Term IRI Term label Parent term IRI Parent term label Alternative term Definition http://purl.obolibrary.org/obo/SO_0002166 ref_miRNA http://purl.obolibrary.org/obo/SO_0000276 miRNA A ref_miRNA (RefSeq-miRNA) sequence is assigned at the creation of a new mature miRNA entry in a database. The ref_miRNA sequence designation remains unchanged even if a different isomiR is later shown to be expressed at a higher level. A ref_miRNA can be produced by one or multiple pre-miRNA. http://purl.obolibrary.org/obo/SO_0002167 isomiR http://purl.obolibrary.org/obo/SO_0000276 miRNA IsomiRs are all the bona fide variants of a mature product. IsomiRs should be connected to the ref_miRNA it is most likely to be the variant of. Some isomiRs can be variations of one or multiple ref_miRNA. http://purl.obolibrary.org/obo/SO_0002221 eukaryotic_promoter http://purl.obolibrary.org/obo/SO_0000167 promoter A regulatory_region including the Transcription Start Site (TSS) of a gene and serving as a platform for Pre-Initiation Complex (PIC) assembly, enabling transcription of a gene under certain conditions. http://purl.obolibrary.org/obo/SO_0002222 prokaryotic_promoter http://purl.obolibrary.org/obo/SO_0000167 promoter A regulatory_region essential for the specific initiation of transcription at a defined location in a DNA molecule, although this location might not be one single base. It is recognized by a specific RNA polymerase(RNAP)-holoenzyme, and this recognition is not necessarily autonomous. http://purl.obolibrary.org/obo/SO_0002231 self_cleaving_ribozyme http://purl.obolibrary.org/obo/SO_0000374 ribozyme An RNA that catalyzes its own cleavage. http://purl.obolibrary.org/obo/SO_0002295 transcription_factor_regulatory_site http://purl.obolibrary.org/obo/SO_0000235 TF_binding_site A TF_binding_site that is involved in regulation of expression. http://purl.obolibrary.org/obo/SO_0002296 TFRS_module http://purl.obolibrary.org/obo/SO_0001055 transcriptional_cis_regulatory_region The possible discontinuous stretch of DNA that is the combination of one or several TFRSs whose bound TFs work jointly in the regulation of a promoter. http://purl.obolibrary.org/obo/SO_0002297 TFRS_collection http://purl.obolibrary.org/obo/SO_0001055 transcriptional_cis_regulatory_region The possible discontinous stretch of DNA that encompass all the TFRSs that regulate a promoter. http://purl.obolibrary.org/obo/SO_0002298 simple_operon http://purl.obolibrary.org/obo/SO_0000178 operon An operon whose transcription is coordinated on a single transcription unit. http://purl.obolibrary.org/obo/SO_0002299 complex_operon http://purl.obolibrary.org/obo/SO_0000178 operon An operon whose transcription is coordinated on several mutually overlapping transcription units transcribed in the same direction and sharing at least one gene. http://purl.obolibrary.org/obo/SO_0002300 unit_of_gene_expression http://purl.obolibrary.org/obo/SO_0001411 biological_region Transcription units or transcribed coding sequences. http://purl.obolibrary.org/obo/SO_0002301 transcription_unit http://purl.obolibrary.org/obo/SO_0002300 unit_of_gene_expression DNA regions delimited by different nonspurious TSS-TTS pairs. http://purl.obolibrary.org/obo/SO_0002302 simple_regulon http://purl.obolibrary.org/obo/SO_1001284 regulon A regulon defined by considering one regulatory gene product. http://purl.obolibrary.org/obo/SO_0002303 complex_regulon http://purl.obolibrary.org/obo/SO_1001284 regulon A regulon defined by considering the units of expression regulated by a specified set of regulatory gene products. http://purl.obolibrary.org/obo/SO_0002343 cytosolic_rRNA http://purl.obolibrary.org/obo/SO_0000252 rRNA Cytosolic rRNA is an RNA component of the small or large subunits of cytosolic ribosomes. http://purl.obolibrary.org/obo/SO_0000018 linkage_group http://purl.obolibrary.org/obo/SO_0001411 biological_region A group of loci that can be grouped in a linear order representing the different degrees of linkage among the genes concerned. http://purl.obolibrary.org/obo/SO_0000087 nuclear_gene http://purl.obolibrary.org/obo/SO_0000704 gene A gene from nuclear sequence. http://purl.obolibrary.org/obo/SO_0000088 mt_gene http://purl.obolibrary.org/obo/SO_0000704 gene A gene located in mitochondrial sequence. http://purl.obolibrary.org/obo/SO_0000089 kinetoplast_gene http://purl.obolibrary.org/obo/SO_0000088 mt_gene A gene located in kinetoplast sequence. http://purl.obolibrary.org/obo/SO_0000090 plastid_gene http://purl.obolibrary.org/obo/SO_0000704 gene A gene from plastid sequence. http://purl.obolibrary.org/obo/SO_0000091 apicoplast_gene http://purl.obolibrary.org/obo/SO_0000090 plastid_gene A gene from apicoplast sequence. http://purl.obolibrary.org/obo/SO_0000092 ct_gene http://purl.obolibrary.org/obo/SO_0000090 plastid_gene A gene from chloroplast sequence. http://purl.obolibrary.org/obo/SO_0000093 chromoplast_gene http://purl.obolibrary.org/obo/SO_0000090 plastid_gene A gene from chromoplast_sequence. http://purl.obolibrary.org/obo/SO_0000094 cyanelle_gene http://purl.obolibrary.org/obo/SO_0000090 plastid_gene A gene from cyanelle sequence. http://purl.obolibrary.org/obo/SO_0000095 leucoplast_gene http://purl.obolibrary.org/obo/SO_0000090 plastid_gene A plastid gene from leucoplast sequence. http://purl.obolibrary.org/obo/SO_0000096 proplastid_gene http://purl.obolibrary.org/obo/SO_0000090 plastid_gene A gene from proplastid sequence. http://purl.obolibrary.org/obo/SO_0000097 nucleomorph_gene http://purl.obolibrary.org/obo/SO_0000704 gene A gene from nucleomorph sequence. http://purl.obolibrary.org/obo/SO_0000098 plasmid_gene http://purl.obolibrary.org/obo/SO_0000704 gene A gene from plasmid sequence. http://purl.obolibrary.org/obo/SO_0000099 proviral_gene http://purl.obolibrary.org/obo/SO_0000704 gene A gene from proviral sequence. http://purl.obolibrary.org/obo/SO_0000100 endogenous_retroviral_gene http://purl.obolibrary.org/obo/SO_0000099 proviral_gene A proviral gene with origin endogenous retrovirus. http://purl.obolibrary.org/obo/SO_0000108 mRNA_with_frameshift http://purl.obolibrary.org/obo/SO_0000234 mRNA An mRNA with a frameshift. http://purl.obolibrary.org/obo/SO_0000111 transposable_element_gene http://purl.obolibrary.org/obo/SO_0000704 gene A gene encoded within a transposable element. For example gag, int, env and pol are the transposable element genes of the TY element in yeast. http://purl.obolibrary.org/obo/SO_0000127 silenced_gene http://purl.obolibrary.org/obo/SO_0000704 gene A gene that is silenced. http://purl.obolibrary.org/obo/SO_0000128 gene_silenced_by_DNA_modification http://purl.obolibrary.org/obo/SO_0000127 silenced_gene A gene that is silenced by DNA modification. http://purl.obolibrary.org/obo/SO_0000129 gene_silenced_by_DNA_methylation http://purl.obolibrary.org/obo/SO_0000128 gene_silenced_by_DNA_modification A gene that is silenced by DNA methylation. http://purl.obolibrary.org/obo/SO_0000138 gene_rearranged_at_DNA_level http://purl.obolibrary.org/obo/SO_0000898 epigenetically_modified_gene An epigenetically modified gene, rearranged at the DNA level. http://purl.obolibrary.org/obo/SO_0000169 RNApol_I_promoter http://purl.obolibrary.org/obo/SO_0002221 eukaryotic_promoter A DNA sequence in eukaryotic DNA to which RNA polymerase I binds, to begin transcription. http://purl.obolibrary.org/obo/SO_0000171 RNApol_III_promoter http://purl.obolibrary.org/obo/SO_0002221 eukaryotic_promoter A DNA sequence in eukaryotic DNA to which RNA polymerase III binds, to begin transcription. http://purl.obolibrary.org/obo/SO_0000239 flanking_region http://purl.obolibrary.org/obo/SO_0001412 topologically_defined_region The sequences extending on either side of a specific region. http://purl.obolibrary.org/obo/SO_0000280 engineered_gene http://purl.obolibrary.org/obo/SO_0000704 gene A gene that is engineered. http://purl.obolibrary.org/obo/SO_0000282 mRNA_with_minus_1_frameshift http://purl.obolibrary.org/obo/SO_0000108 mRNA_with_frameshift An mRNA with a minus 1 frameshift. http://purl.obolibrary.org/obo/SO_0000283 engineered_foreign_transposable_element_gene http://purl.obolibrary.org/obo/SO_0000281 engineered_foreign_gene A transposable_element that is engineered and foreign. http://purl.obolibrary.org/obo/SO_0000285 foreign_gene http://purl.obolibrary.org/obo/SO_0000704 gene A gene that is foreign. http://purl.obolibrary.org/obo/SO_0000287 fusion_gene http://purl.obolibrary.org/obo/SO_0000704 gene A gene that is a fusion. http://purl.obolibrary.org/obo/SO_0000288 engineered_fusion_gene http://purl.obolibrary.org/obo/SO_0000287 fusion_gene A fusion gene that is engineered. http://purl.obolibrary.org/obo/SO_0000307 CpG_island http://purl.obolibrary.org/obo/SO_0001411 biological_region Regions of a few hundred to a few thousand bases in vertebrate genomes that are relatively GC and CpG rich; they are typically unmethylated and often found near the 5' ends of genes. http://purl.obolibrary.org/obo/SO_0000321 mRNA_with_plus_1_frameshift http://purl.obolibrary.org/obo/SO_0000108 mRNA_with_frameshift An mRNA with a plus 1 frameshift. http://purl.obolibrary.org/obo/SO_0000329 mRNA_with_plus_2_frameshift http://purl.obolibrary.org/obo/SO_0000108 mRNA_with_frameshift An mRNA with a plus 2 frameshift. http://purl.obolibrary.org/obo/SO_0000335 mRNA_with_minus_2_frameshift http://purl.obolibrary.org/obo/SO_0000108 mRNA_with_frameshift A mRNA with a minus 2 frameshift. http://purl.obolibrary.org/obo/SO_0000363 floxed_gene http://purl.obolibrary.org/obo/SO_0000902 transgene A transgene that is floxed. http://purl.obolibrary.org/obo/SO_0000364 transposable_element_flanking_region http://purl.obolibrary.org/obo/SO_0000239 flanking_region The region of sequence surrounding a transposable element. http://purl.obolibrary.org/obo/SO_0000366 insertion_site http://purl.obolibrary.org/obo/SO_0000699 junction The junction where an insertion occurred. http://purl.obolibrary.org/obo/SO_0000368 transposable_element_insertion_site http://purl.obolibrary.org/obo/SO_0000366 insertion_site The junction in a genome where a transposable_element has inserted. http://purl.obolibrary.org/obo/SO_0000370 small_regulatory_ncRNA http://purl.obolibrary.org/obo/SO_0002247 sncRNA A non-coding RNA less than 200 nucleotides long, usually with a specific secondary structure, that acts to regulate gene expression. These include short ncRNAs such as piRNA, miRNA and siRNAs (among others). http://purl.obolibrary.org/obo/SO_0000373 recombinationally_inverted_gene http://purl.obolibrary.org/obo/SO_0000456 recombinationally_rearranged_gene A recombinationally rearranged gene by inversion. http://purl.obolibrary.org/obo/SO_0000376 RNA_6S http://purl.obolibrary.org/obo/SO_0000370 small_regulatory_ncRNA A small (184-nt in E. coli) RNA that forms a hairpin type structure. 6S RNA associates with RNA polymerase in a highly specific manner. 6S RNA represses expression from a sigma70-dependent promoter during stationary phase. http://purl.obolibrary.org/obo/SO_0000377 CsrB_RsmB_RNA http://purl.obolibrary.org/obo/SO_0000370 small_regulatory_ncRNA An enterobacterial RNA that binds the CsrA protein. The CsrB RNAs contain a conserved motif CAGGXXG that is found in up to 18 copies and has been suggested to bind CsrA. The Csr regulatory system has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis. In other bacteria such as Erwinia caratovara the RsmA protein has been shown to regulate the production of virulence determinants, such extracellular enzymes. RsmA binds to RsmB regulatory RNA which is also a member of this family. http://purl.obolibrary.org/obo/SO_0000378 DsrA_RNA http://purl.obolibrary.org/obo/SO_0000370 small_regulatory_ncRNA DsrA RNA regulates both transcription, by overcoming transcriptional silencing by the nucleoid-associated H-NS protein, and translation, by promoting efficient translation of the stress sigma factor, RpoS. These two activities of DsrA can be separated by mutation: the first of three stem-loops of the 85 nucleotide RNA is necessary for RpoS translation but not for anti-H-NS action, while the second stem-loop is essential for antisilencing and less critical for RpoS translation. The third stem-loop, which behaves as a transcription terminator, can be substituted by the trp transcription terminator without loss of either DsrA function. The sequence of the first stem-loop of DsrA is complementary with the upstream leader portion of RpoS messenger RNA, suggesting that pairing of DsrA with the RpoS message might be important for translational regulation. http://purl.obolibrary.org/obo/SO_0000384 OxyS_RNA http://purl.obolibrary.org/obo/SO_0000370 small_regulatory_ncRNA A small untranslated RNA which is induced in response to oxidative stress in Escherichia coli. Acts as a global regulator to activate or repress the expression of as many as 40 genes, including the fhlA-encoded transcriptional activator and the rpoS-encoded sigma(s) subunit of RNA polymerase. OxyS is bound by the Hfq protein, that increases the OxyS RNA interaction with its target messages. http://purl.obolibrary.org/obo/SO_0000387 RprA_RNA http://purl.obolibrary.org/obo/SO_0000370 small_regulatory_ncRNA Translational regulation of the stationary phase sigma factor RpoS is mediated by the formation of a double-stranded RNA stem-loop structure in the upstream region of the rpoS messenger RNA, occluding the translation initiation site. Clones carrying rprA (RpoS regulator RNA) increased the translation of RpoS. The rprA gene encodes a 106 nucleotide regulatory RNA. As with DsrA Rfam:RF00014, RprA is predicted to form three stem-loops. Thus, at least two small RNAs, DsrA and RprA, participate in the positive regulation of RpoS translation. Unlike DsrA, RprA does not have an extensive region of complementarity to the RpoS leader, leaving its mechanism of action unclear. RprA is non-essential. http://purl.obolibrary.org/obo/SO_0000388 RRE_RNA http://purl.obolibrary.org/obo/SO_0000370 small_regulatory_ncRNA The Rev response element (RRE) is encoded within the HIV-env gene. Rev is an essential regulatory protein of HIV that binds an internal loop of the RRE leading, encouraging further Rev-RRE binding. This RNP complex is critical for mRNA export and hence for expression of the HIV structural proteins. http://purl.obolibrary.org/obo/SO_0000389 spot_42_RNA http://purl.obolibrary.org/obo/SO_0000370 small_regulatory_ncRNA A 109-nucleotide RNA of E. coli that seems to have a regulatory role on the galactose operon. Changes in Spot 42 levels are implicated in affecting DNA polymerase I levels. http://purl.obolibrary.org/obo/SO_0000451 gene_with_polyadenylated_mRNA http://purl.obolibrary.org/obo/SO_0001217 protein_coding_gene A gene that encodes a polyadenylated mRNA. http://purl.obolibrary.org/obo/SO_0000455 gene_with_mRNA_with_frameshift http://purl.obolibrary.org/obo/SO_0001217 protein_coding_gene A gene that encodes an mRNA with a frameshift. http://purl.obolibrary.org/obo/SO_0000456 recombinationally_rearranged_gene http://purl.obolibrary.org/obo/SO_0000704 gene A gene that is recombinationally rearranged. http://purl.obolibrary.org/obo/SO_0000459 gene_with_trans_spliced_transcript http://purl.obolibrary.org/obo/SO_0000704 gene A gene with a transcript that is trans-spliced. http://purl.obolibrary.org/obo/SO_0000548 gene_with_edited_transcript http://purl.obolibrary.org/obo/SO_0001217 protein_coding_gene A gene that encodes a transcript that is edited. http://purl.obolibrary.org/obo/SO_0000568 bidirectional_promoter http://purl.obolibrary.org/obo/SO_0000167 promoter A promoter that can allow for transcription in both directions. http://purl.obolibrary.org/obo/SO_0000581 cap http://purl.obolibrary.org/obo/SO_0001411 biological_region A structure consisting of a 7-methylguanosine in 5'-5' triphosphate linkage with the first nucleotide of an mRNA. It is added post-transcriptionally, and is not encoded in the DNA. http://purl.obolibrary.org/obo/SO_0000584 tmRNA http://purl.obolibrary.org/obo/SO_0000370 small_regulatory_ncRNA A tmRNA liberates a mRNA from a stalled ribosome. To accomplish this part of the tmRNA is used as a reading frame that ends in a translation stop signal. The broken mRNA is replaced in the ribosome by the tmRNA and translation of the tmRNA leads to addition of a proteolysis tag to the incomplete protein enabling recognition by a protease. Recently a number of permuted tmRNAs genes have been found encoded in two parts. TmRNAs have been identified in eubacteria and some chloroplasts but are absent from archeal and Eukaryote nuclear genomes. http://purl.obolibrary.org/obo/SO_0000609 oligo_U_tail http://purl.obolibrary.org/obo/SO_0001411 biological_region The string of non-encoded U's at the 3' end of a guide RNA (SO:0000602). http://purl.obolibrary.org/obo/SO_0000613 bacterial_RNApol_promoter http://purl.obolibrary.org/obo/SO_0002222 prokaryotic_promoter A DNA sequence to which bacterial RNA polymerase binds, to begin transcription. http://purl.obolibrary.org/obo/SO_0000617 RNApol_III_promoter_type_1 http://purl.obolibrary.org/obo/SO_0000171 RNApol_III_promoter This type of promoter recruits RNA pol III. This promoter is intragenic and includes an A box, an intermediate element, and a C box. This is well conserved in the 5s rRNA promoters across species. http://purl.obolibrary.org/obo/SO_0000618 RNApol_III_promoter_type_2 http://purl.obolibrary.org/obo/SO_0000171 RNApol_III_promoter This type of promoter recruits RNA pol III to transcribe genes mainly for t-RNA. This promoter is intragenic and includes an A box and a B box. http://purl.obolibrary.org/obo/SO_0000621 RNApol_III_promoter_type_3 http://purl.obolibrary.org/obo/SO_0000171 RNApol_III_promoter This type of promoter recruits RNA pol III to transcribe predominantly noncoding RNAs. This promoter contains a proximal sequence element (PSE) and a TATA box upstream of the gene that it regulates. Transcription can also be activated by a distal sequence element (DSE), which is located further upstream. http://purl.obolibrary.org/obo/SO_0000627 insulator http://purl.obolibrary.org/obo/SO_0000727 cis_regulatory_module A regulatory region that 1) when located between a CRM and a gene's promoter prevents the CRM from modulating that genes expression and 2) acts as a chromatin boundary element or barrier that can block the encroachment of condensed chromatin from an adjacent region. http://purl.obolibrary.org/obo/SO_0000633 monocistronic_mRNA http://purl.obolibrary.org/obo/SO_0000665 monocistronic_transcript An mRNA with either a single protein product, or for which the regions encoding all its protein products overlap. http://purl.obolibrary.org/obo/SO_0000634 polycistronic_mRNA http://purl.obolibrary.org/obo/SO_0000078 polycistronic_transcript An mRNA that encodes multiple proteins from at least two non-overlapping regions. http://purl.obolibrary.org/obo/SO_0000647 miRNA_primary_transcript http://purl.obolibrary.org/obo/SO_0000483 nc_primary_transcript A primary transcript encoding a micro RNA. http://purl.obolibrary.org/obo/SO_0000654 maxicircle_gene http://purl.obolibrary.org/obo/SO_0000089 kinetoplast_gene A mitochondrial gene located in a maxicircle. http://purl.obolibrary.org/obo/SO_0000690 gene_with_polycistronic_transcript http://purl.obolibrary.org/obo/SO_0000704 gene A gene that encodes a polycistronic transcript. http://purl.obolibrary.org/obo/SO_0000692 gene_with_dicistronic_transcript http://purl.obolibrary.org/obo/SO_0000690 gene_with_polycistronic_transcript A gene that encodes a dicistronic transcript. http://purl.obolibrary.org/obo/SO_0000693 gene_with_recoded_mRNA http://purl.obolibrary.org/obo/SO_0001217 protein_coding_gene A gene that encodes an mRNA that is recoded. http://purl.obolibrary.org/obo/SO_0000697 gene_with_stop_codon_read_through http://purl.obolibrary.org/obo/SO_0000693 gene_with_recoded_mRNA A gene that encodes a transcript with stop codon readthrough. http://purl.obolibrary.org/obo/SO_0000698 gene_with_stop_codon_redefined_as_pyrrolysine http://purl.obolibrary.org/obo/SO_0000697 gene_with_stop_codon_read_through A gene encoding an mRNA that has the stop codon redefined as pyrrolysine. http://purl.obolibrary.org/obo/SO_0000710 gene_with_stop_codon_redefined_as_selenocysteine http://purl.obolibrary.org/obo/SO_0000697 gene_with_stop_codon_read_through A gene encoding an mRNA that has the stop codon redefined as selenocysteine. http://purl.obolibrary.org/obo/SO_0000711 gene_with_mRNA_recoded_by_translational_bypass http://purl.obolibrary.org/obo/SO_0000693 gene_with_recoded_mRNA A gene with mRNA recoded by translational bypass. http://purl.obolibrary.org/obo/SO_0000712 gene_with_transcript_with_translational_frameshift http://purl.obolibrary.org/obo/SO_0000693 gene_with_recoded_mRNA A gene encoding a transcript that has a translational frameshift. http://purl.obolibrary.org/obo/SO_0000716 dicistronic_mRNA http://purl.obolibrary.org/obo/SO_0000079 dicistronic_transcript An mRNA that has the quality dicistronic. http://purl.obolibrary.org/obo/SO_0000720 foreign_transposable_element http://purl.obolibrary.org/obo/SO_0000101 transposable_element A transposable element that is foreign. http://purl.obolibrary.org/obo/SO_0000721 gene_with_dicistronic_primary_transcript http://purl.obolibrary.org/obo/SO_0000692 gene_with_dicistronic_transcript A gene that encodes a dicistronic primary transcript. http://purl.obolibrary.org/obo/SO_0000722 gene_with_dicistronic_mRNA http://purl.obolibrary.org/obo/SO_0000692 gene_with_dicistronic_transcript A gene that encodes a polycistronic mRNA. http://purl.obolibrary.org/obo/SO_0000727 cis_regulatory_module http://purl.obolibrary.org/obo/SO_0001055 transcriptional_cis_regulatory_region A regulatory region where transcription factor binding sites are clustered to regulate various aspects of transcription activities. (CRMs can be located a few kb to hundreds of kb upstream of the core promoter, in the coding sequence, within introns, or in the untranslated regions (UTR) sequences, and even on a different chromosome). A single gene can be regulated by multiple CRMs to give precise control of its spatial and temporal expression. CRMs function as nodes in large, intertwined regulatory network. CRM DNA accessibility is subject to regulation by dbTFs and transcription co-TFs. http://purl.obolibrary.org/obo/SO_0000734 exemplar_mRNA http://purl.obolibrary.org/obo/SO_0000234 mRNA An exemplar is a representative cDNA sequence for each gene. The exemplar approach is a method that usually involves some initial clustering into gene groups and the subsequent selection of a representative from each gene group. http://purl.obolibrary.org/obo/SO_0000797 natural_transposable_element http://purl.obolibrary.org/obo/SO_0000101 transposable_element TE that exists (or existed) in nature. http://purl.obolibrary.org/obo/SO_0000798 engineered_transposable_element http://purl.obolibrary.org/obo/SO_0000101 transposable_element TE that has been modified by manipulations in vitro. http://purl.obolibrary.org/obo/SO_0000816 rescue_gene http://purl.obolibrary.org/obo/SO_0000704 gene A gene that rescues. http://purl.obolibrary.org/obo/SO_0000818 wild_type_rescue_gene http://purl.obolibrary.org/obo/SO_0000816 rescue_gene A gene that rescues. http://purl.obolibrary.org/obo/SO_0000839 polypeptide_region http://purl.obolibrary.org/obo/SO_0001411 biological_region Biological sequence region that can be assigned to a specific subsequence of a polypeptide. http://purl.obolibrary.org/obo/SO_0000842 gene_component_region http://purl.obolibrary.org/obo/SO_0001411 biological_region A region of a gene that has a specific function. http://purl.obolibrary.org/obo/SO_0000862 capped_mRNA http://purl.obolibrary.org/obo/SO_0000234 mRNA An mRNA that is capped. http://purl.obolibrary.org/obo/SO_0000872 trans_spliced_mRNA http://purl.obolibrary.org/obo/SO_0000479 trans_spliced_transcript An mRNA that is trans-spliced. http://purl.obolibrary.org/obo/SO_0000888 maternally_imprinted_gene http://purl.obolibrary.org/obo/SO_0000898 epigenetically_modified_gene A gene that is maternally_imprinted. http://purl.obolibrary.org/obo/SO_0000889 paternally_imprinted_gene http://purl.obolibrary.org/obo/SO_0000898 epigenetically_modified_gene A gene that is paternally imprinted. http://purl.obolibrary.org/obo/SO_0000890 post_translationally_regulated_gene http://purl.obolibrary.org/obo/SO_0000704 gene A gene that is post translationally regulated. http://purl.obolibrary.org/obo/SO_0000891 negatively_autoregulated_gene http://purl.obolibrary.org/obo/SO_0000704 gene A gene that is negatively autoreguated. http://purl.obolibrary.org/obo/SO_0000892 positively_autoregulated_gene http://purl.obolibrary.org/obo/SO_0000704 gene A gene that is positively autoregulated. http://purl.obolibrary.org/obo/SO_0000896 translationally_regulated_gene http://purl.obolibrary.org/obo/SO_0000704 gene A gene that is translationally regulated. http://purl.obolibrary.org/obo/SO_0000897 allelically_excluded_gene http://purl.obolibrary.org/obo/SO_0000898 epigenetically_modified_gene A gene that is allelically_excluded. http://purl.obolibrary.org/obo/SO_0000898 epigenetically_modified_gene http://purl.obolibrary.org/obo/SO_0000704 gene A gene that is epigenetically modified. http://purl.obolibrary.org/obo/SO_0000929 edited_mRNA http://purl.obolibrary.org/obo/SO_0000873 edited_transcript An mRNA that is edited. http://purl.obolibrary.org/obo/SO_0000941 recombinationally_rearranged_vertebrate_immune_system_gene http://purl.obolibrary.org/obo/SO_0000456 recombinationally_rearranged_gene A recombinationally rearranged gene of the vertebrate immune system. http://purl.obolibrary.org/obo/SO_0000975 minicircle_gene http://purl.obolibrary.org/obo/SO_0000089 kinetoplast_gene A gene found within a minicircle. http://purl.obolibrary.org/obo/SO_0000995 consensus_mRNA http://purl.obolibrary.org/obo/SO_0000994 consensus_region An mRNA sequence produced from an aligment algorithm that uses multiple sequences as input. http://purl.obolibrary.org/obo/SO_0000996 predicted_gene http://purl.obolibrary.org/obo/SO_0000704 gene A region of the genome that has been predicted to be a gene but has not been confirmed by laboratory experiments. http://purl.obolibrary.org/obo/SO_0001058 promoter_targeting_sequence http://purl.obolibrary.org/obo/SO_0001055 transcriptional_cis_regulatory_region A transcriptional_cis_regulatory_region that restricts the activity of a CRM to a single promoter and which functions only when both itself and an insulator are located between the CRM and the promoter. http://purl.obolibrary.org/obo/SO_0001204 Phage_RNA_Polymerase_Promoter http://purl.obolibrary.org/obo/SO_0002311 viral_promoter A region (DNA) to which Bacteriophage RNA polymerase binds, to begin transcription. http://purl.obolibrary.org/obo/SO_0001205 SP6_RNA_Polymerase_Promoter http://purl.obolibrary.org/obo/SO_0001204 Phage_RNA_Polymerase_Promoter A region (DNA) to which the SP6 RNA polymerase binds, to begin transcription. http://purl.obolibrary.org/obo/SO_0001206 T3_RNA_Polymerase_Promoter http://purl.obolibrary.org/obo/SO_0001204 Phage_RNA_Polymerase_Promoter A DNA sequence to which the T3 RNA polymerase binds, to begin transcription. http://purl.obolibrary.org/obo/SO_0001207 T7_RNA_Polymerase_Promoter http://purl.obolibrary.org/obo/SO_0001204 Phage_RNA_Polymerase_Promoter A region (DNA) to which the T7 RNA polymerase binds, to begin transcription. http://purl.obolibrary.org/obo/SO_0001219 retrogene http://purl.obolibrary.org/obo/SO_0000704 gene A gene that has been produced as the product of a reverse transcriptase mediated event. http://purl.obolibrary.org/obo/SO_0001224 gene_silenced_by_RNA_interference http://purl.obolibrary.org/obo/SO_0000127 silenced_gene A gene that is silenced by RNA interference. http://purl.obolibrary.org/obo/SO_0001225 gene_silenced_by_histone_modification http://purl.obolibrary.org/obo/SO_0000127 silenced_gene A gene that is silenced by histone modification. http://purl.obolibrary.org/obo/SO_0001226 gene_silenced_by_histone_methylation http://purl.obolibrary.org/obo/SO_0001225 gene_silenced_by_histone_modification A gene that is silenced by histone methylation. http://purl.obolibrary.org/obo/SO_0001227 gene_silenced_by_histone_deacetylation http://purl.obolibrary.org/obo/SO_0001225 gene_silenced_by_histone_modification A gene that is silenced by histone deacetylation. http://purl.obolibrary.org/obo/SO_0001236 base http://purl.obolibrary.org/obo/SO_0001411 biological_region A base is a sequence feature that corresponds to a single unit of a nucleotide polymer. http://purl.obolibrary.org/obo/SO_0001237 amino_acid http://purl.obolibrary.org/obo/SO_0001411 biological_region A sequence feature that corresponds to a single amino acid residue in a polypeptide. http://purl.obolibrary.org/obo/SO_0001264 gRNA_gene http://purl.obolibrary.org/obo/SO_0001263 ncRNA_gene A noncoding RNA that guides the insertion or deletion of uridine residues in mitochondrial mRNAs. This may also refer to synthetic RNAs used to guide DNA editing using the CRIPSR/Cas9 system. http://purl.obolibrary.org/obo/SO_0001269 SRP_RNA_gene http://purl.obolibrary.org/obo/SO_0001263 ncRNA_gene A gene that encodes a signal recognition particle (SRP) RNA. http://purl.obolibrary.org/obo/SO_0001271 tmRNA_gene http://purl.obolibrary.org/obo/SO_0002342 sncRNA_gene A bacterial RNA with both tRNA and mRNA like properties. http://purl.obolibrary.org/obo/SO_0001412 topologically_defined_region http://purl.obolibrary.org/obo/SO_0000001 region A DNA region within which self-interaction occurs more often than expected by chance because of DNA-looping. http://purl.obolibrary.org/obo/SO_0001431 cryptic_gene http://purl.obolibrary.org/obo/SO_0000704 gene A gene that is not transcribed under normal conditions and is not critical to normal cellular functioning. http://purl.obolibrary.org/obo/SO_0001638 piRNA_gene http://purl.obolibrary.org/obo/SO_0002342 sncRNA_gene A gene that encodes for an piwi associated RNA. http://purl.obolibrary.org/obo/SO_0001645 genetic_marker http://purl.obolibrary.org/obo/SO_0001411 biological_region A measurable sequence feature that varies within a population. http://purl.obolibrary.org/obo/SO_0001669 RNApol_II_core_promoter http://purl.obolibrary.org/obo/SO_0000170 RNApol_II_promoter The minimal portion of the promoter required to properly initiate transcription in RNA polymerase II transcribed genes. http://purl.obolibrary.org/obo/SO_0001671 bacterial_RNApol_promoter_sigma_70_element http://purl.obolibrary.org/obo/SO_0000613 bacterial_RNApol_promoter A DNA sequence to which bacterial RNA polymerase sigma 70 binds, to begin transcription. http://purl.obolibrary.org/obo/SO_0001672 bacterial_RNApol_promoter_sigma54_element http://purl.obolibrary.org/obo/SO_0000613 bacterial_RNApol_promoter A DNA sequence to which bacterial RNA polymerase sigma 54 binds, to begin transcription. http://purl.obolibrary.org/obo/SO_0001687 restriction_enzyme_recognition_site http://purl.obolibrary.org/obo/SO_0001954 restriction_enzyme_region The nucleotide region (usually a palindrome) that is recognized by a restriction enzyme. This may or may not be equal to the restriction enzyme binding site. http://purl.obolibrary.org/obo/SO_0001695 restriction_enzyme_single_strand_overhang http://purl.obolibrary.org/obo/SO_0001954 restriction_enzyme_region A terminal region of DNA sequence where the end of the region is not blunt ended. http://purl.obolibrary.org/obo/SO_0001715 ISRE http://purl.obolibrary.org/obo/SO_0000235 TF_binding_site An ISRE is a transcriptional cis regulatory region, containing the consensus region: YAGTTTC(A/T)YTTTYCC, responsible for increased transcription via interferon binding. http://purl.obolibrary.org/obo/SO_0001720 epigenetically_modified_region http://purl.obolibrary.org/obo/SO_0005836 regulatory_region A biological DNA region implicated in epigenomic changes caused by mechanisms other than changes in the underlying DNA sequence. This includes, nucleosomal histone post-translational modifications, nucleosome depletion to render DNA accessible and post-replicational base modifications such as cytosine modification. http://purl.obolibrary.org/obo/SO_0001739 gene_with_non_canonical_start_codon http://purl.obolibrary.org/obo/SO_0000704 gene A gene with a start codon other than AUG. http://purl.obolibrary.org/obo/SO_0001740 gene_with_start_codon_CUG http://purl.obolibrary.org/obo/SO_0001739 gene_with_non_canonical_start_codon A gene with a translational start codon of CUG. http://purl.obolibrary.org/obo/SO_0001747 open_chromatin_region http://purl.obolibrary.org/obo/SO_0001411 biological_region A DNA sequence that in the normal state of the chromosome corresponds to an unfolded, un-complexed stretch of double-stranded DNA. http://purl.obolibrary.org/obo/SO_0001867 candidate_gene http://purl.obolibrary.org/obo/SO_0000704 gene A gene suspected of being involved in the expression of a trait. http://purl.obolibrary.org/obo/SO_0001868 positional_candidate_gene http://purl.obolibrary.org/obo/SO_0001867 candidate_gene A candidate gene whose association with a trait is based on the gene's location on a chromosome. http://purl.obolibrary.org/obo/SO_0001869 functional_candidate_gene http://purl.obolibrary.org/obo/SO_0001867 candidate_gene A candidate gene whose function has something in common biologically with the trait under investigation. http://purl.obolibrary.org/obo/SO_0001872 rearrangement_region http://purl.obolibrary.org/obo/SO_0001411 biological_region A region of a chromosome, where the chromosome has undergone a large structural rearrangement that altered the genome organization. There is no longer synteny to the reference genome. http://purl.obolibrary.org/obo/SO_0001896 transposable_element_CDS http://purl.obolibrary.org/obo/SO_0000316 CDS A CDS that is part of a transposable element. http://purl.obolibrary.org/obo/SO_0001897 transposable_element_pseudogene http://purl.obolibrary.org/obo/SO_0000336 pseudogene A pseudogene contained within a transposable element. http://purl.obolibrary.org/obo/SO_0001913 bacterial_RNApol_promoter_sigma_ecf_element http://purl.obolibrary.org/obo/SO_0000613 bacterial_RNApol_promoter A bacterial promoter with sigma ecf factor binding dependency. This is a type of bacterial promoters that requires a sigma ECF factor to bind to identified -10 and -35 sequence regions in order to mediate binding of the RNA polymerase to the promoter region as part of transcription initiation. http://purl.obolibrary.org/obo/SO_1001196 cryptogene http://purl.obolibrary.org/obo/SO_0001431 cryptic_gene A maxicircle gene so extensively edited that it cannot be matched to its edited mRNA sequence. http://purl.obolibrary.org/obo/SO_1001261 recoded_mRNA http://purl.obolibrary.org/obo/SO_0000234 mRNA The sequence of a mature mRNA transcript, modified before translation or during translation, usually by special cis-acting signals. http://purl.obolibrary.org/obo/SO_1001264 mRNA_recoded_by_translational_bypass http://purl.obolibrary.org/obo/SO_1001261 recoded_mRNA A recoded_mRNA where translation was suspended at a particular codon and resumed at a particular non-overlapping downstream codon. http://purl.obolibrary.org/obo/SO_1001265 mRNA_recoded_by_codon_redefinition http://purl.obolibrary.org/obo/SO_1001261 recoded_mRNA A recoded_mRNA that was modified by an alteration of codon meaning. http://purl.obolibrary.org/obo/SO_1001275 retron http://purl.obolibrary.org/obo/SO_0001411 biological_region Sequence coding for a short, single-stranded, DNA sequence via a retrotransposed RNA intermediate; characteristic of some microbial genomes. http://purl.obolibrary.org/obo/SO_0002172 sequence_alteration_artifact http://purl.obolibrary.org/obo/SO_0000413 sequence_difference A sequence_alteration where the source of the alteration is due to an artifact in the base-calling or assembly process. http://purl.obolibrary.org/obo/SO_0002173 indel_artifact http://purl.obolibrary.org/obo/SO_0002172 sequence_alteration_artifact An indel that is the result of base-calling or assembly error. http://purl.obolibrary.org/obo/SO_0002174 deletion_artifact http://purl.obolibrary.org/obo/SO_0002172 sequence_alteration_artifact A deletion that is the result of base-calling or assembly error. http://purl.obolibrary.org/obo/SO_0002175 insertion_artifact http://purl.obolibrary.org/obo/SO_0002172 sequence_alteration_artifact An insertion that is the result of base-calling or assembly error. http://purl.obolibrary.org/obo/SO_0002176 substitution_artifact http://purl.obolibrary.org/obo/SO_0002172 sequence_alteration_artifact A substitution that is the result of base-calling or assembly error. http://purl.obolibrary.org/obo/SO_0002177 duplication_artifact http://purl.obolibrary.org/obo/SO_0002175 insertion_artifact A duplication that is the result of base-calling or assembly error. http://purl.obolibrary.org/obo/SO_0002178 SNV_artifact http://purl.obolibrary.org/obo/SO_0002176 substitution_artifact An SNV that is the result of base-calling or assembly error. http://purl.obolibrary.org/obo/SO_0002179 MNV_artifact http://purl.obolibrary.org/obo/SO_0002176 substitution_artifact An MNV that is the result of base-calling or assembly error. http://purl.obolibrary.org/obo/SO_0002187 HERV_insertion http://purl.obolibrary.org/obo/SO_0001837 mobile_element_insertion An insertion of sequence from the HERV family of mobile elements with respect to a reference. http://purl.obolibrary.org/obo/SO_0002214 redundant_inserted_stop_gained http://purl.obolibrary.org/obo/SO_0001992 nonsynonymous_variant A sequence variant whereby at least one base of a codon is changed, resulting in a stop codon inserted next to an existing stop codon. This leads to a polypeptide of the same length. http://purl.obolibrary.org/obo/SO_0002216 Pho7_binding_site http://purl.obolibrary.org/obo/SO_0001659 promoter_element A promoter element with consensus sequence [5'-TCG(G/C)(A/T)xxTTxAA], bound by the transcription factor Pho7. http://purl.obolibrary.org/obo/SO_0002392 increased_enzyme_activity_variant http://purl.obolibrary.org/obo/SO_0001554 polypeptide_function_variant An increase in the activity of an enzyme, as a result of a variant in the gene that encodes the enzyme or a regulatory region. http://purl.obolibrary.org/obo/SO_0002399 inframe_unidirectional_gene_fusion http://purl.obolibrary.org/obo/SO_0002085 unidirectional_gene_fusion A sequence variant whereby two genes, on the same strand have become joined without a disruption of the translational reading frame, because the number of nucleotides between the reading frames of the joined genes is a multiple of three. http://purl.obolibrary.org/obo/SO_0000253 tRNA http://purl.obolibrary.org/obo/SO_0002247 sncRNA Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D, anti-codon, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. Transfer RNAs have two regions of fundamental functional importance: the anti-codon, which is responsible for specific mRNA codon recognition, and the 3' end, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). Transfer RNAs cope with the degeneracy of the genetic code in two manners: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing, i.e. permitting non-standard base-pairing at the 3rd anti-codon position. http://purl.obolibrary.org/obo/SO_0000286 long_terminal_repeat http://purl.obolibrary.org/obo/SO_0000657 repeat_region A sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses. http://purl.obolibrary.org/obo/SO_0000325 rRNA_large_subunit_primary_transcript http://purl.obolibrary.org/obo/SO_0000209 rRNA_primary_transcript A primary transcript encoding a large ribosomal subunit RNA. http://purl.obolibrary.org/obo/SO_0000375 cytosolic_5_8S_rRNA http://purl.obolibrary.org/obo/SO_0000651 cytosolic_LSU_rRNA Cytosolic 5.8S rRNA is an RNA component of the large subunit of cytosolic ribosomes in eukaryotes. http://purl.obolibrary.org/obo/SO_0000407 cytosolic_18S_rRNA http://purl.obolibrary.org/obo/SO_0000650 cytosolic_SSU_rRNA Cytosolic 18S rRNA is an RNA component of the small subunit of cytosolic ribosomes in eukaryotes. http://purl.obolibrary.org/obo/SO_0000624 telomere http://purl.obolibrary.org/obo/SO_0000628 chromosomal_structural_element A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end. http://purl.obolibrary.org/obo/SO_0001002 cytosolic_25S_rRNA http://purl.obolibrary.org/obo/SO_0000651 cytosolic_LSU_rRNA Cytosolic 25S rRNA is an RNA component of the large subunit of cytosolic ribosomes most eukaryotes. http://purl.obolibrary.org/obo/SO_0001789 mating_type_region http://purl.obolibrary.org/obo/SO_0005855 gene_group A specialized region in the genomes of some yeast and fungi, the genes of which regulate mating type. http://purl.obolibrary.org/obo/SO_0001795 regional_centromere http://purl.obolibrary.org/obo/SO_0000577 centromere A regional centromere is a large modular centromere found in fission yeast and higher eukaryotes. It consist of a central core region flanked by inverted inner and outer repeat regions. http://purl.obolibrary.org/obo/SO_0001796 regional_centromere_central_core http://purl.obolibrary.org/obo/SO_0000330 conserved_region A conserved region within the central region of a modular centromere, where the kinetochore is formed. http://purl.obolibrary.org/obo/SO_0001798 regional_centromere_inner_repeat_region http://purl.obolibrary.org/obo/SO_0001797 centromeric_repeat The inner inverted repeat region of a modular centromere and part of the central core surrounding a non-conserved central region. This region is adjacent to the central core, on each chromosome arm. http://purl.obolibrary.org/obo/SO_0001799 regional_centromere_outer_repeat_region http://purl.obolibrary.org/obo/SO_0001797 centromeric_repeat The heterochromatic outer repeat region of a modular centromere. These repeats exist in tandem arrays on both chromosome arms. http://purl.obolibrary.org/obo/SO_0001855 MCB http://purl.obolibrary.org/obo/SO_0001659 promoter_element A promoter element with consensus sequence ACGCGT, bound by the transcription factor complex MBF (MCB-binding factor) and found in promoters of genes expressed during the G1/S transition of the cell cycle. http://purl.obolibrary.org/obo/SO_0001905 regional_centromere_outer_repeat_transcript http://purl.obolibrary.org/obo/SO_0000185 primary_transcript A transcript that is transcribed from the outer repeat region of a regional centromere. http://purl.obolibrary.org/obo/SO_0001958 lariat_intron http://purl.obolibrary.org/obo/SO_0000188 intron A kind of intron whereby the excision is driven by lariat formation. http://purl.obolibrary.org/obo/SO_0001984 silent_mating_type_cassette_array http://purl.obolibrary.org/obo/SO_0005854 gene_cassette_array A gene cassette array that corresponds to a silenced version of a mating type region. http://purl.obolibrary.org/obo/SO_0001985 Okazaki_fragment http://purl.obolibrary.org/obo/SO_0001411 biological_region Any of the DNA segments produced by discontinuous synthesis of the lagging strand during DNA replication. http://purl.obolibrary.org/obo/SO_0001997 subtelomere http://purl.obolibrary.org/obo/SO_0000628 chromosomal_structural_element A heterochromatic region of the chromosome, adjacent to the telomere (on the centromeric side) that contains repetitive DNA and sometimes genes and it is transcribed. http://purl.obolibrary.org/obo/SO_0000348 nucleic_acid http://purl.obolibrary.org/obo/SO_0000443 polymer_attribute An attribute describing a sequence consisting of nucleobases bound to repeating units. The forms found in nature are deoxyribonucleic acid (DNA), where the repeating units are 2-deoxy-D-ribose rings connected to a phosphate backbone, and ribonucleic acid (RNA), where the repeating units are D-ribose rings connected to a phosphate backbone. http://purl.obolibrary.org/obo/SO_0002211 circular_plasmid http://purl.obolibrary.org/obo/SO_0000155 plasmid A self replicating circular nucleic acid molecule that is distinct from a chromosome in the organism. http://purl.obolibrary.org/obo/SO_0002212 linear_plasmid http://purl.obolibrary.org/obo/SO_0000155 plasmid A self replicating linear nucleic acid molecule that is distinct from a chromosome in the organism. They are capped by terminal proteins covalently bound to the 5' ends of the DNA. http://purl.obolibrary.org/obo/SO_0002236 cytosolic_rRNA_18S_gene http://purl.obolibrary.org/obo/SO_0002362 cytosolic_SSU_rRNA_gene A gene which codes for 18S_rRNA, which functions as the small subunit of the ribosome in eukaryotes. http://purl.obolibrary.org/obo/SO_0002237 cytosolic_rRNA_16S_gene http://purl.obolibrary.org/obo/SO_0002362 cytosolic_SSU_rRNA_gene A gene which codes for 16S_rRNA, which functions as the small subunit of the ribosome in prokaryotes. http://purl.obolibrary.org/obo/SO_0002238 cytosolic_rRNA_5S_gene http://purl.obolibrary.org/obo/SO_0002361 cytosolic_LSU_rRNA_gene A gene which codes for 5S_rRNA, which is a portion of the large subunit of the ribosome in both eukaryotes and prokaryotes. http://purl.obolibrary.org/obo/SO_0002239 cytosolic_rRNA_28S_gene http://purl.obolibrary.org/obo/SO_0002361 cytosolic_LSU_rRNA_gene A gene which codes for 28S_rRNA, which functions as a component of the large subunit of the ribosome in eukaryotes. http://purl.obolibrary.org/obo/SO_0002240 cytosolic_rRNA_5_8S_gene http://purl.obolibrary.org/obo/SO_0002361 cytosolic_LSU_rRNA_gene A gene which codes for 5_8S_rRNA (5.8S rRNA), which functions as a component of the large subunit of the ribosome in eukaryotes. http://purl.obolibrary.org/obo/SO_0002242 cytosolic_rRNA_25S_gene http://purl.obolibrary.org/obo/SO_0002361 cytosolic_LSU_rRNA_gene A gene which codes for 25S_rRNA, which functions as a component of the large subunit of the ribosome in some eukaryotes. http://purl.obolibrary.org/obo/SO_0002243 cytosolic_rRNA_23S_gene http://purl.obolibrary.org/obo/SO_0002361 cytosolic_LSU_rRNA_gene A gene which codes for 23S_rRNA, which functions as a component of the large subunit of the ribosome in prokaryotes. http://purl.obolibrary.org/obo/SO_0002257 knob http://purl.obolibrary.org/obo/SO_0000657 repeat_region Cytologically observable heterochromatic regions of chromosomes away from centromeres that contain predominatly large tandem repeats and retrotransposons. http://purl.obolibrary.org/obo/SO_0002258 teb1_recognition_motif http://purl.obolibrary.org/obo/SO_0000713 DNA_motif A binding motif with the consensus sequence TTAGGG to which Teb1 binds. http://purl.obolibrary.org/obo/SO_0002259 polyA_site_cluster http://purl.obolibrary.org/obo/SO_0001411 biological_region A region defined by a cluster of experimentally determined polyadenylation sites, typically less than 25 bp in length and associated with a single polyadenylation signal. http://purl.obolibrary.org/obo/SO_0002260 LARD http://purl.obolibrary.org/obo/SO_0000186 LTR_retrotransposon Large Retrotransposon Derivative elements are long-terminal repeats that contain reverse transcriptase priming sites and are conserved in sequence but contain no open reading frames encoding typical retrotransposon proteins . The LARDs identified in barley and other Triticeae have LTRs ~5.5 kb and an interal domain of ~3.5 kb. LARDs lack coding domains and thus do not encode proteins. http://purl.obolibrary.org/obo/SO_0002261 TRIM http://purl.obolibrary.org/obo/SO_0000186 LTR_retrotransposon TRIM elements have terminal direct repeat sequences of 100-250 bp in length that flank an internal domain of 100–300 bp. TRIMs lack coding domains and thus do not encode proteins. http://purl.obolibrary.org/obo/SO_0000001 region http://purl.obolibrary.org/obo/SO_0000110 sequence_feature A sequence_feature with an extent greater than zero. A nucleotide region is composed of bases and a polypeptide region is composed of amino acids. http://purl.obolibrary.org/obo/SO_0000104 polypeptide http://purl.obolibrary.org/obo/SO_0001411 biological_region A sequence of amino acids linked by peptide bonds which may lack appreciable tertiary structure and may not be liable to irreversible denaturation. http://purl.obolibrary.org/obo/SO_0000148 supercontig http://purl.obolibrary.org/obo/SO_0001876 partial_genomic_sequence_assembly One or more contigs that have been ordered and oriented using end-read information. Contains gaps that are filled with N's. http://purl.obolibrary.org/obo/SO_0000149 contig http://purl.obolibrary.org/obo/SO_0000143 assembly_component A contiguous sequence derived from sequence assembly. Has no gaps, but may contain N's from unavailable bases. http://purl.obolibrary.org/obo/SO_0000276 miRNA http://purl.obolibrary.org/obo/SO_0000370 small_regulatory_ncRNA Small, ~22-nt, RNA molecule that is the endogenous transcript of a miRNA gene (or the product of other non coding RNA genes). Micro RNAs are produced from precursor molecules (SO:0001244) that can form local hairpin structures, which ordinarily are processed (usually via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. Micro RNAs may trigger the cleavage of their target molecules or act as translational repressors. http://purl.obolibrary.org/obo/SO_0000353 sequence_assembly http://purl.obolibrary.org/obo/SO_0001248 assembly A sequence of nucleotides that has been algorithmically derived from an alignment of two or more different sequences. http://purl.obolibrary.org/obo/SO_0000988 circular http://purl.obolibrary.org/obo/SO_0000986 topology_attribute A quality of a nucleotide polymer that has no terminal nucleotide residues. http://purl.obolibrary.org/obo/SO_0001248 assembly http://purl.obolibrary.org/obo/SO_0001410 experimental_feature A region of the genome of known length that is composed by ordering and aligning two or more different regions. http://purl.obolibrary.org/obo/SO_0000105 chromosome_arm http://purl.obolibrary.org/obo/SO_0000830 chromosome_part A region of the chromosome between the centromere and the telomere. Human chromosomes have two arms, the p arm (short) and the q arm (long) which are separated from each other by the centromere. http://purl.obolibrary.org/obo/SO_0000170 RNApol_II_promoter http://purl.obolibrary.org/obo/SO_0002221 eukaryotic_promoter A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription. http://purl.obolibrary.org/obo/SO_0000231 snRNA_primary_transcript http://purl.obolibrary.org/obo/SO_0000483 nc_primary_transcript A primary transcript encoding a small nuclear RNA (SO:0000274). http://purl.obolibrary.org/obo/SO_0000232 snoRNA_primary_transcript http://purl.obolibrary.org/obo/SO_0000483 nc_primary_transcript A primary transcript encoding one or more small nucleolar RNAs (SO:0000275). http://purl.obolibrary.org/obo/SO_0000234 mRNA http://purl.obolibrary.org/obo/SO_0000233 mature_transcript Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns. http://purl.obolibrary.org/obo/SO_0000252 rRNA http://purl.obolibrary.org/obo/SO_0000655 ncRNA rRNA is an RNA component of a ribosome that can provide both structural scaffolding and catalytic activity. http://purl.obolibrary.org/obo/SO_0000274 snRNA http://purl.obolibrary.org/obo/SO_0002247 sncRNA A small nuclear RNA molecule involved in pre-mRNA splicing and processing. http://purl.obolibrary.org/obo/SO_0000275 snoRNA http://purl.obolibrary.org/obo/SO_0002247 sncRNA Small nucleolar RNAs (snoRNAs) are short non-coding RNAs enriched in the nucleolus as components of small nucleolar ribonucleoproteins. They guide ribose methylation and pseudouridylation of rRNAs and snRNAs, and a subgroup regulate excision of rRNAs from rRNA precursor transcripts. snoRNAs may also guide rRNA acetylation and tRNA methylation, and regulate mRNA abundance and alternative splicing. http://purl.obolibrary.org/obo/SO_0000296 origin_of_replication http://purl.obolibrary.org/obo/SO_0001411 biological_region A region of nucleic acid from which replication initiates; includes sequences that are recognized by replication proteins, the site from which the first separation of complementary strands occurs, and specific replication start sites. http://purl.obolibrary.org/obo/SO_0000339 recombination_hotspot http://purl.obolibrary.org/obo/SO_0000298 recombination_feature A region in a genome which promotes recombination. http://purl.obolibrary.org/obo/SO_0000605 intergenic_region http://purl.obolibrary.org/obo/SO_0001411 biological_region A region containing or overlapping no genes that is bounded on either side by a gene, or bounded by a gene and the end of the chromosome. http://purl.obolibrary.org/obo/SO_0000610 polyA_sequence http://purl.obolibrary.org/obo/SO_0001411 biological_region Sequence of about 100 nucleotides of A added to the 3' end of most eukaryotic mRNAs. http://purl.obolibrary.org/obo/SO_0000644 antisense_RNA http://purl.obolibrary.org/obo/SO_0000655 ncRNA Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA. http://purl.obolibrary.org/obo/SO_0000645 antisense_primary_transcript http://purl.obolibrary.org/obo/SO_0000185 primary_transcript The reverse complement of the primary transcript. http://purl.obolibrary.org/obo/SO_0000646 siRNA http://purl.obolibrary.org/obo/SO_0000370 small_regulatory_ncRNA A small RNA molecule that is the product of a longer exogenous or endogenous dsRNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the dsRNA. siRNAs trigger the cleavage of their target molecules. http://purl.obolibrary.org/obo/SO_0000871 polyadenylated_mRNA http://purl.obolibrary.org/obo/SO_0000234 mRNA An mRNA that is polyadenylated. http://purl.obolibrary.org/obo/SO_0001533 cryptic_splice_site http://purl.obolibrary.org/obo/SO_0000162 splice_site A splice site that is in part of the transcript not normally spliced. They occur via mutation or transcriptional error. http://purl.obolibrary.org/obo/SO_0001843 CRE http://purl.obolibrary.org/obo/SO_0001659 promoter_element MERGED DEFINITION: TARGET DEFINITION: A promoter element with consensus sequence TGACGTCA; bound by the ATF/CREB family of transcription factors. -------------------- SOURCE DEFINITION: A promoter element that contains a core sequence TGACGT, bound by a protein complex that regulates transcription of genes encoding PKA pathway components. http://purl.obolibrary.org/obo/SO_0001861 sterol_regulatory_element http://purl.obolibrary.org/obo/SO_0001659 promoter_element A 10-bp promoter element bound by sterol regulatory element binding proteins (SREBPs), found in promoters of genes involved in sterol metabolism. Many variants of the sequence ATCACCCCAC function as SREs. http://purl.obolibrary.org/obo/SO_0001871 PCB http://purl.obolibrary.org/obo/SO_0001659 promoter_element A promoter element with consensus sequence GNAACR, bound by the transcription factor complex PBF (PCB-binding factor) and found in promoters of genes expressed during the M/G1 transition of the cell cycle. http://purl.obolibrary.org/obo/SO_0001914 rDNA_replication_fork_barrier http://purl.obolibrary.org/obo/SO_0000713 DNA_motif A DNA motif that is found in eukaryotic rDNA repeats, and is a site of replication fork pausing. http://purl.obolibrary.org/obo/SO_0001927 telomeric_transcript http://purl.obolibrary.org/obo/SO_0000655 ncRNA A non-coding transcript derived from the transcript of the telomere. http://purl.obolibrary.org/obo/SO_0002021 mating_type_region_replication_fork_barrier http://purl.obolibrary.org/obo/SO_0000713 DNA_motif A DNA motif that is found in eukaryotic rDNA repeats, and is a site of replication fork pausing. http://purl.obolibrary.org/obo/SO_0002025 cis_acting_homologous_chromosome_pairing_region http://purl.obolibrary.org/obo/SO_0000713 DNA_motif A genome region where chromosome pairing occurs preferentially during homologous chromosome pairing during early meiotic prophase of Meiosis I. http://purl.obolibrary.org/obo/SO_0000607 unedited_region http://purl.obolibrary.org/obo/SO_0000579 edited_transcript_feature The region of an edited transcript that will not be edited. http://purl.obolibrary.org/obo/SO_0002189 allelic_pseudogene http://purl.obolibrary.org/obo/SO_0001759 unitary_pseudogene A (unitary) pseudogene that is stable in the population but importantly it has a functional alternative allele also in the population. i.e., one strain may have the gene, another strain may have the pseudogene. MHC haplotypes have allelic pseudogenes. http://purl.obolibrary.org/obo/SO_0002190 enhancer_blocking_element http://purl.obolibrary.org/obo/SO_0000627 insulator A transcriptional cis regulatory region that when located between an enhancer and a gene's promoter prevents the enhancer from modulating the expression of the gene. Sometimes referred to as an insulator but may not include the barrier function of an insulator. http://purl.obolibrary.org/obo/SO_0002191 imprinting_control_region http://purl.obolibrary.org/obo/SO_0001720 epigenetically_modified_region A regulatory region that controls epigenetic imprinting and affects the expression of target genes in an allele- or parent-of-origin-specific manner. Associated regulatory elements may include differentially methylated regions and non-coding RNAs. http://purl.obolibrary.org/obo/SO_0002192 flanking_repeat http://purl.obolibrary.org/obo/SO_0000657 repeat_region A repeat lying outside the sequence for which it has functional significance (eg. transposon insertion target sites). http://purl.obolibrary.org/obo/SO_0002193 processed_pseudogenic_rRNA http://purl.obolibrary.org/obo/SO_0000777 pseudogenic_rRNA The pseudogene has arisen by reverse transcription of a mRNA into cDNA, followed by reintegration into the genome. Therefore, it has lost any intron/exon structure, and it might have a pseudo-polyA-tail. http://purl.obolibrary.org/obo/SO_0002194 unprocessed_pseudogenic_rRNA http://purl.obolibrary.org/obo/SO_0000777 pseudogenic_rRNA The pseudogene has arisen from a copy of the parent gene by duplication followed by accumulation of random mutation. The changes, compared to their functional homolog, include insertions, deletions, premature stop codons, frameshifts and a higher proportion of non-synonymous versus synonymous substitutions. http://purl.obolibrary.org/obo/SO_0002195 unitary_pseudogenic_rRNA http://purl.obolibrary.org/obo/SO_0000777 pseudogenic_rRNA The pseudogene has no parent. It is the original gene, which is functional in some species but disrupted in some way (indels, mutation, recombination) in another species or strain. http://purl.obolibrary.org/obo/SO_0002196 allelic_pseudogenic_rRNA http://purl.obolibrary.org/obo/SO_0000777 pseudogenic_rRNA A (unitary) pseudogene that is stable in the population but importantly it has a functional alternative allele also in the population. i.e., one strain may have the gene, another strain may have the pseudogene. MHC haplotypes have allelic pseudogenes. http://purl.obolibrary.org/obo/SO_0002197 processed_pseudogenic_tRNA http://purl.obolibrary.org/obo/SO_0000778 pseudogenic_tRNA The pseudogene has arisen by reverse transcription of a mRNA into cDNA, followed by reintegration into the genome. Therefore, it has lost any intron/exon structure, and it might have a pseudo-polyA-tail. http://purl.obolibrary.org/obo/SO_0002198 unprocessed_pseudogenic_tRNA http://purl.obolibrary.org/obo/SO_0000778 pseudogenic_tRNA The pseudogene has arisen from a copy of the parent gene by duplication followed by accumulation of random mutation. The changes, compared to their functional homolog, include insertions, deletions, premature stop codons, frameshifts and a higher proportion of non-synonymous versus synonymous substitutions. http://purl.obolibrary.org/obo/SO_0002199 unitary_pseudogenic_tRNA http://purl.obolibrary.org/obo/SO_0000778 pseudogenic_tRNA The pseudogene has no parent. It is the original gene, which is functional in some species but disrupted in some way (indels, mutation, recombination) in another species or strain. http://purl.obolibrary.org/obo/SO_0002200 allelic_pseudogenic_tRNA http://purl.obolibrary.org/obo/SO_0000778 pseudogenic_tRNA A (unitary) pseudogene that is stable in the population but importantly it has a functional alternative allele also in the population. i.e., one strain may have the gene, another strain may have the pseudogene. MHC haplotypes have allelic pseudogenes. http://purl.obolibrary.org/obo/SO_0002201 terminal_repeat http://purl.obolibrary.org/obo/SO_0000657 repeat_region A repeat at the ends of and within the sequence for which it has functional significance other than long terminal repeat. http://purl.obolibrary.org/obo/SO_0002202 repeat_instability_region http://purl.obolibrary.org/obo/SO_0000705 tandem_repeat A repeat region that is prone to expansions and/or contractions. http://purl.obolibrary.org/obo/SO_0002203 replication_start_site http://purl.obolibrary.org/obo/SO_0000296 origin_of_replication A nucleotide site from which replication initiates. http://purl.obolibrary.org/obo/SO_0002204 nucleotide_cleavage_site http://purl.obolibrary.org/obo/SO_0000699 junction A point in nucleic acid where a cleavage event occurs. http://purl.obolibrary.org/obo/SO_0002205 response_element http://purl.obolibrary.org/obo/SO_0001055 transcriptional_cis_regulatory_region A regulatory element that acts in response to a stimulus, usually via transcription factor binding. http://purl.obolibrary.org/obo/SO_0002206 sequence_source http://purl.obolibrary.org/obo/SO_0000400 sequence_attribute Identifies the biological source of the specified span of the sequence http://purl.obolibrary.org/obo/SO_0002207 UNAAAC_motif http://purl.obolibrary.org/obo/SO_0001979 RNA_stability_element A hexameric RNA motif consisting of nucleotides UNAAAC (where N can be any nucleotide) that targets the RNA for degradation. http://purl.obolibrary.org/obo/SO_0002208 long_terminal_repeat_transcript http://purl.obolibrary.org/obo/SO_0000673 transcript An RNA that is transcribed from a long terminal repeat. http://purl.obolibrary.org/obo/SO_0002393 precursor_RNA http://purl.obolibrary.org/obo/SO_0000673 transcript Any RNA species that is not yet the mature RNA product; may include ncRNA, rRNA, tRNA, 5' untranslated region (5'UTR), coding sequences (CDS, exon), intervening sequences (intron) and 3' untranslated region (3'UTR). http://purl.obolibrary.org/obo/SO_0001026 genome http://purl.obolibrary.org/obo/SO_0001260 sequence_collection A genome is the sum of genetic material within a cell or virion. http://purl.obolibrary.org/obo/SO_0001027 genotype http://purl.obolibrary.org/obo/SO_0001507 variant_collection A genotype is a variant genome, complete or incomplete. http://purl.obolibrary.org/obo/SO_0001462 contig_collection http://purl.obolibrary.org/obo/SO_0001085 sequence_conflict A collection of contigs. http://purl.obolibrary.org/obo/SO_0001505 reference_genome http://purl.obolibrary.org/obo/SO_0001026 genome A collection of sequences (often chromosomes) taken as the standard for a given organism and genome assembly. http://purl.obolibrary.org/obo/SO_0001686 quality_value http://purl.obolibrary.org/obo/SO_0001684 experimental_feature_attribute An experimental feature attribute that defines the quality of the feature in a quantitative way, such as a phred quality score. http://purl.obolibrary.org/obo/SO_0000034 morpholino_oligo http://purl.obolibrary.org/obo/SO_0001247 synthetic_oligo Morpholino oligos are synthesized from four different Morpholino subunits, each of which contains one of the four genetic bases (A, C, G, T) linked to a 6-membered morpholine ring. Eighteen to 25 subunits of these four subunit types are joined in a specific order by non-ionic phosphorodiamidate intersubunit linkages to give a Morpholino. http://purl.obolibrary.org/obo/SO_0000143 assembly_component http://purl.obolibrary.org/obo/SO_0001410 experimental_feature A region of known length which may be used to manufacture a longer region. http://purl.obolibrary.org/obo/SO_0000281 engineered_foreign_gene http://purl.obolibrary.org/obo/SO_0000805 engineered_foreign_region A gene that is engineered and foreign. http://purl.obolibrary.org/obo/SO_0000289 microsatellite http://purl.obolibrary.org/obo/SO_0000005 satellite_DNA A repeat_region containing repeat_units of 2 to 10 bp repeated in tandem. http://purl.obolibrary.org/obo/SO_0000337 RNAi_reagent http://purl.obolibrary.org/obo/SO_0000442 ds_oligo A double stranded RNA duplex, at least 20bp long, used experimentally to inhibit gene function by RNA interference. http://purl.obolibrary.org/obo/SO_0000341 chromosome_band http://purl.obolibrary.org/obo/SO_0000830 chromosome_part A cytologically distinguishable feature of a chromosome, often made visible by staining, and usually alternating light and dark. http://purl.obolibrary.org/obo/SO_0000637 engineered_plasmid http://purl.obolibrary.org/obo/SO_0000155 plasmid A plasmid that is engineered. http://purl.obolibrary.org/obo/SO_0000699 junction http://purl.obolibrary.org/obo/SO_0000110 sequence_feature A sequence_feature with an extent of zero. http://purl.obolibrary.org/obo/SO_0000783 engineered http://purl.obolibrary.org/obo/SO_0000733 feature_attribute An attribute to describe a region that was modified in vitro. http://purl.obolibrary.org/obo/SO_0000804 engineered_region http://purl.obolibrary.org/obo/SO_0001409 biomaterial_region A region that is engineered. http://purl.obolibrary.org/obo/SO_0001477 gene_trap_construct http://purl.obolibrary.org/obo/SO_0000637 engineered_plasmid A gene trap construct is a type of engineered plasmid which is designed to integrate into a genome and produce a fusion transcript between exons of the gene into which it inserts and a reporter element in the construct. Gene traps contain a splice acceptor, do not contain promoter elements for the reporter, and are mutagenic. Gene traps may be bicistronic with the second cassette containing a promoter driving an a selectable marker. http://purl.obolibrary.org/obo/SO_0001478 promoter_trap_construct http://purl.obolibrary.org/obo/SO_0000637 engineered_plasmid A promoter trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when inserted in close proximity to a promoter element. Promoter traps typically do not contain promoter elements and are mutagenic. http://purl.obolibrary.org/obo/SO_0001479 enhancer_trap_construct http://purl.obolibrary.org/obo/SO_0000637 engineered_plasmid An enhancer trap construct is a type of engineered plasmid which is designed to integrate into a genome and express a reporter when the expression from a basic minimal promoter is enhanced by genomic enhancer elements. Enhancer traps contain promoter elements and are not usually mutagenic. http://purl.obolibrary.org/obo/SO_0001742 copy_number_gain http://purl.obolibrary.org/obo/SO_0001019 copy_number_variation A sequence alteration whereby the copy number of a given regions is greater than the reference sequence. http://purl.obolibrary.org/obo/SO_0001743 copy_number_loss http://purl.obolibrary.org/obo/SO_0001019 copy_number_variation A sequence alteration whereby the copy number of a given region is less than the reference sequence. http://purl.obolibrary.org/obo/SO_0001744 UPD http://purl.obolibrary.org/obo/SO_0001059 sequence_alteration Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from one parent and no copies of the same chromosome or region from the other parent. http://purl.obolibrary.org/obo/SO_0001745 maternal_uniparental_disomy http://purl.obolibrary.org/obo/SO_0001744 UPD Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the mother and no copies of the same chromosome or region from the father. http://purl.obolibrary.org/obo/SO_0001746 paternal_uniparental_disomy http://purl.obolibrary.org/obo/SO_0001744 UPD Uniparental disomy is a sequence_alteration where a diploid individual receives two copies for all or part of a chromosome from the father and no copies of the same chromosome or region from the mother. http://purl.obolibrary.org/obo/SO_0001784 complex_structural_alteration http://purl.obolibrary.org/obo/SO_1000183 chromosome_structure_variation A structural sequence alteration or rearrangement encompassing one or more genome fragments, with 4 or more breakpoints. http://purl.obolibrary.org/obo/SO_0001785 structural_alteration http://purl.obolibrary.org/obo/SO_0001059 sequence_alteration An alteration of the genome that leads to a change in the structure of one or more chromosomes. http://purl.obolibrary.org/obo/SO_0000004 interior_coding_exon http://purl.obolibrary.org/obo/SO_0000195 coding_exon A coding exon that is not the most 3-prime or the most 5-prime in a given transcript. http://purl.obolibrary.org/obo/SO_0000005 satellite_DNA http://purl.obolibrary.org/obo/SO_0000705 tandem_repeat The many tandem repeats (identical or related) of a short basic repeating unit; many have a base composition or other property different from the genome average that allows them to be separated from the bulk (main band) genomic DNA. http://purl.obolibrary.org/obo/SO_0000006 PCR_product http://purl.obolibrary.org/obo/SO_0000695 reagent A region amplified by a PCR reaction. http://purl.obolibrary.org/obo/SO_0000007 read_pair http://purl.obolibrary.org/obo/SO_0000150 read One of a pair of sequencing reads in which the two members of the pair are related by originating at either end of a clone insert. http://purl.obolibrary.org/obo/SO_0000012 scRNA_primary_transcript http://purl.obolibrary.org/obo/SO_0000483 nc_primary_transcript The primary transcript of any one of several small cytoplasmic RNA molecules present in the cytoplasm and sometimes nucleus of a Eukaryote. http://purl.obolibrary.org/obo/SO_0000013 scRNA http://purl.obolibrary.org/obo/SO_0000655 ncRNA A small non coding RNA sequence, present in the cytoplasm. http://purl.obolibrary.org/obo/SO_0000014 INR_motif http://purl.obolibrary.org/obo/SO_0001660 core_eukaryotic_promoter_element A sequence element characteristic of some RNA polymerase II promoters required for the correct positioning of the polymerase for the start of transcription. Overlaps the TSS. The mammalian consensus sequence is YYAN(T|A)YY; the Drosophila consensus sequence is TCA(G|T)t(T|C). In each the A is at position +1 with respect to the TSS. Functionally similar to the TATA box element. http://purl.obolibrary.org/obo/SO_0000015 DPE_motif http://purl.obolibrary.org/obo/SO_0001660 core_eukaryotic_promoter_element A sequence element characteristic of some RNA polymerase II promoters; Positioned from +28 to +32 with respect to the TSS (+1). Experimental results suggest that the DPE acts in conjunction with the INR_motif to provide a binding site for TFIID in the absence of a TATA box to mediate transcription of TATA-less promoters. Consensus sequence (A|G)G(A|T)(C|T)(G|A|C). http://purl.obolibrary.org/obo/SO_0000016 BREu_motif http://purl.obolibrary.org/obo/SO_0001660 core_eukaryotic_promoter_element A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements at -37 to -32 with respect to the TSS (+1). Consensus sequence is (G|C)(G|C)(G|A)CGCC. Binds TFIIB. http://purl.obolibrary.org/obo/SO_0000017 PSE_motif http://purl.obolibrary.org/obo/SO_0000713 DNA_motif A sequence element characteristic of the promoters of snRNA genes transcribed by RNA polymerase II or by RNA polymerase III. Located between -45 and -60 relative to the TSS. The human PSE_motif consensus sequence is TCACCNTNA(C|G)TNAAAAG(T|G). The basal transcription factor, snRNA-activating protein complex (SNAPc), binds the PSE_motif and is required for the transcription of both RNA polymerase II and III transcribed small-nuclear RNA genes. http://purl.obolibrary.org/obo/SO_0000020 RNA_internal_loop http://purl.obolibrary.org/obo/SO_0000715 RNA_motif A region of double stranded RNA where the bases do not conform to WC base pairing. The loop is closed on both sides by canonical base pairing. If the interruption to base pairing occurs on one strand only, it is known as a bulge. http://purl.obolibrary.org/obo/SO_0000021 asymmetric_RNA_internal_loop http://purl.obolibrary.org/obo/SO_0000020 RNA_internal_loop An internal RNA loop where one of the strands includes more bases than the corresponding region on the other strand. http://purl.obolibrary.org/obo/SO_0000022 A_minor_RNA_motif http://purl.obolibrary.org/obo/SO_0000715 RNA_motif A region forming a motif, composed of adenines, where the minor groove edges are inserted into the minor groove of another helix. http://purl.obolibrary.org/obo/SO_0000023 K_turn_RNA_motif http://purl.obolibrary.org/obo/SO_0000021 asymmetric_RNA_internal_loop The kink turn (K-turn) is an RNA structural motif that creates a sharp (~120 degree) bend between two continuous helices. http://purl.obolibrary.org/obo/SO_0000024 sarcin_like_RNA_motif http://purl.obolibrary.org/obo/SO_0000021 asymmetric_RNA_internal_loop A loop in ribosomal RNA containing the sites of attack for ricin and sarcin. http://purl.obolibrary.org/obo/SO_0000025 symmetric_RNA_internal_loop http://purl.obolibrary.org/obo/SO_0000020 RNA_internal_loop An internal RNA loop where the extent of the loop on both stands is the same size. http://purl.obolibrary.org/obo/SO_0000028 base_pair http://purl.obolibrary.org/obo/SO_0000002 sequence_secondary_structure Two bases paired opposite each other by hydrogen bonds creating a secondary structure. http://purl.obolibrary.org/obo/SO_0000029 WC_base_pair http://purl.obolibrary.org/obo/SO_0000028 base_pair The canonical base pair, where two bases interact via WC edges, with glycosidic bonds oriented cis relative to the axis of orientation. http://purl.obolibrary.org/obo/SO_0000030 sugar_edge_base_pair http://purl.obolibrary.org/obo/SO_0000028 base_pair A type of non-canonical base-pairing. http://purl.obolibrary.org/obo/SO_0000031 aptamer http://purl.obolibrary.org/obo/SO_0000696 oligo DNA or RNA molecules that have been selected from random pools based on their ability to bind other molecules. http://purl.obolibrary.org/obo/SO_0000032 DNA_aptamer http://purl.obolibrary.org/obo/SO_0000031 aptamer DNA molecules that have been selected from random pools based on their ability to bind other molecules. http://purl.obolibrary.org/obo/SO_0000033 RNA_aptamer http://purl.obolibrary.org/obo/SO_0000031 aptamer RNA molecules that have been selected from random pools based on their ability to bind other molecules. http://purl.obolibrary.org/obo/SO_0000035 riboswitch http://purl.obolibrary.org/obo/SO_0000836 mRNA_region A riboswitch is a part of an mRNA that can act as a direct sensor of small molecules to control their own expression. A riboswitch is a cis element in the 5' end of an mRNA, that acts as a direct sensor of metabolites. http://purl.obolibrary.org/obo/SO_0000036 matrix_attachment_site http://purl.obolibrary.org/obo/SO_0000626 chromosomal_regulatory_element A DNA region that is required for the binding of chromatin to the nuclear matrix. http://purl.obolibrary.org/obo/SO_0000037 locus_control_region http://purl.obolibrary.org/obo/SO_0000727 cis_regulatory_module A DNA region that includes DNAse hypersensitive sites located near a gene that confers the high-level, position-independent, and copy number-dependent expression to that gene. http://purl.obolibrary.org/obo/SO_0000039 match_part http://purl.obolibrary.org/obo/SO_0001410 experimental_feature A part of a match, for example an hsp from blast is a match_part. http://purl.obolibrary.org/obo/SO_0000040 genomic_clone http://purl.obolibrary.org/obo/SO_0000151 clone A clone of a DNA region of a genome. http://purl.obolibrary.org/obo/SO_0000043 processed_pseudogene http://purl.obolibrary.org/obo/SO_0000336 pseudogene A pseudogene created via retrotranposition of the mRNA of a functional protein-coding parent gene followed by accumulation of deleterious mutations lacking introns and promoters, often including a polyA tail. http://purl.obolibrary.org/obo/SO_0000044 pseudogene_by_unequal_crossing_over http://purl.obolibrary.org/obo/SO_0001760 non_processed_pseudogene A pseudogene caused by unequal crossing over at recombination. http://purl.obolibrary.org/obo/SO_0000051 probe http://purl.obolibrary.org/obo/SO_0000696 oligo A DNA sequence used experimentally to detect the presence or absence of a complementary nucleic acid. http://purl.obolibrary.org/obo/SO_0000054 aneuploid http://purl.obolibrary.org/obo/SO_1000182 chromosome_number_variation A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number. http://purl.obolibrary.org/obo/SO_0000055 hyperploid http://purl.obolibrary.org/obo/SO_0000054 aneuploid A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as extra chromosomes are present. http://purl.obolibrary.org/obo/SO_0000056 hypoploid http://purl.obolibrary.org/obo/SO_0000054 aneuploid A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number as some chromosomes are missing. http://purl.obolibrary.org/obo/SO_0000057 operator http://purl.obolibrary.org/obo/SO_0001055 transcriptional_cis_regulatory_region A regulatory element of an operon to which activators or repressors bind thereby effecting translation of genes in that operon. http://purl.obolibrary.org/obo/SO_0000059 nuclease_binding_site http://purl.obolibrary.org/obo/SO_0001654 nucleotide_to_protein_binding_site A binding site that, of a nucleotide molecule, that interacts selectively and non-covalently with polypeptide residues of a nuclease. http://purl.obolibrary.org/obo/SO_0000060 compound_chromosome_arm http://purl.obolibrary.org/obo/SO_1000042 compound_chromosome One arm of a compound chromosome. http://purl.obolibrary.org/obo/SO_0000061 restriction_enzyme_binding_site http://purl.obolibrary.org/obo/SO_0000059 nuclease_binding_site A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a restriction enzyme. http://purl.obolibrary.org/obo/SO_0000062 deficient_intrachromosomal_transposition http://purl.obolibrary.org/obo/SO_1000041 intrachromosomal_transposition An intrachromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining. http://purl.obolibrary.org/obo/SO_0000063 deficient_interchromosomal_transposition http://purl.obolibrary.org/obo/SO_1000155 interchromosomal_transposition An interchromosomal transposition whereby a translocation in which one of the four broken ends loses a segment before re-joining. http://purl.obolibrary.org/obo/SO_0000065 free_chromosome_arm http://purl.obolibrary.org/obo/SO_1000183 chromosome_structure_variation A chromosome structure variation whereby an arm exists as an individual chromosome element. http://purl.obolibrary.org/obo/SO_0000068 overlapping http://purl.obolibrary.org/obo/SO_0000067 gene_to_gene_feature An attribute describing a gene that has a sequence that overlaps the sequence of another gene. http://purl.obolibrary.org/obo/SO_0000069 inside_intron http://purl.obolibrary.org/obo/SO_0000068 overlapping An attribute to describe a gene when it is located within the intron of another gene. http://purl.obolibrary.org/obo/SO_0000070 inside_intron_antiparallel http://purl.obolibrary.org/obo/SO_0000069 inside_intron An attribute to describe a gene when it is located within the intron of another gene and on the opposite strand. http://purl.obolibrary.org/obo/SO_0000071 inside_intron_parallel http://purl.obolibrary.org/obo/SO_0000069 inside_intron An attribute to describe a gene when it is located within the intron of another gene and on the same strand. http://purl.obolibrary.org/obo/SO_0000073 five_prime_three_prime_overlap http://purl.obolibrary.org/obo/SO_0000068 overlapping An attribute to describe a gene when the five prime region overlaps with another gene's 3' region. http://purl.obolibrary.org/obo/SO_0000074 five_prime_five_prime_overlap http://purl.obolibrary.org/obo/SO_0000068 overlapping An attribute to describe a gene when the five prime region overlaps with another gene's five prime region. http://purl.obolibrary.org/obo/SO_0000075 three_prime_three_prime_overlap http://purl.obolibrary.org/obo/SO_0000068 overlapping An attribute to describe a gene when the 3' region overlaps with another gene's 3' region. http://purl.obolibrary.org/obo/SO_0000076 three_prime_five_prime_overlap http://purl.obolibrary.org/obo/SO_0000068 overlapping An attribute to describe a gene when the 3' region overlaps with another gene's 5' region. http://purl.obolibrary.org/obo/SO_0000077 antisense http://purl.obolibrary.org/obo/SO_0000068 overlapping A region sequence that is complementary to a sequence of messenger RNA. http://purl.obolibrary.org/obo/SO_0000078 polycistronic_transcript http://purl.obolibrary.org/obo/SO_0000673 transcript A transcript that is polycistronic. http://purl.obolibrary.org/obo/SO_0000079 dicistronic_transcript http://purl.obolibrary.org/obo/SO_0000078 polycistronic_transcript A transcript that is dicistronic. http://purl.obolibrary.org/obo/SO_0000080 operon_member http://purl.obolibrary.org/obo/SO_0000081 gene_array_member A gene that is a member of an operon, which is a set of genes transcribed together as a unit. http://purl.obolibrary.org/obo/SO_0000083 macronuclear_sequence http://purl.obolibrary.org/obo/SO_0000736 organelle_sequence DNA belonging to the macronuclei of ciliates. http://purl.obolibrary.org/obo/SO_0000084 micronuclear_sequence http://purl.obolibrary.org/obo/SO_0000736 organelle_sequence DNA belonging to the micronuclei of a cell. http://purl.obolibrary.org/obo/SO_0000102 expressed_sequence_match http://purl.obolibrary.org/obo/SO_0000347 nucleotide_match A match to an EST or cDNA sequence. http://purl.obolibrary.org/obo/SO_0000103 clone_insert_end http://purl.obolibrary.org/obo/SO_0000699 junction The end of the clone insert. http://purl.obolibrary.org/obo/SO_0000107 sequencing_primer http://purl.obolibrary.org/obo/SO_0000112 primer A single stranded oligo used for polymerase chain reaction. http://purl.obolibrary.org/obo/SO_0000112 primer http://purl.obolibrary.org/obo/SO_0000441 ss_oligo An oligo to which new deoxyribonucleotides can be added by DNA polymerase. http://purl.obolibrary.org/obo/SO_0000113 proviral_region http://purl.obolibrary.org/obo/SO_0001039 integrated_mobile_genetic_element A viral sequence which has integrated into a host genome. http://purl.obolibrary.org/obo/SO_0000114 methylated_cytosine http://purl.obolibrary.org/obo/SO_0001963 modified_cytosine A methylated deoxy-cytosine. http://purl.obolibrary.org/obo/SO_0000116 edited http://purl.obolibrary.org/obo/SO_0000237 transcript_attribute An attribute describing a sequence that is modified by editing. http://purl.obolibrary.org/obo/SO_0000118 transcript_with_translational_frameshift http://purl.obolibrary.org/obo/SO_0000673 transcript A transcript with a translational frameshift. http://purl.obolibrary.org/obo/SO_0000119 regulated http://purl.obolibrary.org/obo/SO_0000401 gene_attribute An attribute to describe a sequence that is regulated. http://purl.obolibrary.org/obo/SO_0000120 protein_coding_primary_transcript http://purl.obolibrary.org/obo/SO_0000185 primary_transcript A primary transcript that, at least in part, encodes one or more proteins. http://purl.obolibrary.org/obo/SO_0000121 forward_primer http://purl.obolibrary.org/obo/SO_0000112 primer A single stranded oligo used for polymerase chain reaction. http://purl.obolibrary.org/obo/SO_0000122 RNA_sequence_secondary_structure http://purl.obolibrary.org/obo/SO_0000002 sequence_secondary_structure A folded RNA sequence. http://purl.obolibrary.org/obo/SO_0000123 transcriptionally_regulated http://purl.obolibrary.org/obo/SO_0000119 regulated An attribute describing a gene that is regulated at transcription. http://purl.obolibrary.org/obo/SO_0000124 transcriptionally_constitutive http://purl.obolibrary.org/obo/SO_0000123 transcriptionally_regulated Expressed in relatively constant amounts without regard to cellular environmental conditions such as the concentration of a particular substrate. http://purl.obolibrary.org/obo/SO_0000125 transcriptionally_induced http://purl.obolibrary.org/obo/SO_0000123 transcriptionally_regulated An inducer molecule is required for transcription to occur. http://purl.obolibrary.org/obo/SO_0000126 transcriptionally_repressed http://purl.obolibrary.org/obo/SO_0000123 transcriptionally_regulated A repressor molecule is required for transcription to stop. http://purl.obolibrary.org/obo/SO_0000130 post_translationally_regulated http://purl.obolibrary.org/obo/SO_0000119 regulated An attribute describing a gene that is regulated after it has been translated. http://purl.obolibrary.org/obo/SO_0000131 translationally_regulated http://purl.obolibrary.org/obo/SO_0000119 regulated An attribute describing a gene that is regulated as it is translated. http://purl.obolibrary.org/obo/SO_0000132 reverse_primer http://purl.obolibrary.org/obo/SO_0000112 primer A single stranded oligo used for polymerase chain reaction. http://purl.obolibrary.org/obo/SO_0000133 epigenetically_modified http://purl.obolibrary.org/obo/SO_0000401 gene_attribute This attribute describes a gene where heritable changes other than those in the DNA sequence occur. These changes include: modification to the DNA (such as DNA methylation, the covalent modification of cytosine), and post-translational modification of histones. http://purl.obolibrary.org/obo/SO_0000134 genomically_imprinted http://purl.obolibrary.org/obo/SO_0000133 epigenetically_modified Imprinted genes are epigenetically modified genes that are expressed monoallelically according to their parent of origin. http://purl.obolibrary.org/obo/SO_0000135 maternally_imprinted http://purl.obolibrary.org/obo/SO_0000134 genomically_imprinted The maternal copy of the gene is modified, rendering it transcriptionally silent. http://purl.obolibrary.org/obo/SO_0000136 paternally_imprinted http://purl.obolibrary.org/obo/SO_0000134 genomically_imprinted The paternal copy of the gene is modified, rendering it transcriptionally silent. http://purl.obolibrary.org/obo/SO_0000137 allelically_excluded http://purl.obolibrary.org/obo/SO_0000133 epigenetically_modified Allelic exclusion is a process occurring in diploid organisms, where a gene is inactivated and not expressed in that cell. http://purl.obolibrary.org/obo/SO_0000140 attenuator http://purl.obolibrary.org/obo/SO_0001680 translation_regulatory_region A sequence segment located within the five prime end of an mRNA that causes premature termination of translation. http://purl.obolibrary.org/obo/SO_0000141 terminator http://purl.obolibrary.org/obo/SO_0001055 transcriptional_cis_regulatory_region The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription. http://purl.obolibrary.org/obo/SO_0000142 DNA_sequence_secondary_structure http://purl.obolibrary.org/obo/SO_0000002 sequence_secondary_structure A folded DNA sequence. http://purl.obolibrary.org/obo/SO_0000145 recoded_codon http://purl.obolibrary.org/obo/SO_0000360 codon A codon that has been redefined at translation. The redefinition may be as a result of translational bypass, translational frameshifting or stop codon readthrough. http://purl.obolibrary.org/obo/SO_0000146 capped http://purl.obolibrary.org/obo/SO_0000237 transcript_attribute An attribute describing when a sequence, usually an mRNA is capped by the addition of a modified guanine nucleotide at the 5' end. http://purl.obolibrary.org/obo/SO_0000147 exon http://purl.obolibrary.org/obo/SO_0000833 transcript_region A region of the transcript sequence within a gene which is not removed from the primary RNA transcript by RNA splicing. http://purl.obolibrary.org/obo/SO_0000151 clone http://purl.obolibrary.org/obo/SO_0000695 reagent A piece of DNA that has been inserted in a vector so that it can be propagated in a host bacterium or some other organism. http://purl.obolibrary.org/obo/SO_0000152 YAC http://purl.obolibrary.org/obo/SO_0000440 vector_replicon Yeast Artificial Chromosome, a vector constructed from the telomeric, centromeric, and replication origin sequences needed for replication in yeast cells. http://purl.obolibrary.org/obo/SO_0000153 BAC http://purl.obolibrary.org/obo/SO_0000440 vector_replicon Bacterial Artificial Chromosome, a cloning vector that can be propagated as mini-chromosomes in a bacterial host. http://purl.obolibrary.org/obo/SO_0000154 PAC http://purl.obolibrary.org/obo/SO_0000440 vector_replicon The P1-derived artificial chromosome are DNA constructs that are derived from the DNA of P1 bacteriophage. They can carry large amounts (about 100-300 kilobases) of other sequences for a variety of bioengineering purposes. It is one type of vector used to clone DNA fragments (100- to 300-kb insert size; average, 150 kb) in Escherichia coli cells. http://purl.obolibrary.org/obo/SO_0000155 plasmid http://purl.obolibrary.org/obo/SO_0001235 replicon A self replicating, using the hosts cellular machinery, often circular nucleic acid molecule that is distinct from a chromosome in the organism. http://purl.obolibrary.org/obo/SO_0000156 cosmid http://purl.obolibrary.org/obo/SO_0000440 vector_replicon A cloning vector that is a hybrid of lambda phages and a plasmid that can be propagated as a plasmid or packaged as a phage,since they retain the lambda cos sites. http://purl.obolibrary.org/obo/SO_0000157 phagemid http://purl.obolibrary.org/obo/SO_0000440 vector_replicon A plasmid which carries within its sequence a bacteriophage replication origin. When the host bacterium is infected with "helper" phage, a phagemid is replicated along with the phage DNA and packaged into phage capsids. http://purl.obolibrary.org/obo/SO_0000158 fosmid http://purl.obolibrary.org/obo/SO_0000440 vector_replicon A cloning vector that utilizes the E. coli F factor. http://purl.obolibrary.org/obo/SO_0000161 methylated_adenine http://purl.obolibrary.org/obo/SO_0001962 modified_adenine A modified base in which adenine has been methylated. http://purl.obolibrary.org/obo/SO_0000163 five_prime_cis_splice_site http://purl.obolibrary.org/obo/SO_0001419 cis_splice_site Intronic 2 bp region bordering the exon, at the 5' edge of the intron. A splice_site that is downstream_adjacent_to exon and starts intron. http://purl.obolibrary.org/obo/SO_0000164 three_prime_cis_splice_site http://purl.obolibrary.org/obo/SO_0001419 cis_splice_site Intronic 2 bp region bordering the exon, at the 3' edge of the intron. A splice_site that is upstream_adjacent_to exon and finishes intron. http://purl.obolibrary.org/obo/SO_0000166 enhancer_bound_by_factor http://purl.obolibrary.org/obo/SO_0000165 enhancer An enhancer bound by a factor. http://purl.obolibrary.org/obo/SO_0000172 CAAT_signal http://purl.obolibrary.org/obo/SO_0000713 DNA_motif Part of a conserved sequence located about 75-bp upstream of the start point of eukaryotic transcription units which may be involved in RNA polymerase binding; consensus=GG(C|T)CAATCT. http://purl.obolibrary.org/obo/SO_0000173 GC_rich_promoter_region http://purl.obolibrary.org/obo/SO_0001659 promoter_element A conserved GC-rich region located upstream of the start point of eukaryotic transcription units which may occur in multiple copies or in either orientation; consensus=GGGCGG. http://purl.obolibrary.org/obo/SO_0000174 TATA_box http://purl.obolibrary.org/obo/SO_0001660 core_eukaryotic_promoter_element A conserved AT-rich septamer found about 25-bp before the start point of many eukaryotic RNA polymerase II transcript units; may be involved in positioning the enzyme for correct initiation; consensus=TATA(A|T)A(A|T). http://purl.obolibrary.org/obo/SO_0000175 minus_10_signal http://purl.obolibrary.org/obo/SO_0000713 DNA_motif A conserved region about 10-bp upstream of the start point of bacterial transcription units which may be involved in binding RNA polymerase; consensus=TAtAaT. This region is associated with sigma factor 70. http://purl.obolibrary.org/obo/SO_0000176 minus_35_signal http://purl.obolibrary.org/obo/SO_0000713 DNA_motif A conserved hexamer about 35-bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA. This region is associated with sigma factor 70. http://purl.obolibrary.org/obo/SO_0000177 cross_genome_match http://purl.obolibrary.org/obo/SO_0000347 nucleotide_match A nucleotide match against a sequence from another organism. http://purl.obolibrary.org/obo/SO_0000178 operon http://purl.obolibrary.org/obo/SO_0005855 gene_group The DNA region of a group of adjacent genes whose transcription is coordinated on one or several mutually overlapping transcription units transcribed in the same direction and sharing at least one gene. http://purl.obolibrary.org/obo/SO_0000179 clone_insert_start http://purl.obolibrary.org/obo/SO_0000699 junction The start of the clone insert. http://purl.obolibrary.org/obo/SO_0000181 translated_nucleotide_match http://purl.obolibrary.org/obo/SO_0000347 nucleotide_match A match against a translated sequence. http://purl.obolibrary.org/obo/SO_0000182 DNA_transposon http://purl.obolibrary.org/obo/SO_0000101 transposable_element A transposon where the mechanism of transposition is via a DNA intermediate. http://purl.obolibrary.org/obo/SO_0000183 non_transcribed_region http://purl.obolibrary.org/obo/SO_0000842 gene_component_region A region of the gene which is not transcribed. http://purl.obolibrary.org/obo/SO_0000184 U2_intron http://purl.obolibrary.org/obo/SO_0000662 spliceosomal_intron A major type of spliceosomal intron spliced by the U2 spliceosome, that includes U1, U2, U4/U6 and U5 snRNAs. http://purl.obolibrary.org/obo/SO_0000189 non_LTR_retrotransposon http://purl.obolibrary.org/obo/SO_0000180 retrotransposon A retrotransposon without long terminal repeat sequences. http://purl.obolibrary.org/obo/SO_0000190 five_prime_intron http://purl.obolibrary.org/obo/SO_0000188 intron An intron that is the most 5-prime in a given transcript. http://purl.obolibrary.org/obo/SO_0000191 interior_intron http://purl.obolibrary.org/obo/SO_0000188 intron An intron that is not the most 3-prime or the most 5-prime in a given transcript. http://purl.obolibrary.org/obo/SO_0000192 three_prime_intron http://purl.obolibrary.org/obo/SO_0000188 intron An intron that is the most 3-prime in a given transcript. http://purl.obolibrary.org/obo/SO_0000193 RFLP_fragment http://purl.obolibrary.org/obo/SO_0000412 restriction_fragment A DNA fragment used as a reagent to detect the polymorphic genomic loci by hybridizing against the genomic DNA digested with a given restriction enzyme. http://purl.obolibrary.org/obo/SO_0000194 LINE_element http://purl.obolibrary.org/obo/SO_0000189 non_LTR_retrotransposon A dispersed repeat family with many copies, each from 1 to 6 kb long. New elements are generated by retroposition of a transcribed copy. Typically the LINE contains 2 ORF's one of which is reverse transcriptase, and 3'and 5' direct repeats. http://purl.obolibrary.org/obo/SO_0000195 coding_exon http://purl.obolibrary.org/obo/SO_0000147 exon An exon whereby at least one base is part of a codon (here, 'codon' is inclusive of the stop_codon). http://purl.obolibrary.org/obo/SO_0000196 five_prime_coding_exon_coding_region http://purl.obolibrary.org/obo/SO_0001215 coding_region_of_exon The sequence of the five_prime_coding_exon that codes for protein. http://purl.obolibrary.org/obo/SO_0000197 three_prime_coding_exon_coding_region http://purl.obolibrary.org/obo/SO_0001215 coding_region_of_exon The sequence of the three_prime_coding_exon that codes for protein. http://purl.obolibrary.org/obo/SO_0000198 noncoding_exon http://purl.obolibrary.org/obo/SO_0000147 exon An exon that does not contain any codons. http://purl.obolibrary.org/obo/SO_0000200 five_prime_coding_exon http://purl.obolibrary.org/obo/SO_0000195 coding_exon The 5' most coding exon. http://purl.obolibrary.org/obo/SO_0000201 interior_exon http://purl.obolibrary.org/obo/SO_0000147 exon An exon that is bounded by 5' and 3' splice sites. http://purl.obolibrary.org/obo/SO_0000202 three_prime_coding_exon http://purl.obolibrary.org/obo/SO_0000195 coding_exon The coding exon that is most 3-prime on a given transcript. http://purl.obolibrary.org/obo/SO_0000203 UTR http://purl.obolibrary.org/obo/SO_0000836 mRNA_region Messenger RNA sequences that are untranslated and lie five prime or three prime to sequences which are translated. http://purl.obolibrary.org/obo/SO_0000204 five_prime_UTR http://purl.obolibrary.org/obo/SO_0000203 UTR A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein. http://purl.obolibrary.org/obo/SO_0000205 three_prime_UTR http://purl.obolibrary.org/obo/SO_0000203 UTR A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein. http://purl.obolibrary.org/obo/SO_0000206 SINE_element http://purl.obolibrary.org/obo/SO_0000189 non_LTR_retrotransposon A repetitive element, a few hundred base pairs long, that is dispersed throughout the genome. A common human SINE is the Alu element. http://purl.obolibrary.org/obo/SO_0000208 terminal_inverted_repeat_element http://purl.obolibrary.org/obo/SO_0000182 DNA_transposon A DNA transposable element defined as having termini with perfect, or nearly perfect short inverted repeats, generally 10 - 40 nucleotides long. http://purl.obolibrary.org/obo/SO_0000211 alanine_tRNA_primary_transcript http://purl.obolibrary.org/obo/SO_0000210 tRNA_primary_transcript A primary transcript encoding alanyl tRNA. http://purl.obolibrary.org/obo/SO_0000212 arginine_tRNA_primary_transcript http://purl.obolibrary.org/obo/SO_0000210 tRNA_primary_transcript A primary transcript encoding arginyl tRNA (SO:0000255). http://purl.obolibrary.org/obo/SO_0000213 asparagine_tRNA_primary_transcript http://purl.obolibrary.org/obo/SO_0000210 tRNA_primary_transcript A primary transcript encoding asparaginyl tRNA (SO:0000256). http://purl.obolibrary.org/obo/SO_0000214 aspartic_acid_tRNA_primary_transcript http://purl.obolibrary.org/obo/SO_0000210 tRNA_primary_transcript A primary transcript encoding aspartyl tRNA (SO:0000257). http://purl.obolibrary.org/obo/SO_0000215 cysteine_tRNA_primary_transcript http://purl.obolibrary.org/obo/SO_0000210 tRNA_primary_transcript A primary transcript encoding cysteinyl tRNA (SO:0000258). http://purl.obolibrary.org/obo/SO_0000216 glutamic_acid_tRNA_primary_transcript http://purl.obolibrary.org/obo/SO_0000210 tRNA_primary_transcript A primary transcript encoding glutaminyl tRNA (SO:0000260). http://purl.obolibrary.org/obo/SO_0000217 glutamine_tRNA_primary_transcript http://purl.obolibrary.org/obo/SO_0000210 tRNA_primary_transcript A primary transcript encoding glutamyl tRNA (SO:0000260). http://purl.obolibrary.org/obo/SO_0000218 glycine_tRNA_primary_transcript http://purl.obolibrary.org/obo/SO_0000210 tRNA_primary_transcript A primary transcript encoding glycyl tRNA (SO:0000263). http://purl.obolibrary.org/obo/SO_0000219 histidine_tRNA_primary_transcript http://purl.obolibrary.org/obo/SO_0000210 tRNA_primary_transcript A primary transcript encoding histidyl tRNA (SO:0000262). http://purl.obolibrary.org/obo/SO_0000220 isoleucine_tRNA_primary_transcript http://purl.obolibrary.org/obo/SO_0000210 tRNA_primary_transcript A primary transcript encoding isoleucyl tRNA (SO:0000263). http://purl.obolibrary.org/obo/SO_0000221 leucine_tRNA_primary_transcript http://purl.obolibrary.org/obo/SO_0000210 tRNA_primary_transcript A primary transcript encoding leucyl tRNA (SO:0000264). http://purl.obolibrary.org/obo/SO_0000222 lysine_tRNA_primary_transcript http://purl.obolibrary.org/obo/SO_0000210 tRNA_primary_transcript A primary transcript encoding lysyl tRNA (SO:0000265). http://purl.obolibrary.org/obo/SO_0000223 methionine_tRNA_primary_transcript http://purl.obolibrary.org/obo/SO_0000210 tRNA_primary_transcript A primary transcript encoding methionyl tRNA (SO:0000266). http://purl.obolibrary.org/obo/SO_0000224 phenylalanine_tRNA_primary_transcript http://purl.obolibrary.org/obo/SO_0000210 tRNA_primary_transcript A primary transcript encoding phenylalanyl tRNA (SO:0000267). http://purl.obolibrary.org/obo/SO_0000225 proline_tRNA_primary_transcript http://purl.obolibrary.org/obo/SO_0000210 tRNA_primary_transcript A primary transcript encoding prolyl tRNA (SO:0000268). http://purl.obolibrary.org/obo/SO_0000226 serine_tRNA_primary_transcript http://purl.obolibrary.org/obo/SO_0000210 tRNA_primary_transcript A primary transcript encoding seryl tRNA (SO:000269). http://purl.obolibrary.org/obo/SO_0000227 threonine_tRNA_primary_transcript http://purl.obolibrary.org/obo/SO_0000210 tRNA_primary_transcript A primary transcript encoding threonyl tRNA (SO:000270). http://purl.obolibrary.org/obo/SO_0000228 tryptophan_tRNA_primary_transcript http://purl.obolibrary.org/obo/SO_0000210 tRNA_primary_transcript A primary transcript encoding tryptophanyl tRNA (SO:000271). http://purl.obolibrary.org/obo/SO_0000229 tyrosine_tRNA_primary_transcript http://purl.obolibrary.org/obo/SO_0000210 tRNA_primary_transcript A primary transcript encoding tyrosyl tRNA (SO:000272). http://purl.obolibrary.org/obo/SO_0000230 valine_tRNA_primary_transcript http://purl.obolibrary.org/obo/SO_0000210 tRNA_primary_transcript A primary transcript encoding valyl tRNA (SO:000273). http://purl.obolibrary.org/obo/SO_0000236 ORF http://purl.obolibrary.org/obo/SO_0000717 reading_frame The in-frame interval between the stop codons of a reading frame which when read as sequential triplets, has the potential of encoding a sequential string of amino acids. TER(NNN)nTER. http://purl.obolibrary.org/obo/SO_0000238 foldback_element http://purl.obolibrary.org/obo/SO_0000182 DNA_transposon A transposable element with extensive secondary structure, characterized by large modular imperfect long inverted repeats. http://purl.obolibrary.org/obo/SO_0000240 chromosome_variation http://purl.obolibrary.org/obo/SO_0001507 variant_collection A deviation in chromosome structure or number. http://purl.obolibrary.org/obo/SO_0000241 internal_UTR http://purl.obolibrary.org/obo/SO_0000203 UTR A UTR bordered by the terminal and initial codons of two CDSs in a polycistronic transcript. Every UTR is either 5', 3' or internal. http://purl.obolibrary.org/obo/SO_0000242 untranslated_region_polycistronic_mRNA http://purl.obolibrary.org/obo/SO_0000203 UTR The untranslated sequence separating the 'cistrons' of multicistronic mRNA. http://purl.obolibrary.org/obo/SO_0000243 internal_ribosome_entry_site http://purl.obolibrary.org/obo/SO_0000139 ribosome_entry_site Sequence element that recruits a ribosomal subunit to internal mRNA for translation initiation. http://purl.obolibrary.org/obo/SO_0000250 modified_RNA_base_feature http://purl.obolibrary.org/obo/SO_0001236 base A post_transcriptionally modified base. http://purl.obolibrary.org/obo/SO_0000254 alanyl_tRNA http://purl.obolibrary.org/obo/SO_0000253 tRNA A tRNA sequence that has an alanine anticodon, and a 3' alanine binding region. http://purl.obolibrary.org/obo/SO_0000256 asparaginyl_tRNA http://purl.obolibrary.org/obo/SO_0000253 tRNA A tRNA sequence that has an asparagine anticodon, and a 3' asparagine binding region. http://purl.obolibrary.org/obo/SO_0000257 aspartyl_tRNA http://purl.obolibrary.org/obo/SO_0000253 tRNA A tRNA sequence that has an aspartic acid anticodon, and a 3' aspartic acid binding region. http://purl.obolibrary.org/obo/SO_0000258 cysteinyl_tRNA http://purl.obolibrary.org/obo/SO_0000253 tRNA A tRNA sequence that has a cysteine anticodon, and a 3' cysteine binding region. http://purl.obolibrary.org/obo/SO_0000259 glutaminyl_tRNA http://purl.obolibrary.org/obo/SO_0000253 tRNA A tRNA sequence that has a glutamine anticodon, and a 3' glutamine binding region. http://purl.obolibrary.org/obo/SO_0000260 glutamyl_tRNA http://purl.obolibrary.org/obo/SO_0000253 tRNA A tRNA sequence that has a glutamic acid anticodon, and a 3' glutamic acid binding region. http://purl.obolibrary.org/obo/SO_0000261 glycyl_tRNA http://purl.obolibrary.org/obo/SO_0000253 tRNA A tRNA sequence that has a glycine anticodon, and a 3' glycine binding region. http://purl.obolibrary.org/obo/SO_0000262 histidyl_tRNA http://purl.obolibrary.org/obo/SO_0000253 tRNA A tRNA sequence that has a histidine anticodon, and a 3' histidine binding region. http://purl.obolibrary.org/obo/SO_0000263 isoleucyl_tRNA http://purl.obolibrary.org/obo/SO_0000253 tRNA A tRNA sequence that has an isoleucine anticodon, and a 3' isoleucine binding region. http://purl.obolibrary.org/obo/SO_0000264 leucyl_tRNA http://purl.obolibrary.org/obo/SO_0000253 tRNA A tRNA sequence that has a leucine anticodon, and a 3' leucine binding region. http://purl.obolibrary.org/obo/SO_0000265 lysyl_tRNA http://purl.obolibrary.org/obo/SO_0000253 tRNA A tRNA sequence that has a lysine anticodon, and a 3' lysine binding region. http://purl.obolibrary.org/obo/SO_0000266 methionyl_tRNA http://purl.obolibrary.org/obo/SO_0000253 tRNA A tRNA sequence that has a methionine anticodon, and a 3' methionine binding region. http://purl.obolibrary.org/obo/SO_0000267 phenylalanyl_tRNA http://purl.obolibrary.org/obo/SO_0000253 tRNA A tRNA sequence that has a phenylalanine anticodon, and a 3' phenylalanine binding region. http://purl.obolibrary.org/obo/SO_0000268 prolyl_tRNA http://purl.obolibrary.org/obo/SO_0000253 tRNA A tRNA sequence that has a proline anticodon, and a 3' proline binding region. http://purl.obolibrary.org/obo/SO_0000269 seryl_tRNA http://purl.obolibrary.org/obo/SO_0000253 tRNA A tRNA sequence that has a serine anticodon, and a 3' serine binding region. http://purl.obolibrary.org/obo/SO_0000270 threonyl_tRNA http://purl.obolibrary.org/obo/SO_0000253 tRNA A tRNA sequence that has a threonine anticodon, and a 3' threonine binding region. http://purl.obolibrary.org/obo/SO_0000271 tryptophanyl_tRNA http://purl.obolibrary.org/obo/SO_0000253 tRNA A tRNA sequence that has a tryptophan anticodon, and a 3' tryptophan binding region. http://purl.obolibrary.org/obo/SO_0000272 tyrosyl_tRNA http://purl.obolibrary.org/obo/SO_0000253 tRNA A tRNA sequence that has a tyrosine anticodon, and a 3' tyrosine binding region. http://purl.obolibrary.org/obo/SO_0000273 valyl_tRNA http://purl.obolibrary.org/obo/SO_0000253 tRNA A tRNA sequence that has a valine anticodon, and a 3' valine binding region. http://purl.obolibrary.org/obo/SO_0000277 bound_by_factor http://purl.obolibrary.org/obo/SO_0000733 feature_attribute An attribute describing a sequence that is bound by another molecule. http://purl.obolibrary.org/obo/SO_0000278 transcript_bound_by_nucleic_acid http://purl.obolibrary.org/obo/SO_0000673 transcript A transcript that is bound by a nucleic acid. http://purl.obolibrary.org/obo/SO_0000279 transcript_bound_by_protein http://purl.obolibrary.org/obo/SO_0000673 transcript A transcript that is bound by a protein. http://purl.obolibrary.org/obo/SO_0000290 dinucleotide_repeat_microsatellite_feature http://purl.obolibrary.org/obo/SO_0000289 microsatellite A region of a repeating dinucleotide sequence (two bases). http://purl.obolibrary.org/obo/SO_0000291 trinucleotide_repeat_microsatellite_feature http://purl.obolibrary.org/obo/SO_0000289 microsatellite A region of a repeating trinucleotide sequence (three bases). http://purl.obolibrary.org/obo/SO_0000293 engineered_foreign_repetitive_element http://purl.obolibrary.org/obo/SO_0000657 repeat_region A repetitive element that is engineered and foreign. http://purl.obolibrary.org/obo/SO_0000294 inverted_repeat http://purl.obolibrary.org/obo/SO_0000657 repeat_region The sequence is complementarily repeated on the opposite strand. It is a palindrome, and it may, or may not be hyphenated. Examples: GCTGATCAGC, or GCTGA-----TCAGC. http://purl.obolibrary.org/obo/SO_0000295 U12_intron http://purl.obolibrary.org/obo/SO_0000662 spliceosomal_intron A type of spliceosomal intron spliced by the U12 spliceosome, that includes U11, U12, U4atac/U6atac and U5 snRNAs. http://purl.obolibrary.org/obo/SO_0000297 D_loop http://purl.obolibrary.org/obo/SO_0001411 biological_region Displacement loop; a region within mitochondrial DNA in which a short stretch of RNA is paired with one strand of DNA, displacing the original partner DNA strand in this region; also used to describe the displacement of a region of one strand of duplex DNA by a single stranded invader in the reaction catalyzed by RecA protein. http://purl.obolibrary.org/obo/SO_0000299 specific_recombination_site http://purl.obolibrary.org/obo/SO_0000669 sequence_rearrangement_feature A location where recombination or occurs during mitosis or meiosis. http://purl.obolibrary.org/obo/SO_0000300 recombination_feature_of_rearranged_gene http://purl.obolibrary.org/obo/SO_0000299 specific_recombination_site A location where a gene is rearranged due to recombination during mitosis or meiosis. http://purl.obolibrary.org/obo/SO_0000301 vertebrate_immune_system_gene_recombination_feature http://purl.obolibrary.org/obo/SO_0000300 recombination_feature_of_rearranged_gene A feature where recombination has occurred for the purpose of generating a diversity in the immune system. http://purl.obolibrary.org/obo/SO_0000302 J_gene_recombination_feature http://purl.obolibrary.org/obo/SO_0000939 vertebrate_immune_system_gene_recombination_signal_feature Recombination signal including J-heptamer, J-spacer and J-nonamer in 5' of J-region of a J-gene or J-sequence. http://purl.obolibrary.org/obo/SO_0000303 clip http://purl.obolibrary.org/obo/SO_0000835 primary_transcript_region Part of the primary transcript that is clipped off during processing. http://purl.obolibrary.org/obo/SO_0000305 modified_DNA_base http://purl.obolibrary.org/obo/SO_0001720 epigenetically_modified_region A modified nucleotide, i.e. a nucleotide other than A, T, C. G. http://purl.obolibrary.org/obo/SO_0000306 methylated_DNA_base_feature http://purl.obolibrary.org/obo/SO_0000305 modified_DNA_base A nucleotide modified by methylation. http://purl.obolibrary.org/obo/SO_0000312 experimentally_determined http://purl.obolibrary.org/obo/SO_0000789 validated Attribute to describe a feature that has been experimentally verified. http://purl.obolibrary.org/obo/SO_0000313 stem_loop http://purl.obolibrary.org/obo/SO_0000122 RNA_sequence_secondary_structure A double-helical region of nucleic acid formed by base-pairing between adjacent (inverted) complementary sequences. http://purl.obolibrary.org/obo/SO_0000314 direct_repeat http://purl.obolibrary.org/obo/SO_0000657 repeat_region A repeat where the same sequence is repeated in the same direction. Example: GCTGA-followed by-GCTGA. http://purl.obolibrary.org/obo/SO_0000315 TSS http://purl.obolibrary.org/obo/SO_0000835 primary_transcript_region The first base where RNA polymerase begins to synthesize the RNA transcript. http://purl.obolibrary.org/obo/SO_0000316 CDS http://purl.obolibrary.org/obo/SO_0000836 mRNA_region A contiguous sequence which begins with, and includes, a start codon and ends with, and includes, a stop codon. http://purl.obolibrary.org/obo/SO_0000317 cDNA_clone http://purl.obolibrary.org/obo/SO_0000151 clone Complementary DNA; A piece of DNA copied from an mRNA and spliced into a vector for propagation in a suitable host. http://purl.obolibrary.org/obo/SO_0000318 start_codon http://purl.obolibrary.org/obo/SO_0000360 codon First codon to be translated by a ribosome. http://purl.obolibrary.org/obo/SO_0000319 stop_codon http://purl.obolibrary.org/obo/SO_0000360 codon In mRNA, a set of three nucleotides that indicates the end of information for protein synthesis. In genomic sequence, a stop codon may be only one or two nucleotides where the additional nucleotides are provided in the RNA via polyadenylation. http://purl.obolibrary.org/obo/SO_0000320 intronic_splice_enhancer http://purl.obolibrary.org/obo/SO_0000344 splice_enhancer Sequences within the intron that modulate splice site selection for some introns. http://purl.obolibrary.org/obo/SO_0000322 nuclease_hypersensitive_site http://purl.obolibrary.org/obo/SO_0002331 accessible_DNA_region A region of nucleotide sequence targeted by a nuclease enzyme that is found cleaved more than would be expected by chance. http://purl.obolibrary.org/obo/SO_0000323 coding_start http://purl.obolibrary.org/obo/SO_0000851 CDS_region The first base to be translated into protein. http://purl.obolibrary.org/obo/SO_0000324 tag http://purl.obolibrary.org/obo/SO_0000696 oligo A nucleotide sequence that may be used to identify a larger sequence. http://purl.obolibrary.org/obo/SO_0000326 SAGE_tag http://purl.obolibrary.org/obo/SO_0000324 tag A short diagnostic sequence tag, serial analysis of gene expression (SAGE), that allows the quantitative and simultaneous analysis of a large number of transcripts. http://purl.obolibrary.org/obo/SO_0000327 coding_end http://purl.obolibrary.org/obo/SO_0000851 CDS_region The last base to be translated into protein. It does not include the stop codon. http://purl.obolibrary.org/obo/SO_0000328 microarray_oligo http://purl.obolibrary.org/obo/SO_0000051 probe A DNA sequence used experimentally to detect the presence or absence of a complementary nucleic acid. http://purl.obolibrary.org/obo/SO_0000331 STS http://purl.obolibrary.org/obo/SO_0000324 tag Short (typically a few hundred base pairs) DNA sequence that has a single occurrence in a genome and whose location and base sequence are known. http://purl.obolibrary.org/obo/SO_0000332 coding_conserved_region http://purl.obolibrary.org/obo/SO_0000330 conserved_region Coding region of sequence similarity by descent from a common ancestor. http://purl.obolibrary.org/obo/SO_0000333 exon_junction http://purl.obolibrary.org/obo/SO_0000699 junction The boundary between two exons in a processed transcript. http://purl.obolibrary.org/obo/SO_0000334 nc_conserved_region http://purl.obolibrary.org/obo/SO_0000330 conserved_region Non-coding region of sequence similarity by descent from a common ancestor. http://purl.obolibrary.org/obo/SO_0000338 MITE http://purl.obolibrary.org/obo/SO_0000208 terminal_inverted_repeat_element A highly repetitive and short (100-500 base pair) transposable element with terminal inverted repeats (TIR) and target site duplication (TSD). MITEs do not encode proteins. http://purl.obolibrary.org/obo/SO_0000342 site_specific_recombination_target_region http://purl.obolibrary.org/obo/SO_0000299 specific_recombination_site A region specifically recognised by a recombinase where recombination can occur during mitosis or meiosis. http://purl.obolibrary.org/obo/SO_0000343 match http://purl.obolibrary.org/obo/SO_0001410 experimental_feature A region of sequence, aligned to another sequence with some statistical significance, using an algorithm such as BLAST or SIM4. http://purl.obolibrary.org/obo/SO_0000344 splice_enhancer http://purl.obolibrary.org/obo/SO_0001056 splicing_regulatory_region Region of a transcript that regulates splicing. http://purl.obolibrary.org/obo/SO_0000345 EST http://purl.obolibrary.org/obo/SO_0000324 tag A tag produced from a single sequencing read from a cDNA clone or PCR product; typically a few hundred base pairs long. http://purl.obolibrary.org/obo/SO_0000346 loxP_site http://purl.obolibrary.org/obo/SO_0000947 resolution_site Cre-Recombination target sequence. http://purl.obolibrary.org/obo/SO_0000347 nucleotide_match http://purl.obolibrary.org/obo/SO_0000343 match A match against a nucleotide sequence. http://purl.obolibrary.org/obo/SO_0000349 protein_match http://purl.obolibrary.org/obo/SO_0000343 match A match against a protein sequence. http://purl.obolibrary.org/obo/SO_0000350 FRT_site http://purl.obolibrary.org/obo/SO_0000948 inversion_site An inversion site found on the Saccharomyces cerevisiae 2 micron plasmid. http://purl.obolibrary.org/obo/SO_0000351 synthetic_sequence http://purl.obolibrary.org/obo/SO_0000443 polymer_attribute An attribute to decide a sequence of nucleotides, nucleotide analogs, or amino acids that has been designed by an experimenter and which may, or may not, correspond with any natural sequence. http://purl.obolibrary.org/obo/SO_0000354 group_1_intron_homing_endonuclease_target_region http://purl.obolibrary.org/obo/SO_0000684 nuclease_sensitive_site A region of intronic nucleotide sequence targeted by a nuclease enzyme. http://purl.obolibrary.org/obo/SO_0000357 flanked http://purl.obolibrary.org/obo/SO_0000733 feature_attribute An attribute describing a region that is bounded either side by a particular kind of region. http://purl.obolibrary.org/obo/SO_0000359 floxed http://purl.obolibrary.org/obo/SO_0000357 flanked An attribute describing sequence that is flanked by Lox-P sites. http://purl.obolibrary.org/obo/SO_0000360 codon http://purl.obolibrary.org/obo/SO_0000851 CDS_region A set of (usually) three nucleotide bases in a DNA or RNA sequence, which together code for a unique amino acid or the termination of translation and are contained within the CDS. http://purl.obolibrary.org/obo/SO_0000361 FRT_flanked http://purl.obolibrary.org/obo/SO_0000357 flanked An attribute to describe sequence that is flanked by the FLP recombinase recognition site, FRT. http://purl.obolibrary.org/obo/SO_0000362 invalidated_by_chimeric_cDNA http://purl.obolibrary.org/obo/SO_0000790 invalidated A cDNA clone constructed from more than one mRNA. Usually an experimental artifact. http://purl.obolibrary.org/obo/SO_0000365 integron http://purl.obolibrary.org/obo/SO_0001039 integrated_mobile_genetic_element A region encoding an integrase which acts at a site adjacent to it (attI_site) to insert DNA which must include but is not limited to an attC_site. http://purl.obolibrary.org/obo/SO_0000367 attI_site http://purl.obolibrary.org/obo/SO_0000946 integration_excision_site A region within an integron, adjacent to an integrase, at which site specific recombination involving an attC_site takes place. http://purl.obolibrary.org/obo/SO_0000371 conjugative_transposon http://purl.obolibrary.org/obo/SO_0000182 DNA_transposon A transposon that encodes function required for conjugation. http://purl.obolibrary.org/obo/SO_0000372 enzymatic_RNA http://purl.obolibrary.org/obo/SO_0000655 ncRNA An RNA sequence that has catalytic activity with or without an associated ribonucleoprotein. http://purl.obolibrary.org/obo/SO_0000374 ribozyme http://purl.obolibrary.org/obo/SO_0000372 enzymatic_RNA An RNA with catalytic activity. http://purl.obolibrary.org/obo/SO_0000379 GcvB_RNA http://purl.obolibrary.org/obo/SO_0000378 DsrA_RNA A small untranslated RNA involved in expression of the dipeptide and oligopeptide transport systems in Escherichia coli. http://purl.obolibrary.org/obo/SO_0000380 hammerhead_ribozyme http://purl.obolibrary.org/obo/SO_0000715 RNA_motif A small catalytic RNA motif that catalyzes self-cleavage reaction. Its name comes from its secondary structure which resembles a carpenter's hammer. The hammerhead ribozyme is involved in the replication of some viroid and some satellite RNAs. http://purl.obolibrary.org/obo/SO_0000381 group_IIA_intron http://purl.obolibrary.org/obo/SO_0000603 group_II_intron A group II intron that recognizes IBS1/EBS1 and IBS2/EBS2 for the 5-prime exon and gamma/gamma-prime for the 3-prime exon. http://purl.obolibrary.org/obo/SO_0000382 group_IIB_intron http://purl.obolibrary.org/obo/SO_0000603 group_II_intron A group II intron that recognizes IBS1/EBS1 and IBS2/EBS2 for the 5-prime exon and IBS3/EBS3 for the 3-prime exon. http://purl.obolibrary.org/obo/SO_0000383 MicF_RNA http://purl.obolibrary.org/obo/SO_0000644 antisense_RNA A non-translated 93 nt antisense RNA that binds its target ompF mRNA and regulates ompF expression by inhibiting translation and inducing degradation of the message. http://purl.obolibrary.org/obo/SO_0000385 RNase_MRP_RNA http://purl.obolibrary.org/obo/SO_0000372 enzymatic_RNA The RNA molecule essential for the catalytic activity of RNase MRP, an enzymatically active ribonucleoprotein with two distinct roles in eukaryotes. In mitochondria it plays a direct role in the initiation of mitochondrial DNA replication. In the nucleus it is involved in precursor rRNA processing, where it cleaves the internal transcribed spacer 1 between 18S and 5.8S rRNAs. http://purl.obolibrary.org/obo/SO_0000386 RNase_P_RNA http://purl.obolibrary.org/obo/SO_0000372 enzymatic_RNA The RNA component of Ribonuclease P (RNase P), a ubiquitous endoribonuclease, found in archaea, bacteria and eukarya as well as chloroplasts and mitochondria. Its best characterized activity is the generation of mature 5 prime ends of tRNAs by cleaving the 5 prime leader elements of precursor-tRNAs. Cellular RNase Ps are ribonucleoproteins. RNA from bacterial RNase Ps retains its catalytic activity in the absence of the protein subunit, i.e. it is a ribozyme. Isolated eukaryotic and archaeal RNase P RNA has not been shown to retain its catalytic function, but is still essential for the catalytic activity of the holoenzyme. Although the archaeal and eukaryotic holoenzymes have a much greater protein content than the bacterial ones, the RNA cores from all the three lineages are homologous. Helices corresponding to P1, P2, P3, P4, and P10/11 are common to all cellular RNase P RNAs. Yet, there is considerable sequence variation, particularly among the eukaryotic RNAs. http://purl.obolibrary.org/obo/SO_0000390 telomerase_RNA http://purl.obolibrary.org/obo/SO_0000655 ncRNA The RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA. http://purl.obolibrary.org/obo/SO_0000391 U1_snRNA http://purl.obolibrary.org/obo/SO_0000274 snRNA U1 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Its 5' end forms complementary base pairs with the 5' splice junction, thus defining the 5' donor site of an intron. There are significant differences in sequence and secondary structure between metazoan and yeast U1 snRNAs, the latter being much longer (568 nucleotides as compared to 164 nucleotides in human). Nevertheless, secondary structure predictions suggest that all U1 snRNAs share a 'common core' consisting of helices I, II, the proximal region of III, and IV. http://purl.obolibrary.org/obo/SO_0000392 U2_snRNA http://purl.obolibrary.org/obo/SO_0000274 snRNA U2 is a small nuclear RNA (snRNA) component of the spliceosome (involved in pre-mRNA splicing). Complementary binding between U2 snRNA (in an area lying towards the 5' end but 3' to hairpin I) and the branchpoint sequence (BPS) of the intron results in the bulging out of an unpaired adenine, on the BPS, which initiates a nucleophilic attack at the intronic 5' splice site, thus starting the first of two transesterification reactions that mediate splicing. http://purl.obolibrary.org/obo/SO_0000393 U4_snRNA http://purl.obolibrary.org/obo/SO_0000274 snRNA U4 small nuclear RNA (U4 snRNA) is a component of the major U2-dependent spliceosome. It forms a duplex with U6, and with each splicing round, it is displaced from U6 (and the spliceosome) in an ATP-dependent manner, allowing U6 to refold and create the active site for splicing catalysis. A recycling process involving protein Prp24 re-anneals U4 and U6. http://purl.obolibrary.org/obo/SO_0000394 U4atac_snRNA http://purl.obolibrary.org/obo/SO_0000274 snRNA An snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U6atac_snRNA (SO:0000397). http://purl.obolibrary.org/obo/SO_0000395 U5_snRNA http://purl.obolibrary.org/obo/SO_0000274 snRNA U5 RNA is a component of both types of known spliceosome. The precise function of this molecule is unknown, though it is known that the 5' loop is required for splice site selection and p220 binding, and that both the 3' stem-loop and the Sm site are important for Sm protein binding and cap methylation. http://purl.obolibrary.org/obo/SO_0000396 U6_snRNA http://purl.obolibrary.org/obo/SO_0000274 snRNA U6 snRNA is a component of the spliceosome which is involved in splicing pre-mRNA. The putative secondary structure consensus base pairing is confined to a short 5' stem loop, but U6 snRNA is thought to form extensive base-pair interactions with U4 snRNA. http://purl.obolibrary.org/obo/SO_0000397 U6atac_snRNA http://purl.obolibrary.org/obo/SO_0000274 snRNA U6atac_snRNA is an snRNA required for the splicing of the minor U12-dependent class of eukaryotic nuclear introns. It forms a base paired complex with U4atac_snRNA (SO:0000394). http://purl.obolibrary.org/obo/SO_0000398 U11_snRNA http://purl.obolibrary.org/obo/SO_0000274 snRNA U11 snRNA plays a role in splicing of the minor U12-dependent class of eukaryotic nuclear introns, similar to U1 snRNA in the major class spliceosome it base pairs to the conserved 5' splice site sequence. http://purl.obolibrary.org/obo/SO_0000399 U12_snRNA http://purl.obolibrary.org/obo/SO_0000274 snRNA The U12 small nuclear (snRNA), together with U4atac/U6atac, U5, and U11 snRNAs and associated proteins, forms a spliceosome that cleaves a divergent class of low-abundance pre-mRNA introns. http://purl.obolibrary.org/obo/SO_0000403 U14_snoRNA http://purl.obolibrary.org/obo/SO_0000593 C_D_box_snoRNA U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region (known as the Y-domain) which is essential for function. A similar structure, but with a different consensus sequence, is found in plants, but is absent in vertebrates. http://purl.obolibrary.org/obo/SO_0000404 vault_RNA http://purl.obolibrary.org/obo/SO_0000655 ncRNA A family of RNAs are found as part of the enigmatic vault ribonucleoprotein complex. The complex consists of a major vault protein (MVP), two minor vault proteins (VPARP and TEP1), and several small untranslated RNA molecules. It has been suggested that the vault complex is involved in drug resistance. http://purl.obolibrary.org/obo/SO_0000405 Y_RNA http://purl.obolibrary.org/obo/SO_0000655 ncRNA Y RNAs are components of the Ro ribonucleoprotein particle (Ro RNP), in association with Ro60 and La proteins. The Y RNAs and Ro60 and La proteins are well conserved, but the function of the Ro RNP is not known. In humans the RNA component can be one of four small RNAs: hY1, hY3, hY4 and hY5. These small RNAs are predicted to fold into a conserved secondary structure containing three stem structures. The largest of the four, hY1, contains an additional hairpin. http://purl.obolibrary.org/obo/SO_0000406 twintron http://purl.obolibrary.org/obo/SO_0000188 intron An intron within an intron. Twintrons are group II or III introns, into which another group II or III intron has been transposed. http://purl.obolibrary.org/obo/SO_0000411 rescue_region http://purl.obolibrary.org/obo/SO_0000695 reagent A region that rescues. http://purl.obolibrary.org/obo/SO_0000412 restriction_fragment http://purl.obolibrary.org/obo/SO_0000143 assembly_component A region of polynucleotide sequence produced by digestion with a restriction endonuclease. http://purl.obolibrary.org/obo/SO_0000413 sequence_difference http://purl.obolibrary.org/obo/SO_0000700 remark A region where the sequence differs from that of a specified sequence. http://purl.obolibrary.org/obo/SO_0000414 invalidated_by_genomic_contamination http://purl.obolibrary.org/obo/SO_0000790 invalidated An attribute to describe a feature that is invalidated due to genomic contamination. http://purl.obolibrary.org/obo/SO_0000415 invalidated_by_genomic_polyA_primed_cDNA http://purl.obolibrary.org/obo/SO_0000790 invalidated An attribute to describe a feature that is invalidated due to polyA priming. http://purl.obolibrary.org/obo/SO_0000416 invalidated_by_partial_processing http://purl.obolibrary.org/obo/SO_0000790 invalidated An attribute to describe a feature that is invalidated due to partial processing. http://purl.obolibrary.org/obo/SO_0000417 polypeptide_domain http://purl.obolibrary.org/obo/SO_0100021 polypeptide_conserved_region A structurally or functionally defined protein region. In proteins with multiple domains, the combination of the domains determines the function of the protein. A region which has been shown to recur throughout evolution. http://purl.obolibrary.org/obo/SO_0000419 mature_protein_region http://purl.obolibrary.org/obo/SO_0000839 polypeptide_region The polypeptide sequence that remains when the cleaved peptide regions have been cleaved from the immature peptide. http://purl.obolibrary.org/obo/SO_0000420 five_prime_terminal_inverted_repeat http://purl.obolibrary.org/obo/SO_0000481 terminal_inverted_repeat An inverted repeat (SO:0000294) occurring at the 5-prime termini of a DNA transposon. http://purl.obolibrary.org/obo/SO_0000421 three_prime_terminal_inverted_repeat http://purl.obolibrary.org/obo/SO_0000481 terminal_inverted_repeat An inverted repeat (SO:0000294) occurring at the 3-prime termini of a DNA transposon. http://purl.obolibrary.org/obo/SO_0000422 U5_LTR_region http://purl.obolibrary.org/obo/SO_0000848 LTR_component The U5 segment of the long terminal repeats. http://purl.obolibrary.org/obo/SO_0000423 R_LTR_region http://purl.obolibrary.org/obo/SO_0000848 LTR_component The R segment of the long terminal repeats. http://purl.obolibrary.org/obo/SO_0000424 U3_LTR_region http://purl.obolibrary.org/obo/SO_0000848 LTR_component The U3 segment of the long terminal repeats. http://purl.obolibrary.org/obo/SO_0000425 five_prime_LTR http://purl.obolibrary.org/obo/SO_0000286 long_terminal_repeat The long terminal repeat found at the five-prime end of the sequence to be inserted into the host genome. http://purl.obolibrary.org/obo/SO_0000426 three_prime_LTR http://purl.obolibrary.org/obo/SO_0000286 long_terminal_repeat The long terminal repeat found at the three-prime end of the sequence to be inserted into the host genome. http://purl.obolibrary.org/obo/SO_0000427 R_five_prime_LTR_region http://purl.obolibrary.org/obo/SO_0000850 five_prime_LTR_component The R segment of the three-prime long terminal repeat. http://purl.obolibrary.org/obo/SO_0000428 U5_five_prime_LTR_region http://purl.obolibrary.org/obo/SO_0000850 five_prime_LTR_component The U5 segment of the three-prime long terminal repeat. http://purl.obolibrary.org/obo/SO_0000429 U3_five_prime_LTR_region http://purl.obolibrary.org/obo/SO_0000850 five_prime_LTR_component The U3 segment of the three-prime long terminal repeat. http://purl.obolibrary.org/obo/SO_0000430 R_three_prime_LTR_region http://purl.obolibrary.org/obo/SO_0000849 three_prime_LTR_component The R segment of the three-prime long terminal repeat. http://purl.obolibrary.org/obo/SO_0000431 U3_three_prime_LTR_region http://purl.obolibrary.org/obo/SO_0000849 three_prime_LTR_component The U3 segment of the three-prime long terminal repeat. http://purl.obolibrary.org/obo/SO_0000432 U5_three_prime_LTR_region http://purl.obolibrary.org/obo/SO_0000849 three_prime_LTR_component The U5 segment of the three-prime long terminal repeat. http://purl.obolibrary.org/obo/SO_0000433 non_LTR_retrotransposon_polymeric_tract http://purl.obolibrary.org/obo/SO_0000657 repeat_region A polymeric tract, such as poly(dA), within a non_LTR_retrotransposon. http://purl.obolibrary.org/obo/SO_0000434 target_site_duplication http://purl.obolibrary.org/obo/SO_0000314 direct_repeat A sequence of the target DNA that is duplicated when a transposable element or phage inserts; usually found at each end the insertion. http://purl.obolibrary.org/obo/SO_0000435 RR_tract http://purl.obolibrary.org/obo/SO_0000330 conserved_region A polypurine tract within an LTR_retrotransposon. http://purl.obolibrary.org/obo/SO_0000436 ARS http://purl.obolibrary.org/obo/SO_0000296 origin_of_replication A sequence that can autonomously replicate, as a plasmid, when transformed into a bacterial host. http://purl.obolibrary.org/obo/SO_0000439 inverted_ring_chromosome http://purl.obolibrary.org/obo/SO_1000045 ring_chromosome A ring chromosome is a chromosome whose arms have fused together to form a ring in an inverted fashion, often with the loss of the ends of the chromosome. http://purl.obolibrary.org/obo/SO_0000440 vector_replicon http://purl.obolibrary.org/obo/SO_0001235 replicon A replicon that has been modified to act as a vector for foreign sequence. http://purl.obolibrary.org/obo/SO_0000441 ss_oligo http://purl.obolibrary.org/obo/SO_0000696 oligo A single stranded oligonucleotide. http://purl.obolibrary.org/obo/SO_0000442 ds_oligo http://purl.obolibrary.org/obo/SO_0000696 oligo A double stranded oligonucleotide. http://purl.obolibrary.org/obo/SO_0000444 three_prime_noncoding_exon http://purl.obolibrary.org/obo/SO_0000198 noncoding_exon Non-coding exon in the 3' UTR. http://purl.obolibrary.org/obo/SO_0000445 five_prime_noncoding_exon http://purl.obolibrary.org/obo/SO_0000198 noncoding_exon Non-coding exon in the 5' UTR. http://purl.obolibrary.org/obo/SO_0000446 UTR_intron http://purl.obolibrary.org/obo/SO_0000188 intron Intron located in the untranslated region. http://purl.obolibrary.org/obo/SO_0000447 five_prime_UTR_intron http://purl.obolibrary.org/obo/SO_0000446 UTR_intron An intron located in the 5' UTR. http://purl.obolibrary.org/obo/SO_0000448 three_prime_UTR_intron http://purl.obolibrary.org/obo/SO_0000446 UTR_intron An intron located in the 3' UTR. http://purl.obolibrary.org/obo/SO_0000449 random_sequence http://purl.obolibrary.org/obo/SO_0000351 synthetic_sequence A sequence of nucleotides or amino acids which, by design, has a "random" order of components, given a predetermined input frequency of these components. http://purl.obolibrary.org/obo/SO_0000450 interband http://purl.obolibrary.org/obo/SO_0000830 chromosome_part A light region between two darkly staining bands in a polytene chromosome. http://purl.obolibrary.org/obo/SO_0000453 chromosomal_transposition http://purl.obolibrary.org/obo/SO_1000183 chromosome_structure_variation A chromosome structure variant whereby a region of a chromosome has been transferred to another position. Among interchromosomal rearrangements, the term transposition is reserved for that class in which the telomeres of the chromosomes involved are coupled (that is to say, form the two ends of a single DNA molecule) as in wild-type. http://purl.obolibrary.org/obo/SO_0000454 rasiRNA http://purl.obolibrary.org/obo/SO_0001035 piRNA A 17-28-nt, small interfering RNA derived from transcripts of repetitive elements. http://purl.obolibrary.org/obo/SO_0000457 interchromosomal_duplication http://purl.obolibrary.org/obo/SO_1000037 chromosomal_duplication A chromosome duplication involving an insertion from another chromosome. http://purl.obolibrary.org/obo/SO_0000458 D_gene_segment http://purl.obolibrary.org/obo/SO_0000460 vertebrate_immunoglobulin_T_cell_receptor_segment Germline genomic DNA including D-region with 5' UTR and 3' UTR, also designated as D-segment. http://purl.obolibrary.org/obo/SO_0000460 vertebrate_immunoglobulin_T_cell_receptor_segment http://purl.obolibrary.org/obo/SO_0000301 vertebrate_immune_system_gene_recombination_feature Germline genomic DNA with the sequence for a V, D, C, or J portion of an immunoglobulin/T-cell receptor. http://purl.obolibrary.org/obo/SO_0000461 inversion_derived_bipartite_deficiency http://purl.obolibrary.org/obo/SO_1000029 chromosomal_deletion A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at each end of the inversion. http://purl.obolibrary.org/obo/SO_0000463 encodes_alternately_spliced_transcripts http://purl.obolibrary.org/obo/SO_0000401 gene_attribute A gene that encodes more than one transcript. http://purl.obolibrary.org/obo/SO_0000464 decayed_exon http://purl.obolibrary.org/obo/SO_0000462 pseudogenic_region A non-functional descendant of an exon. http://purl.obolibrary.org/obo/SO_0000465 inversion_derived_deficiency_plus_duplication http://purl.obolibrary.org/obo/SO_1000038 intrachromosomal_duplication A chromosome deletion whereby a chromosome is generated by recombination between two inversions; there is a deficiency at one end of the inversion and a duplication at the other end of the inversion. http://purl.obolibrary.org/obo/SO_0000466 V_gene_segment http://purl.obolibrary.org/obo/SO_0000460 vertebrate_immunoglobulin_T_cell_receptor_segment Germline genomic DNA including L-part1, V-intron and V-exon, with the 5' UTR and 3' UTR. http://purl.obolibrary.org/obo/SO_0000467 post_translationally_regulated_by_protein_stability http://purl.obolibrary.org/obo/SO_0000130 post_translationally_regulated An attribute describing a gene sequence where the resulting protein is regulated by the stability of the resulting protein. http://purl.obolibrary.org/obo/SO_0000468 golden_path_fragment http://purl.obolibrary.org/obo/SO_0000143 assembly_component One of the pieces of sequence that make up a golden path. http://purl.obolibrary.org/obo/SO_0000469 post_translationally_regulated_by_protein_modification http://purl.obolibrary.org/obo/SO_0000130 post_translationally_regulated An attribute describing a gene sequence where the resulting protein is modified to regulate it. http://purl.obolibrary.org/obo/SO_0000470 J_gene_segment http://purl.obolibrary.org/obo/SO_0000460 vertebrate_immunoglobulin_T_cell_receptor_segment Germline genomic DNA of an immunoglobulin/T-cell receptor gene including J-region with 5' UTR (SO:0000204) and 3' UTR (SO:0000205), also designated as J-segment. http://purl.obolibrary.org/obo/SO_0000471 autoregulated http://purl.obolibrary.org/obo/SO_0000123 transcriptionally_regulated The gene product is involved in its own transcriptional regulation. http://purl.obolibrary.org/obo/SO_0000472 tiling_path http://purl.obolibrary.org/obo/SO_0000353 sequence_assembly A set of regions which overlap with minimal polymorphism to form a linear sequence. http://purl.obolibrary.org/obo/SO_0000473 negatively_autoregulated http://purl.obolibrary.org/obo/SO_0000471 autoregulated The gene product is involved in its own transcriptional regulation where it decreases transcription. http://purl.obolibrary.org/obo/SO_0000474 tiling_path_fragment http://purl.obolibrary.org/obo/SO_0000143 assembly_component A piece of sequence that makes up a tiling_path (SO:0000472). http://purl.obolibrary.org/obo/SO_0000475 positively_autoregulated http://purl.obolibrary.org/obo/SO_0000471 autoregulated The gene product is involved in its own transcriptional regulation, where it increases transcription. http://purl.obolibrary.org/obo/SO_0000476 contig_read http://purl.obolibrary.org/obo/SO_0000150 read A DNA sequencer read which is part of a contig. http://purl.obolibrary.org/obo/SO_0000478 C_gene_segment http://purl.obolibrary.org/obo/SO_0000460 vertebrate_immunoglobulin_T_cell_receptor_segment Genomic DNA of immunoglobulin/T-cell receptor gene including C-region (and introns if present) with 5' UTR (SO:0000204) and 3' UTR (SO:0000205). http://purl.obolibrary.org/obo/SO_0000479 trans_spliced_transcript http://purl.obolibrary.org/obo/SO_0000673 transcript A transcript that is trans-spliced. http://purl.obolibrary.org/obo/SO_0000480 tiling_path_clone http://purl.obolibrary.org/obo/SO_0000474 tiling_path_fragment A clone which is part of a tiling path. A tiling path is a set of sequencing substrates, typically clones, which have been selected in order to efficiently cover a region of the genome in preparation for sequencing and assembly. http://purl.obolibrary.org/obo/SO_0000481 terminal_inverted_repeat http://purl.obolibrary.org/obo/SO_0000294 inverted_repeat An inverted repeat (SO:0000294) occurring at the termini of a DNA transposon. http://purl.obolibrary.org/obo/SO_0000482 vertebrate_immunoglobulin_T_cell_receptor_gene_cluster http://purl.obolibrary.org/obo/SO_0000301 vertebrate_immune_system_gene_recombination_feature Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration. http://purl.obolibrary.org/obo/SO_0000484 three_prime_coding_exon_noncoding_region http://purl.obolibrary.org/obo/SO_0001214 noncoding_region_of_exon The sequence of the 3' exon that is not coding. http://purl.obolibrary.org/obo/SO_0000485 DJ_J_cluster http://purl.obolibrary.org/obo/SO_0000938 vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene, and one J-gene. http://purl.obolibrary.org/obo/SO_0000486 five_prime_coding_exon_noncoding_region http://purl.obolibrary.org/obo/SO_0001214 noncoding_region_of_exon The sequence of the 5' exon preceding the start codon. http://purl.obolibrary.org/obo/SO_0000487 VDJ_J_C_cluster http://purl.obolibrary.org/obo/SO_0000938 vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene, one J-gene and one C-gene. http://purl.obolibrary.org/obo/SO_0000488 VDJ_J_cluster http://purl.obolibrary.org/obo/SO_0000938 vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one J-gene. http://purl.obolibrary.org/obo/SO_0000489 VJ_C_cluster http://purl.obolibrary.org/obo/SO_0000938 vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one C-gene. http://purl.obolibrary.org/obo/SO_0000490 VJ_J_C_cluster http://purl.obolibrary.org/obo/SO_0000938 vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene, one J-gene and one C-gene. http://purl.obolibrary.org/obo/SO_0000491 VJ_J_cluster http://purl.obolibrary.org/obo/SO_0000938 vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VJ-gene and one J-gene. http://purl.obolibrary.org/obo/SO_0000492 D_gene_recombination_feature http://purl.obolibrary.org/obo/SO_0000939 vertebrate_immune_system_gene_recombination_signal_feature Recombination signal including D-heptamer, D-spacer and D-nonamer in 5' of D-region of a D-gene or D-sequence. http://purl.obolibrary.org/obo/SO_0000493 three_prime_D_heptamer http://purl.obolibrary.org/obo/SO_0000561 heptamer_of_recombination_feature_of_vertebrate_immune_system_gene 7 nucleotide recombination site like CACAGTG, part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene. http://purl.obolibrary.org/obo/SO_0000494 three_prime_D_nonamer http://purl.obolibrary.org/obo/SO_0000562 nonamer_of_recombination_feature_of_vertebrate_immune_system_gene A 9 nucleotide recombination site (e.g. ACAAAAACC), part of a 3' D-recombination signal sequence of an immunoglobulin/T-cell receptor gene. http://purl.obolibrary.org/obo/SO_0000495 three_prime_D_spacer http://purl.obolibrary.org/obo/SO_0000563 vertebrate_immune_system_gene_recombination_spacer A 12 or 23 nucleotide spacer between the 3'D-HEPTAMER and 3'D-NONAMER of a 3'D-RS. http://purl.obolibrary.org/obo/SO_0000496 five_prime_D_heptamer http://purl.obolibrary.org/obo/SO_0000561 heptamer_of_recombination_feature_of_vertebrate_immune_system_gene 7 nucleotide recombination site (e.g. CACTGTG), part of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene. http://purl.obolibrary.org/obo/SO_0000497 five_prime_D_nonamer http://purl.obolibrary.org/obo/SO_0000562 nonamer_of_recombination_feature_of_vertebrate_immune_system_gene 9 nucleotide recombination site (e.g. GGTTTTTGT), part of a five_prime_D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene. http://purl.obolibrary.org/obo/SO_0000498 five_prime_D_spacer http://purl.obolibrary.org/obo/SO_0000563 vertebrate_immune_system_gene_recombination_spacer 12 or 23 nucleotide spacer between the 5' D-heptamer (SO:0000496) and 5' D-nonamer (SO:0000497) of a 5' D-recombination signal sequence (SO:0000556) of an immunoglobulin/T-cell receptor gene. http://purl.obolibrary.org/obo/SO_0000499 virtual_sequence http://purl.obolibrary.org/obo/SO_0000353 sequence_assembly A continuous piece of sequence similar to the 'virtual contig' concept of the Ensembl database. http://purl.obolibrary.org/obo/SO_0000500 Hoogsteen_base_pair http://purl.obolibrary.org/obo/SO_0000028 base_pair A type of non-canonical base-pairing. This is less energetically favourable than watson crick base pairing. Hoogsteen GC base pairs only have two hydrogen bonds. http://purl.obolibrary.org/obo/SO_0000501 reverse_Hoogsteen_base_pair http://purl.obolibrary.org/obo/SO_0000028 base_pair A type of non-canonical base-pairing. http://purl.obolibrary.org/obo/SO_0000504 D_DJ_C_cluster http://purl.obolibrary.org/obo/SO_0000938 vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene and one C-gene. http://purl.obolibrary.org/obo/SO_0000505 D_DJ_cluster http://purl.obolibrary.org/obo/SO_0000938 vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene and one DJ-gene. http://purl.obolibrary.org/obo/SO_0000506 D_DJ_J_C_cluster http://purl.obolibrary.org/obo/SO_0000938 vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, one J-gene and one C-gene. http://purl.obolibrary.org/obo/SO_0000507 pseudogenic_exon http://purl.obolibrary.org/obo/SO_0000462 pseudogenic_region A non functional descendant of an exon, part of a pseudogene. http://purl.obolibrary.org/obo/SO_0000508 D_DJ_J_cluster http://purl.obolibrary.org/obo/SO_0000938 vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one D-gene, one DJ-gene, and one J-gene. http://purl.obolibrary.org/obo/SO_0000509 D_J_C_cluster http://purl.obolibrary.org/obo/SO_0000482 vertebrate_immunoglobulin_T_cell_receptor_gene_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene, one J-gene and one C-gene. http://purl.obolibrary.org/obo/SO_0000510 VD_gene_segment http://purl.obolibrary.org/obo/SO_0000936 vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including L-part1, V-intron and V-D-exon, with the 5' UTR (SO:0000204) and 3' UTR (SO:0000205). http://purl.obolibrary.org/obo/SO_0000511 J_C_cluster http://purl.obolibrary.org/obo/SO_0000482 vertebrate_immunoglobulin_T_cell_receptor_gene_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one J-gene and one C-gene. http://purl.obolibrary.org/obo/SO_0000512 inversion_derived_deficiency_plus_aneuploid http://purl.obolibrary.org/obo/SO_1000029 chromosomal_deletion A chromosomal deletion whereby a chromosome generated by recombination between two inversions; has a deficiency at one end and presumed to have a deficiency or duplication at the other end of the inversion. http://purl.obolibrary.org/obo/SO_0000513 J_cluster http://purl.obolibrary.org/obo/SO_0000482 vertebrate_immunoglobulin_T_cell_receptor_gene_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one J-gene. http://purl.obolibrary.org/obo/SO_0000514 J_nonamer http://purl.obolibrary.org/obo/SO_0000562 nonamer_of_recombination_feature_of_vertebrate_immune_system_gene 9 nucleotide recombination site (e.g. GGTTTTTGT), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene. http://purl.obolibrary.org/obo/SO_0000515 J_heptamer http://purl.obolibrary.org/obo/SO_0000561 heptamer_of_recombination_feature_of_vertebrate_immune_system_gene 7 nucleotide recombination site (e.g. CACAGTG), part of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene. http://purl.obolibrary.org/obo/SO_0000516 pseudogenic_transcript http://purl.obolibrary.org/obo/SO_0000462 pseudogenic_region A non functional descendant of a transcript, part of a pseudogene. http://purl.obolibrary.org/obo/SO_0000517 J_spacer http://purl.obolibrary.org/obo/SO_0000563 vertebrate_immune_system_gene_recombination_spacer 12 or 23 nucleotide spacer between the J-nonamer and the J-heptamer of a J-gene recombination feature of an immunoglobulin/T-cell receptor gene. http://purl.obolibrary.org/obo/SO_0000518 V_DJ_cluster http://purl.obolibrary.org/obo/SO_0000938 vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one DJ-gene. http://purl.obolibrary.org/obo/SO_0000519 V_DJ_J_cluster http://purl.obolibrary.org/obo/SO_0000938 vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one J-gene. http://purl.obolibrary.org/obo/SO_0000520 V_VDJ_C_cluster http://purl.obolibrary.org/obo/SO_0000938 vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one C-gene. http://purl.obolibrary.org/obo/SO_0000521 V_VDJ_cluster http://purl.obolibrary.org/obo/SO_0000938 vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VDJ-gene. http://purl.obolibrary.org/obo/SO_0000522 V_VDJ_J_cluster http://purl.obolibrary.org/obo/SO_0000938 vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene and one J-gene. http://purl.obolibrary.org/obo/SO_0000523 V_VJ_C_cluster http://purl.obolibrary.org/obo/SO_0000938 vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one C-gene. http://purl.obolibrary.org/obo/SO_0000524 V_VJ_cluster http://purl.obolibrary.org/obo/SO_0000938 vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene and one VJ-gene. http://purl.obolibrary.org/obo/SO_0000525 V_VJ_J_cluster http://purl.obolibrary.org/obo/SO_0000938 vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene and one J-gene. http://purl.obolibrary.org/obo/SO_0000526 V_cluster http://purl.obolibrary.org/obo/SO_0000482 vertebrate_immunoglobulin_T_cell_receptor_gene_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one V-gene. http://purl.obolibrary.org/obo/SO_0000527 V_D_DJ_C_cluster http://purl.obolibrary.org/obo/SO_0000938 vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one C-gene. http://purl.obolibrary.org/obo/SO_0000528 V_D_DJ_cluster http://purl.obolibrary.org/obo/SO_0000938 vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene. http://purl.obolibrary.org/obo/SO_0000529 V_D_DJ_J_C_cluster http://purl.obolibrary.org/obo/SO_0000938 vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene, one J-gene and one C-gene. http://purl.obolibrary.org/obo/SO_0000530 V_D_DJ_J_cluster http://purl.obolibrary.org/obo/SO_0000938 vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one D-gene, one DJ-gene and one J-gene. http://purl.obolibrary.org/obo/SO_0000531 V_D_J_C_cluster http://purl.obolibrary.org/obo/SO_0000938 vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene and one C-gene. http://purl.obolibrary.org/obo/SO_0000532 V_D_J_cluster http://purl.obolibrary.org/obo/SO_0000938 vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one D-gene and one J-gene. http://purl.obolibrary.org/obo/SO_0000533 V_heptamer http://purl.obolibrary.org/obo/SO_0000561 heptamer_of_recombination_feature_of_vertebrate_immune_system_gene 7 nucleotide recombination site (e.g. CACAGTG), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene. http://purl.obolibrary.org/obo/SO_0000534 V_J_cluster http://purl.obolibrary.org/obo/SO_0000482 vertebrate_immunoglobulin_T_cell_receptor_gene_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene and one J-gene. http://purl.obolibrary.org/obo/SO_0000535 V_J_C_cluster http://purl.obolibrary.org/obo/SO_0000482 vertebrate_immunoglobulin_T_cell_receptor_gene_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one V-gene, one J-gene and one C-gene. http://purl.obolibrary.org/obo/SO_0000536 V_nonamer http://purl.obolibrary.org/obo/SO_0000562 nonamer_of_recombination_feature_of_vertebrate_immune_system_gene 9 nucleotide recombination site (e.g. ACAAAAACC), part of V-gene recombination feature of an immunoglobulin/T-cell receptor gene. http://purl.obolibrary.org/obo/SO_0000537 V_spacer http://purl.obolibrary.org/obo/SO_0000563 vertebrate_immune_system_gene_recombination_spacer 12 or 23 nucleotide spacer between the V-heptamer and the V-nonamer of a V-gene recombination feature of an immunoglobulin/T-cell receptor gene. http://purl.obolibrary.org/obo/SO_0000538 V_gene_recombination_feature http://purl.obolibrary.org/obo/SO_0000939 vertebrate_immune_system_gene_recombination_signal_feature Recombination signal including V-heptamer, V-spacer and V-nonamer in 3' of V-region of a V-gene or V-sequence of an immunoglobulin/T-cell receptor gene. http://purl.obolibrary.org/obo/SO_0000539 DJ_C_cluster http://purl.obolibrary.org/obo/SO_0000938 vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one DJ-gene and one C-gene. http://purl.obolibrary.org/obo/SO_0000540 DJ_J_C_cluster http://purl.obolibrary.org/obo/SO_0000938 vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster Genomic DNA in rearranged configuration including at least one D-J-GENE, one J-GENE and one C-GENE. http://purl.obolibrary.org/obo/SO_0000541 VDJ_C_cluster http://purl.obolibrary.org/obo/SO_0000938 vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one VDJ-gene and one C-gene. http://purl.obolibrary.org/obo/SO_0000542 V_DJ_C_cluster http://purl.obolibrary.org/obo/SO_0000938 vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene and one C-gene. http://purl.obolibrary.org/obo/SO_0000544 helitron http://purl.obolibrary.org/obo/SO_0000182 DNA_transposon A rolling circle transposon. Autonomous helitrons encode a 5'-to-3' DNA helicase and nuclease/ligase similar to those encoded by known rolling-circle replicons. http://purl.obolibrary.org/obo/SO_0000545 recoding_pseudoknot http://purl.obolibrary.org/obo/SO_0000591 pseudoknot The pseudoknots involved in recoding are unique in that, as they play their role as a structure, they are immediately unfolded and their now linear sequence serves as a template for decoding. http://purl.obolibrary.org/obo/SO_0000546 designed_sequence http://purl.obolibrary.org/obo/SO_0000351 synthetic_sequence An oligonucleotide sequence that was designed by an experimenter that may or may not correspond with any natural sequence. http://purl.obolibrary.org/obo/SO_0000547 inversion_derived_bipartite_duplication http://purl.obolibrary.org/obo/SO_1000038 intrachromosomal_duplication A chromosome generated by recombination between two inversions; there is a duplication at each end of the inversion. http://purl.obolibrary.org/obo/SO_0000549 inversion_derived_duplication_plus_aneuploid http://purl.obolibrary.org/obo/SO_1000038 intrachromosomal_duplication A chromosome generated by recombination between two inversions; has a duplication at one end and presumed to have a deficiency or duplication at the other end of the inversion. http://purl.obolibrary.org/obo/SO_0000550 aneuploid_chromosome http://purl.obolibrary.org/obo/SO_1000183 chromosome_structure_variation A chromosome structural variation whereby either a chromosome exists in addition to the normal chromosome complement or is lacking. http://purl.obolibrary.org/obo/SO_0000551 polyA_signal_sequence http://purl.obolibrary.org/obo/SO_0001055 transcriptional_cis_regulatory_region The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA. http://purl.obolibrary.org/obo/SO_0000552 Shine_Dalgarno_sequence http://purl.obolibrary.org/obo/SO_0000139 ribosome_entry_site A region in the 5' UTR that pairs with the 16S rRNA during formation of the preinitiation complex. http://purl.obolibrary.org/obo/SO_0000553 polyA_site http://purl.obolibrary.org/obo/SO_0000699 junction The site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation. The boundary between the UTR and the polyA sequence. http://purl.obolibrary.org/obo/SO_0000555 five_prime_clip http://purl.obolibrary.org/obo/SO_0000303 clip 5' most region of a precursor transcript that is clipped off during processing. http://purl.obolibrary.org/obo/SO_0000556 five_prime_D_recombination_signal_sequence http://purl.obolibrary.org/obo/SO_0000492 D_gene_recombination_feature Recombination signal of an immunoglobulin/T-cell receptor gene, including the 5' D-nonamer (SO:0000497), 5' D-spacer (SO:0000498), and 5' D-heptamer (SO:0000396) in 5' of the D-region of a D-gene, or in 5' of the D-region of DJ-gene. http://purl.obolibrary.org/obo/SO_0000557 three_prime_clip http://purl.obolibrary.org/obo/SO_0000303 clip 3'-most region of a precursor transcript that is clipped off during processing. http://purl.obolibrary.org/obo/SO_0000558 C_cluster http://purl.obolibrary.org/obo/SO_0000482 vertebrate_immunoglobulin_T_cell_receptor_gene_cluster Genomic DNA of immunoglobulin/T-cell receptor gene including more than one C-gene. http://purl.obolibrary.org/obo/SO_0000559 D_cluster http://purl.obolibrary.org/obo/SO_0000482 vertebrate_immunoglobulin_T_cell_receptor_gene_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including more than one D-gene. http://purl.obolibrary.org/obo/SO_0000560 D_J_cluster http://purl.obolibrary.org/obo/SO_0000482 vertebrate_immunoglobulin_T_cell_receptor_gene_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in germline configuration including at least one D-gene and one J-gene. http://purl.obolibrary.org/obo/SO_0000561 heptamer_of_recombination_feature_of_vertebrate_immune_system_gene http://purl.obolibrary.org/obo/SO_0000939 vertebrate_immune_system_gene_recombination_signal_feature Seven nucleotide recombination site (e.g. CACAGTG), part of V-gene, D-gene or J-gene recombination feature of an immunoglobulin or T-cell receptor gene. http://purl.obolibrary.org/obo/SO_0000562 nonamer_of_recombination_feature_of_vertebrate_immune_system_gene http://purl.obolibrary.org/obo/SO_0000939 vertebrate_immune_system_gene_recombination_signal_feature Nine nucleotide recombination site, part of V-gene, D-gene or J-gene recombination feature of an immunoglobulin or T-cell receptor gene. http://purl.obolibrary.org/obo/SO_0000563 vertebrate_immune_system_gene_recombination_spacer http://purl.obolibrary.org/obo/SO_0000301 vertebrate_immune_system_gene_recombination_feature A 12 or 23 nucleotide spacer between two regions of an immunoglobulin/T-cell receptor gene that may be rearranged by recombinase. http://purl.obolibrary.org/obo/SO_0000564 V_DJ_J_C_cluster http://purl.obolibrary.org/obo/SO_0000938 vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one DJ-gene, one J-gene and one C-gene. http://purl.obolibrary.org/obo/SO_0000565 V_VDJ_J_C_cluster http://purl.obolibrary.org/obo/SO_0000938 vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VDJ-gene, one J-gene and one C-gene. http://purl.obolibrary.org/obo/SO_0000566 V_VJ_J_C_cluster http://purl.obolibrary.org/obo/SO_0000938 vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration including at least one V-gene, one VJ-gene, one J-gene and one C-gene. http://purl.obolibrary.org/obo/SO_0000567 inversion_derived_aneuploid_chromosome http://purl.obolibrary.org/obo/SO_0000550 aneuploid_chromosome A chromosome may be generated by recombination between two inversions; presumed to have a deficiency or duplication at each end of the inversion. http://purl.obolibrary.org/obo/SO_0000569 retrotransposed http://purl.obolibrary.org/obo/SO_0000733 feature_attribute An attribute of a feature that occurred as the product of a reverse transcriptase mediated event. http://purl.obolibrary.org/obo/SO_0000570 three_prime_D_recombination_signal_sequence http://purl.obolibrary.org/obo/SO_0000492 D_gene_recombination_feature Recombination signal of an immunoglobulin/T-cell receptor gene, including the 3' D-heptamer (SO:0000493), 3' D-spacer, and 3' D-nonamer (SO:0000494) in 3' of the D-region of a D-gene. http://purl.obolibrary.org/obo/SO_0000571 miRNA_encoding http://purl.obolibrary.org/obo/SO_0000011 non_protein_coding A region that can be transcribed into a microRNA (miRNA). http://purl.obolibrary.org/obo/SO_0000572 DJ_gene_segment http://purl.obolibrary.org/obo/SO_0000936 vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA including D-J-region with 5' UTR and 3' UTR, also designated as D-J-segment. http://purl.obolibrary.org/obo/SO_0000573 rRNA_encoding http://purl.obolibrary.org/obo/SO_0000011 non_protein_coding A region that can be transcribed into a ribosomal RNA (rRNA). http://purl.obolibrary.org/obo/SO_0000574 VDJ_gene_segment http://purl.obolibrary.org/obo/SO_0000936 vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-D-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205). http://purl.obolibrary.org/obo/SO_0000575 scRNA_encoding http://purl.obolibrary.org/obo/SO_0000011 non_protein_coding A region that can be transcribed into a small cytoplasmic RNA (scRNA). http://purl.obolibrary.org/obo/SO_0000576 VJ_gene_segment http://purl.obolibrary.org/obo/SO_0000936 vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment Rearranged genomic DNA of immunoglobulin/T-cell receptor gene including L-part1, V-intron and V-J-exon, with the 5'UTR (SO:0000204) and 3'UTR (SO:0000205). http://purl.obolibrary.org/obo/SO_0000579 edited_transcript_feature http://purl.obolibrary.org/obo/SO_0000833 transcript_region A locatable feature on a transcript that is edited. http://purl.obolibrary.org/obo/SO_0000580 methylation_guide_snoRNA_primary_transcript http://purl.obolibrary.org/obo/SO_0000232 snoRNA_primary_transcript A primary transcript encoding a methylation guide small nucleolar RNA. http://purl.obolibrary.org/obo/SO_0000582 rRNA_cleavage_snoRNA_primary_transcript http://purl.obolibrary.org/obo/SO_0000232 snoRNA_primary_transcript A primary transcript encoding an rRNA cleavage snoRNA. http://purl.obolibrary.org/obo/SO_0000583 pre_edited_region http://purl.obolibrary.org/obo/SO_0000579 edited_transcript_feature The region of a transcript that will be edited. http://purl.obolibrary.org/obo/SO_0000585 C_D_box_snoRNA_encoding http://purl.obolibrary.org/obo/SO_0000578 snoRNA_encoding snoRNA that is associated with guiding methylation of nucleotides. It contains two short conserved sequence motifs: C (RUGAUGA) near the 5-prime end and D (CUGA) near the 3-prime end. http://purl.obolibrary.org/obo/SO_0000586 tmRNA_primary_transcript http://purl.obolibrary.org/obo/SO_0000483 nc_primary_transcript A primary transcript encoding a tmRNA (SO:0000584). http://purl.obolibrary.org/obo/SO_0000587 group_I_intron http://purl.obolibrary.org/obo/SO_0000588 autocatalytically_spliced_intron Group I catalytic introns are large self-splicing ribozymes. They catalyze their own excision from mRNA, tRNA and rRNA precursors in a wide range of organisms. The core secondary structure consists of 9 paired regions (P1-P9). These fold to essentially two domains, the P4-P6 domain (formed from the stacking of P5, P4, P6 and P6a helices) and the P3-P9 domain (formed from the P8, P3, P7 and P9 helices). Group I catalytic introns often have long ORFs inserted in loop regions. http://purl.obolibrary.org/obo/SO_0000588 autocatalytically_spliced_intron http://purl.obolibrary.org/obo/SO_0000188 intron A self spliced intron. http://purl.obolibrary.org/obo/SO_0000589 SRP_RNA_primary_transcript http://purl.obolibrary.org/obo/SO_0000483 nc_primary_transcript A primary transcript encoding a signal recognition particle RNA. http://purl.obolibrary.org/obo/SO_0000591 pseudoknot http://purl.obolibrary.org/obo/SO_0000002 sequence_secondary_structure A tertiary structure in RNA where nucleotides in a loop form base pairs with a region of RNA downstream of the loop. http://purl.obolibrary.org/obo/SO_0000592 H_pseudoknot http://purl.obolibrary.org/obo/SO_0000591 pseudoknot A pseudoknot which contains two stems and at least two loops. http://purl.obolibrary.org/obo/SO_0000593 C_D_box_snoRNA http://purl.obolibrary.org/obo/SO_0000275 snoRNA Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C' and D', are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for snoRNA stability, processing, nucleolar targeting and function. A small number of box C/D snoRNAs are involved in rRNA processing; most, however, are known or predicted to serve as guide RNAs in ribose methylation of rRNA. Targeting involves direct base pairing of the snoRNA at the rRNA site to be modified and selection of a rRNA nucleotide a fixed distance from box D or D'. http://purl.obolibrary.org/obo/SO_0000594 H_ACA_box_snoRNA http://purl.obolibrary.org/obo/SO_0000275 snoRNA Members of the box H/ACA family contain an ACA triplet, exactly 3 nt upstream from the 3' end and an H-box in a hinge region that links two structurally similar functional domains of the molecule. Both boxes are important for snoRNA biosynthesis and function. A few box H/ACA snoRNAs are involved in rRNA processing; most others are known or predicted to participate in selection of uridine nucleosides in rRNA to be converted to pseudouridines. Site selection is mediated by direct base pairing of the snoRNA with rRNA through one or both targeting domains. http://purl.obolibrary.org/obo/SO_0000595 C_D_box_snoRNA_primary_transcript http://purl.obolibrary.org/obo/SO_0000232 snoRNA_primary_transcript A primary transcript encoding a small nucleolar RNA of the box C/D family. http://purl.obolibrary.org/obo/SO_0000596 H_ACA_box_snoRNA_primary_transcript http://purl.obolibrary.org/obo/SO_0000232 snoRNA_primary_transcript A primary transcript encoding a small nucleolar RNA of the box H/ACA family. http://purl.obolibrary.org/obo/SO_0000602 guide_RNA http://purl.obolibrary.org/obo/SO_0000655 ncRNA A short 3'-uridylated RNA that can form a duplex (except for its post-transcriptionally added oligo_U tail (SO:0000609)) with a stretch of mature edited mRNA. http://purl.obolibrary.org/obo/SO_0000603 group_II_intron http://purl.obolibrary.org/obo/SO_0000588 autocatalytically_spliced_intron Group II introns are found in rRNA, tRNA and mRNA of organelles in fungi, plants and protists, and also in mRNA in bacteria. They are large self-splicing ribozymes and have 6 structural domains (usually designated dI to dVI). A subset of group II introns also encode essential splicing proteins in intronic ORFs. The length of these introns can therefore be up to 3kb. Splicing occurs in almost identical fashion to nuclear pre-mRNA splicing with two transesterification steps. The 2' hydroxyl of a bulged adenosine in domain VI attacks the 5' splice site, followed by nucleophilic attack on the 3' splice site by the 3' OH of the upstream exon. Protein machinery is required for splicing in vivo, and long range intron to intron and intron-exon interactions are important for splice site positioning. Group II introns are further sub-classified into groups IIA and IIB which differ in splice site consensus, distance of bulged A from 3' splice site, some tertiary interactions, and intronic ORF phylogeny. http://purl.obolibrary.org/obo/SO_0000604 editing_block http://purl.obolibrary.org/obo/SO_0000579 edited_transcript_feature Edited mRNA sequence mediated by a single guide RNA (SO:0000602). http://purl.obolibrary.org/obo/SO_0000606 editing_domain http://purl.obolibrary.org/obo/SO_0000579 edited_transcript_feature Edited mRNA sequence mediated by two or more overlapping guide RNAs (SO:0000602). http://purl.obolibrary.org/obo/SO_0000608 H_ACA_box_snoRNA_encoding http://purl.obolibrary.org/obo/SO_0000578 snoRNA_encoding snoRNA that is associated with guiding polyuridylation. It contains two short conserved sequence motifs: H box (ANANNA) and ACA (ACA). http://purl.obolibrary.org/obo/SO_0000611 branch_site http://purl.obolibrary.org/obo/SO_0000841 spliceosomal_intron_region A pyrimidine rich sequence near the 3' end of an intron to which the 5'end becomes covalently bound during nuclear splicing. The resulting structure resembles a lariat. http://purl.obolibrary.org/obo/SO_0000612 polypyrimidine_tract http://purl.obolibrary.org/obo/SO_0000841 spliceosomal_intron_region The polypyrimidine tract is one of the cis-acting sequence elements directing intron removal in pre-mRNA splicing. http://purl.obolibrary.org/obo/SO_0000614 bacterial_terminator http://purl.obolibrary.org/obo/SO_0000141 terminator A terminator signal for bacterial transcription. http://purl.obolibrary.org/obo/SO_0000615 terminator_of_type_2_RNApol_III_promoter http://purl.obolibrary.org/obo/SO_0000951 eukaryotic_terminator A terminator signal for RNA polymerase III transcription. http://purl.obolibrary.org/obo/SO_0000616 transcription_end_site http://purl.obolibrary.org/obo/SO_0000835 primary_transcript_region The base where transcription ends. http://purl.obolibrary.org/obo/SO_0000619 A_box http://purl.obolibrary.org/obo/SO_0001660 core_eukaryotic_promoter_element A variably distant linear promoter region recognized by TFIIIC, with consensus sequence TGGCnnAGTGG. http://purl.obolibrary.org/obo/SO_0000620 B_box http://purl.obolibrary.org/obo/SO_0001660 core_eukaryotic_promoter_element A variably distant linear promoter region recognized by TFIIIC, with consensus sequence AGGTTCCAnnCC. http://purl.obolibrary.org/obo/SO_0000622 C_box http://purl.obolibrary.org/obo/SO_0001660 core_eukaryotic_promoter_element An RNA polymerase III type 1 promoter with consensus sequence CAnnCCn. http://purl.obolibrary.org/obo/SO_0000623 snRNA_encoding http://purl.obolibrary.org/obo/SO_0000011 non_protein_coding A region that can be transcribed into a small nuclear RNA (snRNA). http://purl.obolibrary.org/obo/SO_0000625 silencer http://purl.obolibrary.org/obo/SO_0000727 cis_regulatory_module A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control. http://purl.obolibrary.org/obo/SO_0000626 chromosomal_regulatory_element http://purl.obolibrary.org/obo/SO_0000830 chromosome_part Regions of the chromosome that are important for regulating binding of chromosomes to the nuclear matrix. http://purl.obolibrary.org/obo/SO_0000629 five_prime_open_reading_frame http://purl.obolibrary.org/obo/SO_0000836 mRNA_region An open reading frame found within the 5' UTR that can be translated and stall the translation of the downstream open reading frame. http://purl.obolibrary.org/obo/SO_0000630 upstream_AUG_codon http://purl.obolibrary.org/obo/SO_0000837 UTR_region A start codon upstream of the ORF. http://purl.obolibrary.org/obo/SO_0000631 polycistronic_primary_transcript http://purl.obolibrary.org/obo/SO_0000185 primary_transcript A primary transcript encoding for more than one gene product. http://purl.obolibrary.org/obo/SO_0000632 monocistronic_primary_transcript http://purl.obolibrary.org/obo/SO_0000185 primary_transcript A primary transcript encoding for one gene product. http://purl.obolibrary.org/obo/SO_0000635 mini_exon_donor_RNA http://purl.obolibrary.org/obo/SO_0000185 primary_transcript A primary transcript that donates the spliced leader to other mRNA. http://purl.obolibrary.org/obo/SO_0000636 spliced_leader_RNA http://purl.obolibrary.org/obo/SO_0000835 primary_transcript_region Snall nuclear RNAs that are incorporated into the pre-mRNAs to replace the 5' end in some eukaryotes. http://purl.obolibrary.org/obo/SO_0000638 transcribed_spacer_region http://purl.obolibrary.org/obo/SO_0000838 rRNA_primary_transcript_region Part of an rRNA transcription unit that is transcribed but discarded during maturation, not giving rise to any part of rRNA. http://purl.obolibrary.org/obo/SO_0000639 internal_transcribed_spacer_region http://purl.obolibrary.org/obo/SO_0000638 transcribed_spacer_region Non-coding regions of DNA sequence that separate genes coding for the 28S, 5.8S, and 18S ribosomal RNAs. http://purl.obolibrary.org/obo/SO_0000640 external_transcribed_spacer_region http://purl.obolibrary.org/obo/SO_0000638 transcribed_spacer_region Non-coding regions of DNA that precede the sequence that codes for the ribosomal RNA. http://purl.obolibrary.org/obo/SO_0000641 tetranucleotide_repeat_microsatellite_feature http://purl.obolibrary.org/obo/SO_0000289 microsatellite A region of a repeating tetranucleotide sequence (four bases). http://purl.obolibrary.org/obo/SO_0000642 SRP_RNA_encoding http://purl.obolibrary.org/obo/SO_0000011 non_protein_coding A region that can be transcribed into a signal recognition particle RNA (SRP RNA). http://purl.obolibrary.org/obo/SO_0000643 minisatellite http://purl.obolibrary.org/obo/SO_0000005 satellite_DNA A repeat region containing tandemly repeated sequences having a unit length of 10 to 40 bp. http://purl.obolibrary.org/obo/SO_0000652 cytosolic_5S_rRNA http://purl.obolibrary.org/obo/SO_0000651 cytosolic_LSU_rRNA Cytosolic 5S rRNA is an RNA component of the large subunit of cytosolic ribosomes in both prokaryotes and eukaryotes. http://purl.obolibrary.org/obo/SO_0000653 cytosolic_28S_rRNA http://purl.obolibrary.org/obo/SO_0000651 cytosolic_LSU_rRNA Cytosolic 28S rRNA is an RNA component of the large subunit of cytosolic ribosomes in metazoan eukaryotes. http://purl.obolibrary.org/obo/SO_0000656 stRNA_encoding http://purl.obolibrary.org/obo/SO_0000011 non_protein_coding A region that can be transcribed into a small temporal RNA (stRNA). Found in roundworm development. http://purl.obolibrary.org/obo/SO_0000658 dispersed_repeat http://purl.obolibrary.org/obo/SO_0000657 repeat_region A repeat that is located at dispersed sites in the genome. http://purl.obolibrary.org/obo/SO_0000659 tmRNA_encoding http://purl.obolibrary.org/obo/SO_0000011 non_protein_coding A region that can be transcribed into a transfer-messenger RNA (tmRNA). http://purl.obolibrary.org/obo/SO_0000662 spliceosomal_intron http://purl.obolibrary.org/obo/SO_0000188 intron An intron which is spliced by the spliceosome. http://purl.obolibrary.org/obo/SO_0000664 introgressed_chromosome_region http://purl.obolibrary.org/obo/SO_0000830 chromosome_part A region of a chromosome that has been introduced by backcrossing with a separate species. http://purl.obolibrary.org/obo/SO_0000665 monocistronic_transcript http://purl.obolibrary.org/obo/SO_0000673 transcript A transcript that is monocistronic. http://purl.obolibrary.org/obo/SO_0000666 mobile_intron http://purl.obolibrary.org/obo/SO_0001037 mobile_genetic_element An intron (mitochondrial, chloroplast, nuclear or prokaryotic) that encodes a double strand sequence specific endonuclease allowing for mobility. http://purl.obolibrary.org/obo/SO_0000668 EST_match http://purl.obolibrary.org/obo/SO_0000102 expressed_sequence_match A match against an EST sequence. http://purl.obolibrary.org/obo/SO_0000669 sequence_rearrangement_feature http://purl.obolibrary.org/obo/SO_0000298 recombination_feature A feature where a segment of DNA has been rearranged from what it was in the parent cell. http://purl.obolibrary.org/obo/SO_0000670 chromosome_breakage_sequence http://purl.obolibrary.org/obo/SO_0000669 sequence_rearrangement_feature A sequence within the micronuclear DNA of ciliates at which chromosome breakage and telomere addition occurs during nuclear differentiation. http://purl.obolibrary.org/obo/SO_0000671 internal_eliminated_sequence http://purl.obolibrary.org/obo/SO_0000669 sequence_rearrangement_feature A sequence eliminated from the genome of ciliates during nuclear differentiation. http://purl.obolibrary.org/obo/SO_0000672 macronucleus_destined_segment http://purl.obolibrary.org/obo/SO_0000669 sequence_rearrangement_feature A sequence that is conserved, although rearranged relative to the micronucleus, in the macronucleus of a ciliate genome. http://purl.obolibrary.org/obo/SO_0000676 canonical_three_prime_splice_site http://purl.obolibrary.org/obo/SO_0000164 three_prime_cis_splice_site The canonical 3' splice site has the sequence "AG". http://purl.obolibrary.org/obo/SO_0000677 canonical_five_prime_splice_site http://purl.obolibrary.org/obo/SO_0000163 five_prime_cis_splice_site The canonical 5' splice site has the sequence "GT". http://purl.obolibrary.org/obo/SO_0000678 non_canonical_three_prime_splice_site http://purl.obolibrary.org/obo/SO_0000164 three_prime_cis_splice_site A 3' splice site that does not have the sequence "AG". http://purl.obolibrary.org/obo/SO_0000679 non_canonical_five_prime_splice_site http://purl.obolibrary.org/obo/SO_0000163 five_prime_cis_splice_site A 5' splice site which does not have the sequence "GT". http://purl.obolibrary.org/obo/SO_0000680 non_canonical_start_codon http://purl.obolibrary.org/obo/SO_0000318 start_codon A start codon that is not the usual AUG sequence. http://purl.obolibrary.org/obo/SO_0000681 aberrant_processed_transcript http://purl.obolibrary.org/obo/SO_0000673 transcript A transcript that has been processed "incorrectly", for example by the failure of splicing of one or more exons. http://purl.obolibrary.org/obo/SO_0000683 exonic_splice_enhancer http://purl.obolibrary.org/obo/SO_0000344 splice_enhancer Exonic splicing enhancers (ESEs) facilitate exon definition by assisting in the recruitment of splicing factors to the adjacent intron. http://purl.obolibrary.org/obo/SO_0000684 nuclease_sensitive_site http://purl.obolibrary.org/obo/SO_0000059 nuclease_binding_site A region of nucleotide sequence targeted by a nuclease enzyme. http://purl.obolibrary.org/obo/SO_0000685 DNaseI_hypersensitive_site http://purl.obolibrary.org/obo/SO_0000322 nuclease_hypersensitive_site DNA region representing open chromatin structure that is hypersensitive to digestion by DNase I. http://purl.obolibrary.org/obo/SO_0000686 translocation_element http://purl.obolibrary.org/obo/SO_1000044 chromosomal_translocation A chromosomal translocation whereby the chromosomes carrying non-homologous centromeres may be recovered independently. These chromosomes are described as translocation elements. This occurs for some translocations, particularly but not exclusively, reciprocal translocations. http://purl.obolibrary.org/obo/SO_0000687 deletion_junction http://purl.obolibrary.org/obo/SO_0000699 junction The space between two bases in a sequence which marks the position where a deletion has occurred. http://purl.obolibrary.org/obo/SO_0000688 golden_path http://purl.obolibrary.org/obo/SO_0000353 sequence_assembly A set of subregions selected from sequence contigs which when concatenated form a nonredundant linear sequence. http://purl.obolibrary.org/obo/SO_0000689 cDNA_match http://purl.obolibrary.org/obo/SO_0000102 expressed_sequence_match A match against cDNA sequence. http://purl.obolibrary.org/obo/SO_0000691 cleaved_initiator_methionine http://purl.obolibrary.org/obo/SO_0100011 cleaved_peptide_region The initiator methionine that has been cleaved from a mature polypeptide sequence. http://purl.obolibrary.org/obo/SO_0000695 reagent http://purl.obolibrary.org/obo/SO_0001409 biomaterial_region A sequence used in experiment. http://purl.obolibrary.org/obo/SO_0000696 oligo http://purl.obolibrary.org/obo/SO_0000695 reagent A short oligonucleotide sequence, of length on the order of 10's of bases; either single or double stranded. http://purl.obolibrary.org/obo/SO_0000700 remark http://purl.obolibrary.org/obo/SO_0001410 experimental_feature A comment about the sequence. http://purl.obolibrary.org/obo/SO_0000701 possible_base_call_error http://purl.obolibrary.org/obo/SO_0000413 sequence_difference A region of sequence where the validity of the base calling is questionable. http://purl.obolibrary.org/obo/SO_0000702 possible_assembly_error http://purl.obolibrary.org/obo/SO_0000413 sequence_difference A region of sequence where there may have been an error in the assembly. http://purl.obolibrary.org/obo/SO_0000703 experimental_result_region http://purl.obolibrary.org/obo/SO_0000700 remark A region of sequence implicated in an experimental result. http://purl.obolibrary.org/obo/SO_0000705 tandem_repeat http://purl.obolibrary.org/obo/SO_0000657 repeat_region Two or more adjacent copies of a region (of length greater than 1). http://purl.obolibrary.org/obo/SO_0000706 trans_splice_acceptor_site http://purl.obolibrary.org/obo/SO_0001420 trans_splice_site The 3' splice site of the acceptor primary transcript. http://purl.obolibrary.org/obo/SO_0000707 trans_splice_donor_site http://purl.obolibrary.org/obo/SO_0001420 trans_splice_site The 5' five prime splice site region of the donor RNA. http://purl.obolibrary.org/obo/SO_0000708 SL1_acceptor_site http://purl.obolibrary.org/obo/SO_0000706 trans_splice_acceptor_site A trans_splicing_acceptor_site which appends the 22nt SL1 RNA leader sequence to the 5' end of most mRNAs. http://purl.obolibrary.org/obo/SO_0000709 SL2_acceptor_site http://purl.obolibrary.org/obo/SO_0000706 trans_splice_acceptor_site A trans_splicing_acceptor_site which appends the 22nt SL2 RNA leader sequence to the 5' end of mRNAs. SL2 acceptor sites occur in genes in internal segments of polycistronic transcripts. http://purl.obolibrary.org/obo/SO_0000715 RNA_motif http://purl.obolibrary.org/obo/SO_0000714 nucleotide_motif A motif that is active in RNA sequence. http://purl.obolibrary.org/obo/SO_0000717 reading_frame http://purl.obolibrary.org/obo/SO_0001410 experimental_feature A nucleic acid sequence that when read as sequential triplets, has the potential of encoding a sequential string of amino acids. It need not contain the start or stop codon. http://purl.obolibrary.org/obo/SO_0000718 blocked_reading_frame http://purl.obolibrary.org/obo/SO_0000717 reading_frame A reading_frame that is interrupted by one or more stop codons; usually identified through inter-genomic sequence comparisons. http://purl.obolibrary.org/obo/SO_0000719 ultracontig http://purl.obolibrary.org/obo/SO_0001876 partial_genomic_sequence_assembly An ordered and oriented set of scaffolds based on somewhat weaker sets of inferential evidence such as one set of mate pair reads together with supporting evidence from ESTs or location of markers from SNP or microsatellite maps, or cytogenetic localization of contained markers. http://purl.obolibrary.org/obo/SO_0000723 iDNA http://purl.obolibrary.org/obo/SO_0000298 recombination_feature Genomic sequence removed from the genome, as a normal event, by a process of recombination. http://purl.obolibrary.org/obo/SO_0000724 oriT http://purl.obolibrary.org/obo/SO_0000296 origin_of_replication A region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization. http://purl.obolibrary.org/obo/SO_0000728 intein http://purl.obolibrary.org/obo/SO_0100011 cleaved_peptide_region A region of a peptide that is able to excise itself and rejoin the remaining portions with a peptide bond. http://purl.obolibrary.org/obo/SO_0000729 intein_containing http://purl.obolibrary.org/obo/SO_0000010 protein_coding An attribute of protein-coding genes where the initial protein product contains an intein. http://purl.obolibrary.org/obo/SO_0000730 gap http://purl.obolibrary.org/obo/SO_0000143 assembly_component A gap in the sequence of known length. The unknown bases are filled in with N's. http://purl.obolibrary.org/obo/SO_0000731 fragmentary http://purl.obolibrary.org/obo/SO_0000905 status An attribute to describe a feature that is incomplete. http://purl.obolibrary.org/obo/SO_0000732 predicted http://purl.obolibrary.org/obo/SO_0000905 status An attribute describing an unverified region. http://purl.obolibrary.org/obo/SO_0000735 sequence_location http://purl.obolibrary.org/obo/SO_0000400 sequence_attribute The location of a sequence. http://purl.obolibrary.org/obo/SO_0000736 organelle_sequence http://purl.obolibrary.org/obo/SO_0000735 sequence_location A sequence of DNA that originates from a an organelle. http://purl.obolibrary.org/obo/SO_0000737 mitochondrial_sequence http://purl.obolibrary.org/obo/SO_0000736 organelle_sequence DNA belonging to the genome of a mitochondria. http://purl.obolibrary.org/obo/SO_0000738 nuclear_sequence http://purl.obolibrary.org/obo/SO_0000735 sequence_location DNA belonging to the nuclear genome of cell. http://purl.obolibrary.org/obo/SO_0000739 nucleomorphic_sequence http://purl.obolibrary.org/obo/SO_0000736 organelle_sequence DNA belonging to the genome of a plastid such as a chloroplast. The nucleomorph is the nuclei of the plastic. http://purl.obolibrary.org/obo/SO_0000740 plastid_sequence http://purl.obolibrary.org/obo/SO_0000736 organelle_sequence DNA belonging to the genome of a plastid such as a chloroplast. http://purl.obolibrary.org/obo/SO_0000741 kinetoplast http://purl.obolibrary.org/obo/SO_0001026 genome A kinetoplast is an interlocked network of thousands of minicircles and tens of maxicircles, located near the base of the flagellum of some protozoan species. http://purl.obolibrary.org/obo/SO_0000742 maxicircle http://purl.obolibrary.org/obo/SO_0001235 replicon A maxicircle is a replicon, part of a kinetoplast, that contains open reading frames and replicates via a rolling circle method. http://purl.obolibrary.org/obo/SO_0000743 apicoplast_sequence http://purl.obolibrary.org/obo/SO_0000740 plastid_sequence DNA belonging to the genome of an apicoplast, a non-photosynthetic plastid. http://purl.obolibrary.org/obo/SO_0000744 chromoplast_sequence http://purl.obolibrary.org/obo/SO_0000740 plastid_sequence DNA belonging to the genome of a chromoplast, a colored plastid for synthesis and storage of pigments. http://purl.obolibrary.org/obo/SO_0000745 chloroplast_sequence http://purl.obolibrary.org/obo/SO_0000740 plastid_sequence DNA belonging to the genome of a chloroplast, a green plastid for photosynthesis. http://purl.obolibrary.org/obo/SO_0000746 cyanelle_sequence http://purl.obolibrary.org/obo/SO_0000740 plastid_sequence DNA belonging to the genome of a cyanelle, a photosynthetic plastid found in algae. http://purl.obolibrary.org/obo/SO_0000747 leucoplast_sequence http://purl.obolibrary.org/obo/SO_0000740 plastid_sequence DNA belonging to the genome of a leucoplast, a colorless plastid generally containing starch or oil. http://purl.obolibrary.org/obo/SO_0000748 proplastid_sequence http://purl.obolibrary.org/obo/SO_0000740 plastid_sequence DNA belonging to the genome of a proplastid such as an immature chloroplast. http://purl.obolibrary.org/obo/SO_0000749 plasmid_location http://purl.obolibrary.org/obo/SO_0000735 sequence_location The location of DNA that has come from a plasmid sequence. http://purl.obolibrary.org/obo/SO_0000750 amplification_origin http://purl.obolibrary.org/obo/SO_0000296 origin_of_replication An origin_of_replication that is used for the amplification of a chromosomal nucleic acid sequence. http://purl.obolibrary.org/obo/SO_0000751 proviral_location http://purl.obolibrary.org/obo/SO_0000735 sequence_location The location of DNA that has come from a viral origin. http://purl.obolibrary.org/obo/SO_0000753 clone_insert http://purl.obolibrary.org/obo/SO_0000695 reagent The region of sequence that has been inserted and is being propagated by the clone. http://purl.obolibrary.org/obo/SO_0000754 lambda_vector http://purl.obolibrary.org/obo/SO_0000440 vector_replicon The lambda bacteriophage is the vector for the linear lambda clone. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome. http://purl.obolibrary.org/obo/SO_0000755 plasmid_vector http://purl.obolibrary.org/obo/SO_0000440 vector_replicon A plasmid that has been generated to act as a vector for foreign sequence. http://purl.obolibrary.org/obo/SO_0000756 cDNA http://purl.obolibrary.org/obo/SO_0000352 DNA DNA synthesized by reverse transcriptase using RNA as a template. http://purl.obolibrary.org/obo/SO_0000757 single_stranded_cDNA http://purl.obolibrary.org/obo/SO_0000756 cDNA DNA synthesized from RNA by reverse transcriptase, single stranded. http://purl.obolibrary.org/obo/SO_0000758 double_stranded_cDNA http://purl.obolibrary.org/obo/SO_0000756 cDNA DNA synthesized from RNA by reverse transcriptase that has been copied by PCR to make it double stranded. http://purl.obolibrary.org/obo/SO_0000766 pyrrolysyl_tRNA http://purl.obolibrary.org/obo/SO_0000253 tRNA A tRNA sequence that has a pyrrolysine anticodon, and a 3' pyrrolysine binding region. http://purl.obolibrary.org/obo/SO_0000768 episome http://purl.obolibrary.org/obo/SO_0000155 plasmid A plasmid that may integrate with a chromosome. http://purl.obolibrary.org/obo/SO_0000769 tmRNA_coding_piece http://purl.obolibrary.org/obo/SO_0000847 tmRNA_region The region of a two-piece tmRNA that bears the reading frame encoding the proteolysis tag. The tmRNA gene undergoes circular permutation in some groups of bacteria. Processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together. http://purl.obolibrary.org/obo/SO_0000770 tmRNA_acceptor_piece http://purl.obolibrary.org/obo/SO_0000847 tmRNA_region The acceptor region of a two-piece tmRNA that when mature is charged at its 3' end with alanine. The tmRNA gene undergoes circular permutation in some groups of bacteria; processing of the transcripts from such a gene leaves the mature tmRNA in two pieces, base-paired together. http://purl.obolibrary.org/obo/SO_0000772 genomic_island http://purl.obolibrary.org/obo/SO_0001039 integrated_mobile_genetic_element A genomic island is an integrated mobile genetic element, characterized by size (over 10 Kb). It that has features that suggest a foreign origin. These can include nucleotide distribution (oligonucleotides signature, CG content etc.) that differs from the bulk of the chromosome and/or genes suggesting DNA mobility. http://purl.obolibrary.org/obo/SO_0000773 pathogenic_island http://purl.obolibrary.org/obo/SO_0000772 genomic_island Mobile genetic elements that contribute to rapid changes in virulence potential. They are present on the genomes of pathogenic strains but absent from the genomes of non pathogenic members of the same or related species. http://purl.obolibrary.org/obo/SO_0000774 metabolic_island http://purl.obolibrary.org/obo/SO_0000772 genomic_island A transmissible element containing genes involved in metabolism, analogous to the pathogenicity islands of gram negative bacteria. http://purl.obolibrary.org/obo/SO_0000775 adaptive_island http://purl.obolibrary.org/obo/SO_0000772 genomic_island An adaptive island is a genomic island that provides an adaptive advantage to the host. http://purl.obolibrary.org/obo/SO_0000776 symbiosis_island http://purl.obolibrary.org/obo/SO_0000772 genomic_island A transmissible element containing genes involved in symbiosis, analogous to the pathogenicity islands of gram negative bacteria. http://purl.obolibrary.org/obo/SO_0000777 pseudogenic_rRNA http://purl.obolibrary.org/obo/SO_0000516 pseudogenic_transcript A non functional descendant of an rRNA. http://purl.obolibrary.org/obo/SO_0000778 pseudogenic_tRNA http://purl.obolibrary.org/obo/SO_0000516 pseudogenic_transcript A non functional descendent of a tRNA. http://purl.obolibrary.org/obo/SO_0000779 engineered_episome http://purl.obolibrary.org/obo/SO_0000768 episome An episome that is engineered. http://purl.obolibrary.org/obo/SO_0000781 transgenic http://purl.obolibrary.org/obo/SO_0000733 feature_attribute Attribute describing sequence that has been integrated with foreign sequence. http://purl.obolibrary.org/obo/SO_0000782 natural http://purl.obolibrary.org/obo/SO_0000733 feature_attribute An attribute describing a feature that occurs in nature. http://purl.obolibrary.org/obo/SO_0000784 foreign http://purl.obolibrary.org/obo/SO_0000733 feature_attribute An attribute to describe a region from another species. http://purl.obolibrary.org/obo/SO_0000785 cloned_region http://purl.obolibrary.org/obo/SO_0000695 reagent The region of sequence that has been inserted and is being propagated by the clone. http://purl.obolibrary.org/obo/SO_0000789 validated http://purl.obolibrary.org/obo/SO_0000905 status An attribute to describe a feature that has been proven. http://purl.obolibrary.org/obo/SO_0000790 invalidated http://purl.obolibrary.org/obo/SO_0000905 status An attribute describing a feature that is invalidated. http://purl.obolibrary.org/obo/SO_0000794 engineered_rescue_region http://purl.obolibrary.org/obo/SO_0000411 rescue_region A rescue region that is engineered. http://purl.obolibrary.org/obo/SO_0000795 rescue_mini_gene http://purl.obolibrary.org/obo/SO_0000815 mini_gene A mini_gene that rescues. http://purl.obolibrary.org/obo/SO_0000796 transgenic_transposable_element http://purl.obolibrary.org/obo/SO_0000101 transposable_element TE that has been modified in vitro, including insertion of DNA derived from a source other than the originating TE. http://purl.obolibrary.org/obo/SO_0000799 engineered_foreign_transposable_element http://purl.obolibrary.org/obo/SO_0000805 engineered_foreign_region A transposable_element that is engineered and foreign. http://purl.obolibrary.org/obo/SO_0000800 assortment_derived_duplication http://purl.obolibrary.org/obo/SO_0001504 assortment_derived_variation A multi-chromosome duplication aberration generated by reassortment of other aberration components. http://purl.obolibrary.org/obo/SO_0000801 assortment_derived_deficiency_plus_duplication http://purl.obolibrary.org/obo/SO_0001504 assortment_derived_variation A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency and a duplication. http://purl.obolibrary.org/obo/SO_0000802 assortment_derived_deficiency http://purl.obolibrary.org/obo/SO_0001504 assortment_derived_variation A multi-chromosome deficiency aberration generated by reassortment of other aberration components. http://purl.obolibrary.org/obo/SO_0000803 assortment_derived_aneuploid http://purl.obolibrary.org/obo/SO_0001504 assortment_derived_variation A multi-chromosome aberration generated by reassortment of other aberration components; presumed to have a deficiency or a duplication. http://purl.obolibrary.org/obo/SO_0000805 engineered_foreign_region http://purl.obolibrary.org/obo/SO_0000804 engineered_region A region that is engineered and foreign. http://purl.obolibrary.org/obo/SO_0000806 fusion http://purl.obolibrary.org/obo/SO_0000733 feature_attribute When two regions of DNA are joined together that are not normally together. http://purl.obolibrary.org/obo/SO_0000807 engineered_tag http://purl.obolibrary.org/obo/SO_0000324 tag A tag that is engineered. http://purl.obolibrary.org/obo/SO_0000808 validated_cDNA_clone http://purl.obolibrary.org/obo/SO_0000317 cDNA_clone A cDNA clone that has been validated. http://purl.obolibrary.org/obo/SO_0000809 invalidated_cDNA_clone http://purl.obolibrary.org/obo/SO_0000317 cDNA_clone A cDNA clone that is invalid. http://purl.obolibrary.org/obo/SO_0000810 chimeric_cDNA_clone http://purl.obolibrary.org/obo/SO_0000809 invalidated_cDNA_clone A cDNA clone invalidated because it is chimeric. http://purl.obolibrary.org/obo/SO_0000811 genomically_contaminated_cDNA_clone http://purl.obolibrary.org/obo/SO_0000809 invalidated_cDNA_clone A cDNA clone invalidated by genomic contamination. http://purl.obolibrary.org/obo/SO_0000812 polyA_primed_cDNA_clone http://purl.obolibrary.org/obo/SO_0000809 invalidated_cDNA_clone A cDNA clone invalidated by polyA priming. http://purl.obolibrary.org/obo/SO_0000813 partially_processed_cDNA_clone http://purl.obolibrary.org/obo/SO_0000809 invalidated_cDNA_clone A cDNA invalidated clone by partial processing. http://purl.obolibrary.org/obo/SO_0000814 rescue http://purl.obolibrary.org/obo/SO_0000733 feature_attribute An attribute describing a region's ability, when introduced to a mutant organism, to re-establish (rescue) a phenotype. http://purl.obolibrary.org/obo/SO_0000815 mini_gene http://purl.obolibrary.org/obo/SO_0000236 ORF By definition, minigenes are short open-reading frames (ORF), usually encoding approximately 9 to 20 amino acids, which are expressed in vivo (as distinct from being synthesized as peptide or protein ex vivo and subsequently injected). The in vivo synthesis confers a distinct advantage: the expressed sequences can enter both antigen presentation pathways, MHC I (inducing CD8+ T- cells, which are usually cytotoxic T-lymphocytes (CTL)) and MHC II (inducing CD4+ T-cells, usually 'T-helpers' (Th)); and can encounter B-cells, inducing antibody responses. Three main vector approaches have been used to deliver minigenes: viral vectors, bacterial vectors and plasmid DNA. http://purl.obolibrary.org/obo/SO_0000817 wild_type http://purl.obolibrary.org/obo/SO_0000733 feature_attribute An attribute describing sequence with the genotype found in nature and/or standard laboratory stock. http://purl.obolibrary.org/obo/SO_0000819 mitochondrial_chromosome http://purl.obolibrary.org/obo/SO_0000340 chromosome A chromosome originating in a mitochondria. http://purl.obolibrary.org/obo/SO_0000820 chloroplast_chromosome http://purl.obolibrary.org/obo/SO_0000340 chromosome A chromosome originating in a chloroplast. http://purl.obolibrary.org/obo/SO_0000821 chromoplast_chromosome http://purl.obolibrary.org/obo/SO_0000340 chromosome A chromosome originating in a chromoplast. http://purl.obolibrary.org/obo/SO_0000822 cyanelle_chromosome http://purl.obolibrary.org/obo/SO_0000340 chromosome A chromosome originating in a cyanelle. http://purl.obolibrary.org/obo/SO_0000823 leucoplast_chromosome http://purl.obolibrary.org/obo/SO_0000340 chromosome A chromosome with origin in a leucoplast. http://purl.obolibrary.org/obo/SO_0000824 macronuclear_chromosome http://purl.obolibrary.org/obo/SO_0000340 chromosome A chromosome originating in a macronucleus. http://purl.obolibrary.org/obo/SO_0000825 micronuclear_chromosome http://purl.obolibrary.org/obo/SO_0000340 chromosome A chromosome originating in a micronucleus. http://purl.obolibrary.org/obo/SO_0000828 nuclear_chromosome http://purl.obolibrary.org/obo/SO_0000340 chromosome A chromosome originating in a nucleus. http://purl.obolibrary.org/obo/SO_0000829 nucleomorphic_chromosome http://purl.obolibrary.org/obo/SO_0000340 chromosome A chromosome originating in a nucleomorph. http://purl.obolibrary.org/obo/SO_0000834 mature_transcript_region http://purl.obolibrary.org/obo/SO_0000833 transcript_region A region of a mature transcript. http://purl.obolibrary.org/obo/SO_0000836 mRNA_region http://purl.obolibrary.org/obo/SO_0000834 mature_transcript_region A region of an mRNA. http://purl.obolibrary.org/obo/SO_0000837 UTR_region http://purl.obolibrary.org/obo/SO_0000836 mRNA_region A region of UTR. http://purl.obolibrary.org/obo/SO_0000838 rRNA_primary_transcript_region http://purl.obolibrary.org/obo/SO_0000835 primary_transcript_region A region of an rRNA primary transcript. http://purl.obolibrary.org/obo/SO_0000840 repeat_component http://purl.obolibrary.org/obo/SO_0001412 topologically_defined_region A region of a repeated sequence. http://purl.obolibrary.org/obo/SO_0000841 spliceosomal_intron_region http://purl.obolibrary.org/obo/SO_0000835 primary_transcript_region A region within an intron. http://purl.obolibrary.org/obo/SO_0000847 tmRNA_region http://purl.obolibrary.org/obo/SO_0000834 mature_transcript_region A region of a tmRNA. http://purl.obolibrary.org/obo/SO_0000848 LTR_component http://purl.obolibrary.org/obo/SO_0000840 repeat_component The long terminal repeat found at the ends of the sequence to be inserted into the host genome. http://purl.obolibrary.org/obo/SO_0000849 three_prime_LTR_component http://purl.obolibrary.org/obo/SO_0000848 LTR_component A component of the three-prime long terminal repeat. http://purl.obolibrary.org/obo/SO_0000850 five_prime_LTR_component http://purl.obolibrary.org/obo/SO_0000848 LTR_component A component of the five-prime long terminal repeat. http://purl.obolibrary.org/obo/SO_0000851 CDS_region http://purl.obolibrary.org/obo/SO_0000836 mRNA_region A region of a CDS. http://purl.obolibrary.org/obo/SO_0000852 exon_region http://purl.obolibrary.org/obo/SO_0000833 transcript_region A region of an exon. http://purl.obolibrary.org/obo/SO_0000853 homologous_region http://purl.obolibrary.org/obo/SO_0000330 conserved_region A region that is homologous to another region. http://purl.obolibrary.org/obo/SO_0000854 paralogous_region http://purl.obolibrary.org/obo/SO_0000853 homologous_region A homologous_region that is paralogous to another region. http://purl.obolibrary.org/obo/SO_0000855 orthologous_region http://purl.obolibrary.org/obo/SO_0000853 homologous_region A homologous_region that is orthologous to another region. http://purl.obolibrary.org/obo/SO_0000856 conserved http://purl.obolibrary.org/obo/SO_0000733 feature_attribute A region that is similar or identical across more than one species. http://purl.obolibrary.org/obo/SO_0000857 homologous http://purl.obolibrary.org/obo/SO_0000856 conserved Similarity due to common ancestry. http://purl.obolibrary.org/obo/SO_0000858 orthologous http://purl.obolibrary.org/obo/SO_0000857 homologous An attribute describing a kind of homology where divergence occurred after a speciation event. http://purl.obolibrary.org/obo/SO_0000859 paralogous http://purl.obolibrary.org/obo/SO_0000857 homologous An attribute describing a kind of homology where divergence occurred after a duplication event. http://purl.obolibrary.org/obo/SO_0000860 syntenic http://purl.obolibrary.org/obo/SO_0000856 conserved Attribute describing sequence regions occurring in same order on chromosome of different species. http://purl.obolibrary.org/obo/SO_0000861 capped_primary_transcript http://purl.obolibrary.org/obo/SO_0000185 primary_transcript A primary transcript that is capped. http://purl.obolibrary.org/obo/SO_0000864 exemplar http://purl.obolibrary.org/obo/SO_0000863 mRNA_attribute An attribute describing a sequence is representative of a class of similar sequences. http://purl.obolibrary.org/obo/SO_0000865 frameshift http://purl.obolibrary.org/obo/SO_0000863 mRNA_attribute An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is not divisible by 3. http://purl.obolibrary.org/obo/SO_0000866 minus_1_frameshift http://purl.obolibrary.org/obo/SO_0000865 frameshift A frameshift caused by deleting one base. http://purl.obolibrary.org/obo/SO_0000867 minus_2_frameshift http://purl.obolibrary.org/obo/SO_0000865 frameshift A frameshift caused by deleting two bases. http://purl.obolibrary.org/obo/SO_0000868 plus_1_frameshift http://purl.obolibrary.org/obo/SO_0000865 frameshift A frameshift caused by inserting one base. http://purl.obolibrary.org/obo/SO_0000869 plus_2_framshift http://purl.obolibrary.org/obo/SO_0000865 frameshift A frameshift caused by inserting two bases. http://purl.obolibrary.org/obo/SO_0000870 trans_spliced http://purl.obolibrary.org/obo/SO_0000237 transcript_attribute An attribute describing transcript sequence that is created by splicing exons from diferent genes. http://purl.obolibrary.org/obo/SO_0000873 edited_transcript http://purl.obolibrary.org/obo/SO_0000673 transcript A transcript that is edited. http://purl.obolibrary.org/obo/SO_0000874 edited_transcript_by_A_to_I_substitution http://purl.obolibrary.org/obo/SO_0000873 edited_transcript A transcript that has been edited by A to I substitution. http://purl.obolibrary.org/obo/SO_0000875 bound_by_protein http://purl.obolibrary.org/obo/SO_0000277 bound_by_factor An attribute describing a sequence that is bound by a protein. http://purl.obolibrary.org/obo/SO_0000876 bound_by_nucleic_acid http://purl.obolibrary.org/obo/SO_0000277 bound_by_factor An attribute describing a sequence that is bound by a nucleic acid. http://purl.obolibrary.org/obo/SO_0000877 alternatively_spliced http://purl.obolibrary.org/obo/SO_0000237 transcript_attribute An attribute describing a situation where a gene may encode for more than 1 transcript. http://purl.obolibrary.org/obo/SO_0000878 monocistronic http://purl.obolibrary.org/obo/SO_0000237 transcript_attribute An attribute describing a sequence that contains the code for one gene product. http://purl.obolibrary.org/obo/SO_0000879 dicistronic http://purl.obolibrary.org/obo/SO_0000880 polycistronic An attribute describing a sequence that contains the code for two gene products. http://purl.obolibrary.org/obo/SO_0000880 polycistronic http://purl.obolibrary.org/obo/SO_0000237 transcript_attribute An attribute describing a sequence that contains the code for more than one gene product. http://purl.obolibrary.org/obo/SO_0000881 recoded http://purl.obolibrary.org/obo/SO_0000863 mRNA_attribute An attribute describing an mRNA sequence that has been reprogrammed at translation, causing localized alterations. http://purl.obolibrary.org/obo/SO_0000882 codon_redefined http://purl.obolibrary.org/obo/SO_0000881 recoded An attribute describing the alteration of codon meaning. http://purl.obolibrary.org/obo/SO_0000883 stop_codon_read_through http://purl.obolibrary.org/obo/SO_0000145 recoded_codon A stop codon redefined to be a new amino acid. http://purl.obolibrary.org/obo/SO_0000884 stop_codon_redefined_as_pyrrolysine http://purl.obolibrary.org/obo/SO_0000883 stop_codon_read_through A stop codon redefined to be the new amino acid, pyrrolysine. http://purl.obolibrary.org/obo/SO_0000885 stop_codon_redefined_as_selenocysteine http://purl.obolibrary.org/obo/SO_0000883 stop_codon_read_through A stop codon redefined to be the new amino acid, selenocysteine. http://purl.obolibrary.org/obo/SO_0000886 recoded_by_translational_bypass http://purl.obolibrary.org/obo/SO_0000881 recoded Recoded mRNA where a block of nucleotides is not translated. http://purl.obolibrary.org/obo/SO_0000887 translationally_frameshifted http://purl.obolibrary.org/obo/SO_0000881 recoded Recoding by frameshifting a particular site. http://purl.obolibrary.org/obo/SO_0000893 silenced http://purl.obolibrary.org/obo/SO_0000126 transcriptionally_repressed An attribute describing an epigenetic process where a gene is inactivated at transcriptional or translational level. http://purl.obolibrary.org/obo/SO_0000894 silenced_by_DNA_modification http://purl.obolibrary.org/obo/SO_0000893 silenced An attribute describing an epigenetic process where a gene is inactivated by DNA modifications, resulting in repression of transcription. http://purl.obolibrary.org/obo/SO_0000895 silenced_by_DNA_methylation http://purl.obolibrary.org/obo/SO_0000894 silenced_by_DNA_modification An attribute describing an epigenetic process where a gene is inactivated by DNA methylation, resulting in repression of transcription. http://purl.obolibrary.org/obo/SO_0000903 endogenous_retroviral_sequence http://purl.obolibrary.org/obo/SO_0000751 proviral_location Endogenous DNA sequence that are likely to have arisen from retroviruses. http://purl.obolibrary.org/obo/SO_0000904 rearranged_at_DNA_level http://purl.obolibrary.org/obo/SO_0000133 epigenetically_modified An attribute to describe the sequence of a feature, where the DNA is rearranged. http://purl.obolibrary.org/obo/SO_0000905 status http://purl.obolibrary.org/obo/SO_0000733 feature_attribute An attribute describing the status of a feature, based on the available evidence. http://purl.obolibrary.org/obo/SO_0000906 independently_known http://purl.obolibrary.org/obo/SO_0000905 status Attribute to describe a feature that is independently known - not predicted. http://purl.obolibrary.org/obo/SO_0000907 supported_by_sequence_similarity http://purl.obolibrary.org/obo/SO_0000732 predicted An attribute to describe a feature that has been predicted using sequence similarity techniques. http://purl.obolibrary.org/obo/SO_0000908 supported_by_domain_match http://purl.obolibrary.org/obo/SO_0000907 supported_by_sequence_similarity An attribute to describe a feature that has been predicted using sequence similarity of a known domain. http://purl.obolibrary.org/obo/SO_0000909 supported_by_EST_or_cDNA http://purl.obolibrary.org/obo/SO_0000907 supported_by_sequence_similarity An attribute to describe a feature that has been predicted using sequence similarity to EST or cDNA data. http://purl.obolibrary.org/obo/SO_0000910 orphan http://purl.obolibrary.org/obo/SO_0000732 predicted A gene whose predicted amino acid sequence is unsupported by any experimental evidence or by any match with any other known sequence. http://purl.obolibrary.org/obo/SO_0000911 predicted_by_ab_initio_computation http://purl.obolibrary.org/obo/SO_0000732 predicted An attribute describing a feature that is predicted by a computer program that did not rely on sequence similarity. http://purl.obolibrary.org/obo/SO_0000912 asx_turn http://purl.obolibrary.org/obo/SO_0001128 polypeptide_turn_motif A motif of three consecutive residues and one H-bond in which: residue(i) is Aspartate or Asparagine (Asx), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2). http://purl.obolibrary.org/obo/SO_0000913 cloned_cDNA_insert http://purl.obolibrary.org/obo/SO_0000753 clone_insert A clone insert made from cDNA. http://purl.obolibrary.org/obo/SO_0000914 cloned_genomic_insert http://purl.obolibrary.org/obo/SO_0000753 clone_insert A clone insert made from genomic DNA. http://purl.obolibrary.org/obo/SO_0000915 engineered_insert http://purl.obolibrary.org/obo/SO_0000753 clone_insert A clone insert that is engineered. http://purl.obolibrary.org/obo/SO_0000930 guide_RNA_region http://purl.obolibrary.org/obo/SO_0000834 mature_transcript_region A region of guide RNA. http://purl.obolibrary.org/obo/SO_0000931 anchor_region http://purl.obolibrary.org/obo/SO_0000930 guide_RNA_region A region of a guide_RNA that base-pairs to a target mRNA. http://purl.obolibrary.org/obo/SO_0000932 pre_edited_mRNA http://purl.obolibrary.org/obo/SO_0000120 protein_coding_primary_transcript A primary transcript that, at least in part, encodes one or more proteins that has not been edited. http://purl.obolibrary.org/obo/SO_0000933 intermediate http://purl.obolibrary.org/obo/SO_0000733 feature_attribute An attribute to describe a feature between stages of processing. http://purl.obolibrary.org/obo/SO_0000934 miRNA_target_site http://purl.obolibrary.org/obo/SO_0001655 nucleotide_binding_site A miRNA target site is a binding site where the molecule is a micro RNA. http://purl.obolibrary.org/obo/SO_0000935 edited_CDS http://purl.obolibrary.org/obo/SO_0000316 CDS A CDS that is edited. http://purl.obolibrary.org/obo/SO_0000936 vertebrate_immunoglobulin_T_cell_receptor_rearranged_segment http://purl.obolibrary.org/obo/SO_0000301 vertebrate_immune_system_gene_recombination_feature Genomic DNA of immunoglobulin/T-cell receptor gene in partially rearranged genomic DNA. http://purl.obolibrary.org/obo/SO_0000938 vertebrate_immunoglobulin_T_cell_receptor_rearranged_gene_cluster http://purl.obolibrary.org/obo/SO_0000301 vertebrate_immune_system_gene_recombination_feature Genomic DNA of immunoglobulin/T-cell receptor gene in rearranged configuration. http://purl.obolibrary.org/obo/SO_0000939 vertebrate_immune_system_gene_recombination_signal_feature http://purl.obolibrary.org/obo/SO_0000301 vertebrate_immune_system_gene_recombination_feature Feature used for the recombination of genomic material for the purpose of generating diversity of the immune system. http://purl.obolibrary.org/obo/SO_0000940 recombinationally_rearranged http://purl.obolibrary.org/obo/SO_0000733 feature_attribute A gene that is recombinationally rearranged. http://purl.obolibrary.org/obo/SO_0000942 attP_site http://purl.obolibrary.org/obo/SO_0000946 integration_excision_site An integration/excision site of a phage chromosome at which a recombinase acts to insert the phage DNA at a cognate integration/excision site on a bacterial chromosome. http://purl.obolibrary.org/obo/SO_0000943 attB_site http://purl.obolibrary.org/obo/SO_0000946 integration_excision_site An integration/excision site of a bacterial chromosome at which a recombinase acts to insert foreign DNA containing a cognate integration/excision site. http://purl.obolibrary.org/obo/SO_0000944 attL_site http://purl.obolibrary.org/obo/SO_0000946 integration_excision_site A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attB_site and the 3' portion of attP_site. http://purl.obolibrary.org/obo/SO_0000945 attR_site http://purl.obolibrary.org/obo/SO_0000946 integration_excision_site A region that results from recombination between attP_site and attB_site, composed of the 5' portion of attP_site and the 3' portion of attB_site. http://purl.obolibrary.org/obo/SO_0000946 integration_excision_site http://purl.obolibrary.org/obo/SO_0000342 site_specific_recombination_target_region A region specifically recognised by a recombinase, which inserts or removes another region marked by a distinct cognate integration/excision site. http://purl.obolibrary.org/obo/SO_0000947 resolution_site http://purl.obolibrary.org/obo/SO_0000342 site_specific_recombination_target_region A region specifically recognized by a recombinase, which separates a physically contiguous circle of DNA into two physically separate circles. http://purl.obolibrary.org/obo/SO_0000948 inversion_site http://purl.obolibrary.org/obo/SO_0000342 site_specific_recombination_target_region A region specifically recognised by a recombinase, which inverts the region flanked by a pair of sites. http://purl.obolibrary.org/obo/SO_0000949 dif_site http://purl.obolibrary.org/obo/SO_0000947 resolution_site A site at which replicated bacterial circular chromosomes are decatenated by site specific resolvase. http://purl.obolibrary.org/obo/SO_0000950 attC_site http://purl.obolibrary.org/obo/SO_0000946 integration_excision_site An attC site is a sequence required for the integration of a DNA of an integron. http://purl.obolibrary.org/obo/SO_0000951 eukaryotic_terminator http://purl.obolibrary.org/obo/SO_0000141 terminator A signal for RNA polymerase to terminate transcription. http://purl.obolibrary.org/obo/SO_0000952 oriV http://purl.obolibrary.org/obo/SO_0000296 origin_of_replication An origin of vegetative replication in plasmids and phages. http://purl.obolibrary.org/obo/SO_0000953 oriC http://purl.obolibrary.org/obo/SO_0000296 origin_of_replication An origin of bacterial chromosome replication. http://purl.obolibrary.org/obo/SO_0000954 DNA_chromosome http://purl.obolibrary.org/obo/SO_0000340 chromosome Structural unit composed of a self-replicating, DNA molecule. http://purl.obolibrary.org/obo/SO_0000955 double_stranded_DNA_chromosome http://purl.obolibrary.org/obo/SO_0000954 DNA_chromosome Structural unit composed of a self-replicating, double-stranded DNA molecule. http://purl.obolibrary.org/obo/SO_0000956 single_stranded_DNA_chromosome http://purl.obolibrary.org/obo/SO_0000954 DNA_chromosome Structural unit composed of a self-replicating, single-stranded DNA molecule. http://purl.obolibrary.org/obo/SO_0000957 linear_double_stranded_DNA_chromosome http://purl.obolibrary.org/obo/SO_0000955 double_stranded_DNA_chromosome Structural unit composed of a self-replicating, double-stranded, linear DNA molecule. http://purl.obolibrary.org/obo/SO_0000958 circular_double_stranded_DNA_chromosome http://purl.obolibrary.org/obo/SO_0000955 double_stranded_DNA_chromosome Structural unit composed of a self-replicating, double-stranded, circular DNA molecule. http://purl.obolibrary.org/obo/SO_0000959 linear_single_stranded_DNA_chromosome http://purl.obolibrary.org/obo/SO_0000956 single_stranded_DNA_chromosome Structural unit composed of a self-replicating, single-stranded, linear DNA molecule. http://purl.obolibrary.org/obo/SO_0000960 circular_single_stranded_DNA_chromosome http://purl.obolibrary.org/obo/SO_0000956 single_stranded_DNA_chromosome Structural unit composed of a self-replicating, single-stranded, circular DNA molecule. http://purl.obolibrary.org/obo/SO_0000961 RNA_chromosome http://purl.obolibrary.org/obo/SO_0000340 chromosome Structural unit composed of a self-replicating, RNA molecule. http://purl.obolibrary.org/obo/SO_0000962 single_stranded_RNA_chromosome http://purl.obolibrary.org/obo/SO_0000961 RNA_chromosome Structural unit composed of a self-replicating, single-stranded RNA molecule. http://purl.obolibrary.org/obo/SO_0000963 linear_single_stranded_RNA_chromosome http://purl.obolibrary.org/obo/SO_0000962 single_stranded_RNA_chromosome Structural unit composed of a self-replicating, single-stranded, linear RNA molecule. http://purl.obolibrary.org/obo/SO_0000964 linear_double_stranded_RNA_chromosome http://purl.obolibrary.org/obo/SO_0000965 double_stranded_RNA_chromosome Structural unit composed of a self-replicating, double-stranded, linear RNA molecule. http://purl.obolibrary.org/obo/SO_0000965 double_stranded_RNA_chromosome http://purl.obolibrary.org/obo/SO_0000961 RNA_chromosome Structural unit composed of a self-replicating, double-stranded RNA molecule. http://purl.obolibrary.org/obo/SO_0000966 circular_single_stranded_RNA_chromosome http://purl.obolibrary.org/obo/SO_0000962 single_stranded_RNA_chromosome Structural unit composed of a self-replicating, single-stranded, circular DNA molecule. http://purl.obolibrary.org/obo/SO_0000967 circular_double_stranded_RNA_chromosome http://purl.obolibrary.org/obo/SO_0000965 double_stranded_RNA_chromosome Structural unit composed of a self-replicating, double-stranded, circular RNA molecule. http://purl.obolibrary.org/obo/SO_0000973 insertion_sequence http://purl.obolibrary.org/obo/SO_0000208 terminal_inverted_repeat_element A terminal_inverted_repeat_element that is bacterial and only encodes the functions required for its transposition between these inverted repeats. http://purl.obolibrary.org/obo/SO_0000976 cryptic http://purl.obolibrary.org/obo/SO_0000733 feature_attribute A feature_attribute describing a feature that is not manifest under normal conditions. http://purl.obolibrary.org/obo/SO_0000978 template_region http://purl.obolibrary.org/obo/SO_0000930 guide_RNA_region A region of a guide_RNA that specifies the insertions and deletions of bases in the editing of a target mRNA. http://purl.obolibrary.org/obo/SO_0000979 gRNA_encoding http://purl.obolibrary.org/obo/SO_0000011 non_protein_coding A non-protein_coding gene that encodes a guide_RNA. http://purl.obolibrary.org/obo/SO_0000980 minicircle http://purl.obolibrary.org/obo/SO_0001235 replicon A minicircle is a replicon, part of a kinetoplast, that encodes for guide RNAs. http://purl.obolibrary.org/obo/SO_0000981 rho_dependent_bacterial_terminator http://purl.obolibrary.org/obo/SO_0000614 bacterial_terminator A transcription terminator that is dependent upon Rho. http://purl.obolibrary.org/obo/SO_0000982 rho_independent_bacterial_terminator http://purl.obolibrary.org/obo/SO_0000614 bacterial_terminator A transcription terminator that is not dependent upon Rho. Rather, the mRNA contains a sequence that allows it to base-pair with itself and make a stem-loop structure. http://purl.obolibrary.org/obo/SO_0000983 strand_attribute http://purl.obolibrary.org/obo/SO_0000733 feature_attribute The attribute of how many strands are present in a nucleotide polymer. http://purl.obolibrary.org/obo/SO_0000984 single http://purl.obolibrary.org/obo/SO_0000983 strand_attribute When a nucleotide polymer has only one strand. http://purl.obolibrary.org/obo/SO_0000985 double http://purl.obolibrary.org/obo/SO_0000983 strand_attribute When a nucleotide polymer has two strands that are reverse-complement to one another and pair together. http://purl.obolibrary.org/obo/SO_0000986 topology_attribute http://purl.obolibrary.org/obo/SO_0000443 polymer_attribute The attribute of whether a nucleotide polymer is linear or circular. http://purl.obolibrary.org/obo/SO_0000987 linear http://purl.obolibrary.org/obo/SO_0000986 topology_attribute A quality of a nucleotide polymer that has a 3'-terminal residue and a 5'-terminal residue. http://purl.obolibrary.org/obo/SO_0000989 class_II_RNA http://purl.obolibrary.org/obo/SO_0000655 ncRNA Small non-coding RNA (59-60 nt long) containing 5' and 3' ends that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm. http://purl.obolibrary.org/obo/SO_0000990 class_I_RNA http://purl.obolibrary.org/obo/SO_0000655 ncRNA Small non-coding RNA (55-65 nt long) containing highly conserved 5' and 3' ends (16 and 8 nt, respectively) that are predicted to come together to form a stem structure. Identified in the social amoeba Dictyostelium discoideum and localized in the cytoplasm. http://purl.obolibrary.org/obo/SO_0000991 genomic_DNA http://purl.obolibrary.org/obo/SO_0000352 DNA DNA located in the genome and able to be transmitted to the offspring. http://purl.obolibrary.org/obo/SO_0000992 BAC_cloned_genomic_insert http://purl.obolibrary.org/obo/SO_0000914 cloned_genomic_insert A region of DNA that has been inserted into the bacterial genome using a bacterial artificial chromosome. http://purl.obolibrary.org/obo/SO_0000993 consensus http://purl.obolibrary.org/obo/SO_0000905 status A sequence produced from an aligment algorithm that uses multiple sequences as input. http://purl.obolibrary.org/obo/SO_0000994 consensus_region http://purl.obolibrary.org/obo/SO_0001410 experimental_feature A region that has a known consensus sequence. http://purl.obolibrary.org/obo/SO_0000997 gene_fragment http://purl.obolibrary.org/obo/SO_0000842 gene_component_region A portion of a gene that is not the complete gene. http://purl.obolibrary.org/obo/SO_0000998 recursive_splice_site http://purl.obolibrary.org/obo/SO_0001419 cis_splice_site A recursive splice site is a splice site which subdivides a large intron. Recursive splicing is a mechanism that splices large introns by sub dividing the intron at non exonic elements and alternate exons. http://purl.obolibrary.org/obo/SO_0001000 cytosolic_16S_rRNA http://purl.obolibrary.org/obo/SO_0000650 cytosolic_SSU_rRNA Cytosolic 16S rRNA is an RNA component of the small subunit of cytosolic ribosomes in prokaryotes. http://purl.obolibrary.org/obo/SO_0001001 cytosolic_23S_rRNA http://purl.obolibrary.org/obo/SO_0000651 cytosolic_LSU_rRNA Cytosolic 23S rRNA is an RNA component of the large subunit of cytosolic ribosomes in prokaryotes. http://purl.obolibrary.org/obo/SO_0001003 solo_LTR http://purl.obolibrary.org/obo/SO_0000286 long_terminal_repeat A recombination product between the 2 LTR of the same element. http://purl.obolibrary.org/obo/SO_0001004 low_complexity http://purl.obolibrary.org/obo/SO_0000905 status When a sequence does not contain an equal distribution of all four possible nucleotide bases or does not contain all nucleotide bases. http://purl.obolibrary.org/obo/SO_0001005 low_complexity_region http://purl.obolibrary.org/obo/SO_0001410 experimental_feature A region where the DNA does not contain an equal distrubution of all four possible nucleotides or does not contain all four nucleotides. http://purl.obolibrary.org/obo/SO_0001006 prophage http://purl.obolibrary.org/obo/SO_0000113 proviral_region A phage genome after it has established in the host genome in a latent/immune state either as a plasmid or as an integrated "island". http://purl.obolibrary.org/obo/SO_0001007 cryptic_prophage http://purl.obolibrary.org/obo/SO_0000772 genomic_island A remnant of an integrated prophage in the host genome or an "island" in the host genome that includes phage like-genes. http://purl.obolibrary.org/obo/SO_0001008 tetraloop http://purl.obolibrary.org/obo/SO_0000313 stem_loop A base-paired stem with loop of 4 non-hydrogen bonded nucleotides. http://purl.obolibrary.org/obo/SO_0001009 DNA_constraint_sequence http://purl.obolibrary.org/obo/SO_0000442 ds_oligo A double-stranded DNA used to control macromolecular structure and function. http://purl.obolibrary.org/obo/SO_0001010 i_motif http://purl.obolibrary.org/obo/SO_0000142 DNA_sequence_secondary_structure A cytosine rich domain whereby strands associate both inter- and intramolecularly at moderately acidic pH. http://purl.obolibrary.org/obo/SO_0001011 PNA_oligo http://purl.obolibrary.org/obo/SO_0001247 synthetic_oligo Peptide nucleic acid, is a chemical not known to occur naturally but is artificially synthesized and used in some biological research and medical treatments. The PNA backbone is composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds. http://purl.obolibrary.org/obo/SO_0001012 DNAzyme http://purl.obolibrary.org/obo/SO_0000696 oligo A DNA sequence with catalytic activity. http://purl.obolibrary.org/obo/SO_0001014 intron_domain http://purl.obolibrary.org/obo/SO_0000835 primary_transcript_region An intronic region that has an attribute. http://purl.obolibrary.org/obo/SO_0001015 wobble_base_pair http://purl.obolibrary.org/obo/SO_0000028 base_pair A type of non-canonical base pairing, most commonly between G and U, which is important for the secondary structure of RNAs. It has similar thermodynamic stability to the Watson-Crick pairing. Wobble base pairs only have two hydrogen bonds. Other wobble base pair possibilities are I-A, I-U and I-C. http://purl.obolibrary.org/obo/SO_0001016 internal_guide_sequence http://purl.obolibrary.org/obo/SO_0001014 intron_domain A purine-rich sequence in the group I introns which determines the locations of the splice sites in group I intron splicing and has catalytic activity. http://purl.obolibrary.org/obo/SO_0001017 silent_mutation http://purl.obolibrary.org/obo/SO_0001878 feature_variant A sequence variant that does not affect protein function. Silent mutations may occur in genic ( CDS, UTR, intron etc) and intergenic regions. Silent mutations may have affects on processes such as splicing and regulation. http://purl.obolibrary.org/obo/SO_0001018 epitope http://purl.obolibrary.org/obo/SO_0000409 binding_site A binding site that, in the molecule, interacts selectively and non-covalently with antibodies, B cells or T cells. http://purl.obolibrary.org/obo/SO_0001021 chromosome_breakpoint http://purl.obolibrary.org/obo/SO_0000699 junction A chromosomal region that may sustain a double-strand break, resulting in a recombination event. http://purl.obolibrary.org/obo/SO_0001022 inversion_breakpoint http://purl.obolibrary.org/obo/SO_0001021 chromosome_breakpoint The point within a chromosome where an inversion begins or ends. http://purl.obolibrary.org/obo/SO_0001023 allele http://purl.obolibrary.org/obo/SO_0001507 variant_collection An allele is one of a set of coexisting sequence variants of a gene. http://purl.obolibrary.org/obo/SO_0001025 polymorphic_sequence_variant http://purl.obolibrary.org/obo/SO_0001023 allele A sequence variant that is segregating in one or more natural populations of a species. http://purl.obolibrary.org/obo/SO_0001028 diplotype http://purl.obolibrary.org/obo/SO_0001507 variant_collection A diplotype is a pair of haplotypes from a given individual. It is a genotype where the phase is known. http://purl.obolibrary.org/obo/SO_0001029 direction_attribute http://purl.obolibrary.org/obo/SO_0000733 feature_attribute The attribute of whether the sequence is the same direction as a feature (forward) or the opposite direction as a feature (reverse). http://purl.obolibrary.org/obo/SO_0001030 forward http://purl.obolibrary.org/obo/SO_0001029 direction_attribute Forward is an attribute of the feature, where the feature is in the 5' to 3' direction. http://purl.obolibrary.org/obo/SO_0001031 reverse http://purl.obolibrary.org/obo/SO_0001029 direction_attribute Reverse is an attribute of the feature, where the feature is in the 3' to 5' direction. Again could be applied to primer. http://purl.obolibrary.org/obo/SO_0001032 mitochondrial_DNA http://purl.obolibrary.org/obo/SO_0000737 mitochondrial_sequence DNA belonging to the genome of a mitochondria. http://purl.obolibrary.org/obo/SO_0001033 chloroplast_DNA http://purl.obolibrary.org/obo/SO_0000745 chloroplast_sequence DNA belonging to the genome of a chloroplast, a photosynthetic plastid. http://purl.obolibrary.org/obo/SO_0001034 miRtron http://purl.obolibrary.org/obo/SO_0001014 intron_domain A de-branched intron which mimics the structure of pre-miRNA and enters the miRNA processing pathway without Drosha mediated cleavage. http://purl.obolibrary.org/obo/SO_0001035 piRNA http://purl.obolibrary.org/obo/SO_0000370 small_regulatory_ncRNA A small non coding RNA, part of a silencing system that prevents the spreading of selfish genetic elements. http://purl.obolibrary.org/obo/SO_0001036 arginyl_tRNA http://purl.obolibrary.org/obo/SO_0000253 tRNA A tRNA sequence that has an arginine anticodon, and a 3' arginine binding region. http://purl.obolibrary.org/obo/SO_0001038 extrachromosomal_mobile_genetic_element http://purl.obolibrary.org/obo/SO_0001037 mobile_genetic_element An MGE that is not integrated into the host chromosome. http://purl.obolibrary.org/obo/SO_0001040 integrated_plasmid http://purl.obolibrary.org/obo/SO_0001039 integrated_mobile_genetic_element A plasmid sequence that is integrated within the host chromosome. http://purl.obolibrary.org/obo/SO_0001041 viral_sequence http://purl.obolibrary.org/obo/SO_0001235 replicon The region of nucleotide sequence of a virus, a submicroscopic particle that replicates by infecting a host cell. http://purl.obolibrary.org/obo/SO_0001042 phage_sequence http://purl.obolibrary.org/obo/SO_0001041 viral_sequence The nucleotide sequence of a virus that infects bacteria. http://purl.obolibrary.org/obo/SO_0001043 attCtn_site http://purl.obolibrary.org/obo/SO_0000946 integration_excision_site An attachment site located on a conjugative transposon and used for site-specific integration of a conjugative transposon. http://purl.obolibrary.org/obo/SO_0001044 nuclear_mt_pseudogene http://purl.obolibrary.org/obo/SO_0001760 non_processed_pseudogene A nuclear pseudogene of either coding or non-coding mitochondria derived sequence. http://purl.obolibrary.org/obo/SO_0001045 cointegrated_plasmid http://purl.obolibrary.org/obo/SO_0001039 integrated_mobile_genetic_element A MGE region consisting of two fused plasmids resulting from a replicative transposition event. http://purl.obolibrary.org/obo/SO_0001046 IRLinv_site http://purl.obolibrary.org/obo/SO_0001048 inversion_site_part Component of the inversion site located at the left of a region susceptible to site-specific inversion. http://purl.obolibrary.org/obo/SO_0001047 IRRinv_site http://purl.obolibrary.org/obo/SO_0001048 inversion_site_part Component of the inversion site located at the right of a region susceptible to site-specific inversion. http://purl.obolibrary.org/obo/SO_0001048 inversion_site_part http://purl.obolibrary.org/obo/SO_0000342 site_specific_recombination_target_region A region located within an inversion site. http://purl.obolibrary.org/obo/SO_0001049 defective_conjugative_transposon http://purl.obolibrary.org/obo/SO_0000772 genomic_island An island that contains genes for integration/excision and the gene and site for the initiation of intercellular transfer by conjugation. It can be complemented for transfer by a conjugative transposon. http://purl.obolibrary.org/obo/SO_0001050 repeat_fragment http://purl.obolibrary.org/obo/SO_0000840 repeat_component A portion of a repeat, interrupted by the insertion of another element. http://purl.obolibrary.org/obo/SO_0001054 transposon_fragment http://purl.obolibrary.org/obo/SO_0000840 repeat_component A portion of a transposon, interrupted by the insertion of another element. http://purl.obolibrary.org/obo/SO_0001056 splicing_regulatory_region http://purl.obolibrary.org/obo/SO_0001055 transcriptional_cis_regulatory_region A regulatory_region that modulates splicing. http://purl.obolibrary.org/obo/SO_0001061 propeptide_cleavage_site http://purl.obolibrary.org/obo/SO_0100011 cleaved_peptide_region The propeptide_cleavage_site is the arginine/lysine boundary on a propeptide where cleavage occurs. http://purl.obolibrary.org/obo/SO_0001063 immature_peptide_region http://purl.obolibrary.org/obo/SO_0000839 polypeptide_region An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs. http://purl.obolibrary.org/obo/SO_0001064 active_peptide http://purl.obolibrary.org/obo/SO_0000419 mature_protein_region Active peptides are proteins which are biologically active, released from a precursor molecule. http://purl.obolibrary.org/obo/SO_0001066 compositionally_biased_region_of_peptide http://purl.obolibrary.org/obo/SO_0000839 polypeptide_region Polypeptide region that is rich in a particular amino acid or homopolymeric and greater than three residues in length. http://purl.obolibrary.org/obo/SO_0001067 polypeptide_motif http://purl.obolibrary.org/obo/SO_0100021 polypeptide_conserved_region A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.). http://purl.obolibrary.org/obo/SO_0001068 polypeptide_repeat http://purl.obolibrary.org/obo/SO_0100021 polypeptide_conserved_region A polypeptide_repeat is a single copy of an internal sequence repetition. http://purl.obolibrary.org/obo/SO_0001070 polypeptide_structural_region http://purl.obolibrary.org/obo/SO_0000839 polypeptide_region Region of polypeptide with a given structural property. http://purl.obolibrary.org/obo/SO_0001071 membrane_structure http://purl.obolibrary.org/obo/SO_0001070 polypeptide_structural_region Arrangement of the polypeptide with respect to the lipid bilayer. http://purl.obolibrary.org/obo/SO_0001072 extramembrane_polypeptide_region http://purl.obolibrary.org/obo/SO_0001070 polypeptide_structural_region Polypeptide region that is localized outside of a lipid bilayer. http://purl.obolibrary.org/obo/SO_0001073 cytoplasmic_polypeptide_region http://purl.obolibrary.org/obo/SO_0001072 extramembrane_polypeptide_region Polypeptide region that is localized inside the cytoplasm. http://purl.obolibrary.org/obo/SO_0001074 non_cytoplasmic_polypeptide_region http://purl.obolibrary.org/obo/SO_0001072 extramembrane_polypeptide_region Polypeptide region that is localized outside of a lipid bilayer and outside of the cytoplasm. http://purl.obolibrary.org/obo/SO_0001075 intramembrane_polypeptide_region http://purl.obolibrary.org/obo/SO_0001070 polypeptide_structural_region Polypeptide region present in the lipid bilayer. http://purl.obolibrary.org/obo/SO_0001076 membrane_peptide_loop http://purl.obolibrary.org/obo/SO_0001075 intramembrane_polypeptide_region Polypeptide region localized within the lipid bilayer where both ends traverse the same membrane. http://purl.obolibrary.org/obo/SO_0001077 transmembrane_polypeptide_region http://purl.obolibrary.org/obo/SO_0001075 intramembrane_polypeptide_region Polypeptide region traversing the lipid bilayer. http://purl.obolibrary.org/obo/SO_0001078 polypeptide_secondary_structure http://purl.obolibrary.org/obo/SO_0001070 polypeptide_structural_region A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain. http://purl.obolibrary.org/obo/SO_0001079 polypeptide_structural_motif http://purl.obolibrary.org/obo/SO_0001070 polypeptide_structural_region Motif is a three-dimensional structural element within the chain, which appears also in a variety of other molecules. Unlike a domain, a motif does not need to form a stable globular unit. http://purl.obolibrary.org/obo/SO_0001080 coiled_coil http://purl.obolibrary.org/obo/SO_0001079 polypeptide_structural_motif A coiled coil is a structural motif in proteins, in which alpha-helices are coiled together like the strands of a rope. http://purl.obolibrary.org/obo/SO_0001081 helix_turn_helix http://purl.obolibrary.org/obo/SO_0001079 polypeptide_structural_motif A motif comprising two helices separated by a turn. http://purl.obolibrary.org/obo/SO_0001082 polypeptide_sequencing_information http://purl.obolibrary.org/obo/SO_0000700 remark Incompatibility in the sequence due to some experimental problem. http://purl.obolibrary.org/obo/SO_0001083 non_adjacent_residues http://purl.obolibrary.org/obo/SO_0001082 polypeptide_sequencing_information Indicates that two consecutive residues in a fragment sequence are not consecutive in the full-length protein and that there are a number of unsequenced residues between them. http://purl.obolibrary.org/obo/SO_0001084 non_terminal_residue http://purl.obolibrary.org/obo/SO_0001082 polypeptide_sequencing_information The residue at an extremity of the sequence is not the terminal residue. http://purl.obolibrary.org/obo/SO_0001085 sequence_conflict http://purl.obolibrary.org/obo/SO_0001082 polypeptide_sequencing_information Different sources report differing sequences. http://purl.obolibrary.org/obo/SO_0001086 sequence_uncertainty http://purl.obolibrary.org/obo/SO_0001082 polypeptide_sequencing_information Describes the positions in a sequence where the authors are unsure about the sequence assignment. http://purl.obolibrary.org/obo/SO_0001089 post_translationally_modified_region http://purl.obolibrary.org/obo/SO_0100001 biochemical_region_of_peptide A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein. http://purl.obolibrary.org/obo/SO_0001092 polypeptide_metal_contact http://purl.obolibrary.org/obo/SO_0100002 molecular_contact_region A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with metal ions. http://purl.obolibrary.org/obo/SO_0001093 protein_protein_contact http://purl.obolibrary.org/obo/SO_0000410 protein_binding_site A binding site that, in the protein molecule, interacts selectively and non-covalently with polypeptide residues. http://purl.obolibrary.org/obo/SO_0001094 polypeptide_calcium_ion_contact_site http://purl.obolibrary.org/obo/SO_0001092 polypeptide_metal_contact A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with calcium ions. http://purl.obolibrary.org/obo/SO_0001095 polypeptide_cobalt_ion_contact_site http://purl.obolibrary.org/obo/SO_0001092 polypeptide_metal_contact A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with cobalt ions. http://purl.obolibrary.org/obo/SO_0001096 polypeptide_copper_ion_contact_site http://purl.obolibrary.org/obo/SO_0001092 polypeptide_metal_contact A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with copper ions. http://purl.obolibrary.org/obo/SO_0001097 polypeptide_iron_ion_contact_site http://purl.obolibrary.org/obo/SO_0001092 polypeptide_metal_contact A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with iron ions. http://purl.obolibrary.org/obo/SO_0001098 polypeptide_magnesium_ion_contact_site http://purl.obolibrary.org/obo/SO_0001092 polypeptide_metal_contact A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with magnesium ions. http://purl.obolibrary.org/obo/SO_0001099 polypeptide_manganese_ion_contact_site http://purl.obolibrary.org/obo/SO_0001092 polypeptide_metal_contact A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with manganese ions. http://purl.obolibrary.org/obo/SO_0001100 polypeptide_molybdenum_ion_contact_site http://purl.obolibrary.org/obo/SO_0001092 polypeptide_metal_contact A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with molybdenum ions. http://purl.obolibrary.org/obo/SO_0001101 polypeptide_nickel_ion_contact_site http://purl.obolibrary.org/obo/SO_0001092 polypeptide_metal_contact A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with nickel ions. http://purl.obolibrary.org/obo/SO_0001102 polypeptide_tungsten_ion_contact_site http://purl.obolibrary.org/obo/SO_0001092 polypeptide_metal_contact A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with tungsten ions. http://purl.obolibrary.org/obo/SO_0001103 polypeptide_zinc_ion_contact_site http://purl.obolibrary.org/obo/SO_0001092 polypeptide_metal_contact A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with zinc ions. http://purl.obolibrary.org/obo/SO_0001104 catalytic_residue http://purl.obolibrary.org/obo/SO_0001237 amino_acid Amino acid involved in the activity of an enzyme. http://purl.obolibrary.org/obo/SO_0001105 polypeptide_ligand_contact http://purl.obolibrary.org/obo/SO_0100002 molecular_contact_region Residues which interact with a ligand. http://purl.obolibrary.org/obo/SO_0001106 asx_motif http://purl.obolibrary.org/obo/SO_0001078 polypeptide_secondary_structure A motif of five consecutive residues and two H-bonds in which: Residue(i) is Aspartate or Asparagine (Asx), side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3), main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4). http://purl.obolibrary.org/obo/SO_0001107 beta_bulge http://purl.obolibrary.org/obo/SO_0001078 polypeptide_secondary_structure A motif of three residues within a beta-sheet in which the main chains of two consecutive residues are H-bonded to that of the third, and in which the dihedral angles are as follows: Residue(i): -140 degrees < phi(l) -20 degrees , -90 degrees < psi(l) < 40 degrees. Residue (i+1): -180 degrees < phi < -25 degrees or +120 degrees < phi < +180 degrees, +40 degrees < psi < +180 degrees or -180 degrees < psi < -120 degrees. http://purl.obolibrary.org/obo/SO_0001108 beta_bulge_loop http://purl.obolibrary.org/obo/SO_0001078 polypeptide_secondary_structure A motif of three residues within a beta-sheet consisting of two H-bonds. Beta bulge loops often occur at the loop ends of beta-hairpins. http://purl.obolibrary.org/obo/SO_0001109 beta_bulge_loop_five http://purl.obolibrary.org/obo/SO_0001108 beta_bulge_loop A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+4), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+3), these loops have an RL nest at residues i+2 and i+3. http://purl.obolibrary.org/obo/SO_0001110 beta_bulge_loop_six http://purl.obolibrary.org/obo/SO_0001108 beta_bulge_loop A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+5), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+4), these loops have an RL nest at residues i+3 and i+4. http://purl.obolibrary.org/obo/SO_0001111 beta_strand http://purl.obolibrary.org/obo/SO_0001078 polypeptide_secondary_structure A beta strand describes a single length of polypeptide chain that forms part of a beta sheet. A single continuous stretch of amino acids adopting an extended conformation of hydrogen bonds between the N-O and the C=O of another part of the peptide. This forms a secondary protein structure in which two or more extended polypeptide regions are hydrogen-bonded to one another in a planar array. http://purl.obolibrary.org/obo/SO_0001112 antiparallel_beta_strand http://purl.obolibrary.org/obo/SO_0001111 beta_strand A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (one running N-terminal to C-terminal and one running C-terminal to N-terminal). Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i) and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they form two mutual backbone hydrogen bonds to each other's flanking peptide groups; this is known as a close pair of hydrogen bonds. The peptide backbone dihedral angles (phi, psi) are about (-140 degrees, 135 degrees) in antiparallel sheets. http://purl.obolibrary.org/obo/SO_0001113 parallel_beta_strand http://purl.obolibrary.org/obo/SO_0001111 beta_strand A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (both running N-terminal to C-terminal). This orientation is slightly less stable because it introduces nonplanarity in the inter-strand hydrogen bonding pattern. Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i)and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they do not hydrogen bond to each other; rather, one residue forms hydrogen bonds to the residues that flank the other (but not vice versa). For example, residue i may form hydrogen bonds to residues j - 1 and j + 1; this is known as a wide pair of hydrogen bonds. By contrast, residue j may hydrogen-bond to different residues altogether, or to none at all. The dihedral angles (phi, psi) are about (-120 degrees, 115 degrees) in parallel sheets. http://purl.obolibrary.org/obo/SO_0001114 peptide_helix http://purl.obolibrary.org/obo/SO_0001078 polypeptide_secondary_structure A helix is a secondary_structure conformation where the peptide backbone forms a coil. http://purl.obolibrary.org/obo/SO_0001115 left_handed_peptide_helix http://purl.obolibrary.org/obo/SO_0001114 peptide_helix A left handed helix is a region of peptide where the coiled conformation turns in an anticlockwise, left handed screw. http://purl.obolibrary.org/obo/SO_0001116 right_handed_peptide_helix http://purl.obolibrary.org/obo/SO_0001114 peptide_helix A right handed helix is a region of peptide where the coiled conformation turns in a clockwise, right handed screw. http://purl.obolibrary.org/obo/SO_0001117 alpha_helix http://purl.obolibrary.org/obo/SO_0001116 right_handed_peptide_helix The helix has 3.6 residues per turn which corresponds to a translation of 1.5 angstroms (= 0.15 nm) along the helical axis. Every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier. http://purl.obolibrary.org/obo/SO_0001118 pi_helix http://purl.obolibrary.org/obo/SO_0001116 right_handed_peptide_helix The pi helix has 4.1 residues per turn and a translation of 1.15 (=0.115 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid five residues earlier. http://purl.obolibrary.org/obo/SO_0001119 three_ten_helix http://purl.obolibrary.org/obo/SO_0001116 right_handed_peptide_helix The 3-10 helix has 3 residues per turn with a translation of 2.0 angstroms (=0.2 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid three residues earlier. http://purl.obolibrary.org/obo/SO_0001120 polypeptide_nest_motif http://purl.obolibrary.org/obo/SO_0001078 polypeptide_secondary_structure A motif of two consecutive residues with dihedral angles. Nest should not have Proline as any residue. Nests frequently occur as parts of other motifs such as Schellman loops. http://purl.obolibrary.org/obo/SO_0001121 polypeptide_nest_left_right_motif http://purl.obolibrary.org/obo/SO_0001120 polypeptide_nest_motif A motif of two consecutive residues with dihedral angles: Residue(i): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. http://purl.obolibrary.org/obo/SO_0001122 polypeptide_nest_right_left_motif http://purl.obolibrary.org/obo/SO_0001120 polypeptide_nest_motif A motif of two consecutive residues with dihedral angles: Residue(i): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. http://purl.obolibrary.org/obo/SO_0001123 schellmann_loop http://purl.obolibrary.org/obo/SO_0001078 polypeptide_secondary_structure A motif of six or seven consecutive residues that contains two H-bonds. http://purl.obolibrary.org/obo/SO_0001124 schellmann_loop_seven http://purl.obolibrary.org/obo/SO_0001123 schellmann_loop Wild type: A motif of seven consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+6), the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+5). http://purl.obolibrary.org/obo/SO_0001125 schellmann_loop_six http://purl.obolibrary.org/obo/SO_0001123 schellmann_loop Common Type: A motif of six consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+5) the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+4). http://purl.obolibrary.org/obo/SO_0001126 serine_threonine_motif http://purl.obolibrary.org/obo/SO_0001078 polypeptide_secondary_structure A motif of five consecutive residues and two hydrogen bonds in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3) , the main-chain CO group of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4). http://purl.obolibrary.org/obo/SO_0001127 serine_threonine_staple_motif http://purl.obolibrary.org/obo/SO_0001078 polypeptide_secondary_structure A motif of four or five consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain OH of residue(i) is H-bonded to the main-chain CO of residue(i3) or (i4), Phi angles of residues(i1), (i2) and (i3) are negative. http://purl.obolibrary.org/obo/SO_0001128 polypeptide_turn_motif http://purl.obolibrary.org/obo/SO_0001078 polypeptide_secondary_structure A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues. http://purl.obolibrary.org/obo/SO_0001129 asx_turn_left_handed_type_one http://purl.obolibrary.org/obo/SO_0000912 asx_turn Left handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. http://purl.obolibrary.org/obo/SO_0001130 asx_turn_left_handed_type_two http://purl.obolibrary.org/obo/SO_0000912 asx_turn Left handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. http://purl.obolibrary.org/obo/SO_0001131 asx_turn_right_handed_type_two http://purl.obolibrary.org/obo/SO_0000912 asx_turn Right handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. http://purl.obolibrary.org/obo/SO_0001132 asx_turn_right_handed_type_one http://purl.obolibrary.org/obo/SO_0000912 asx_turn Right handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. http://purl.obolibrary.org/obo/SO_0001133 beta_turn http://purl.obolibrary.org/obo/SO_0001128 polypeptide_turn_motif A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles of the second and third residues, which are the basis for sub-categorization. http://purl.obolibrary.org/obo/SO_0001134 beta_turn_left_handed_type_one http://purl.obolibrary.org/obo/SO_0001133 beta_turn Left handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles:- Residue(i+1): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees. Residue(i+2): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees. http://purl.obolibrary.org/obo/SO_0001135 beta_turn_left_handed_type_two http://purl.obolibrary.org/obo/SO_0001133 beta_turn Left handed type II: A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees > phi > -20 degrees, +80 degrees > psi > +180 degrees. Residue(i+2): +20 degrees > phi > +140 degrees, -40 degrees > psi > +90 degrees. http://purl.obolibrary.org/obo/SO_0001136 beta_turn_right_handed_type_one http://purl.obolibrary.org/obo/SO_0001133 beta_turn Right handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+2): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. http://purl.obolibrary.org/obo/SO_0001137 beta_turn_right_handed_type_two http://purl.obolibrary.org/obo/SO_0001133 beta_turn Right handed type II:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, +80 degrees < psi < +180 degrees. Residue(i+2): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. http://purl.obolibrary.org/obo/SO_0001138 gamma_turn http://purl.obolibrary.org/obo/SO_0001128 polypeptide_turn_motif Gamma turns, defined for 3 residues i,( i+1),( i+2) if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees. http://purl.obolibrary.org/obo/SO_0001139 gamma_turn_classic http://purl.obolibrary.org/obo/SO_0001138 gamma_turn Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=75.0 - psi(i+1)=-64.0. http://purl.obolibrary.org/obo/SO_0001140 gamma_turn_inverse http://purl.obolibrary.org/obo/SO_0001138 gamma_turn Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=-79.0 - psi(i+1)=69.0. http://purl.obolibrary.org/obo/SO_0001141 serine_threonine_turn http://purl.obolibrary.org/obo/SO_0001128 polypeptide_turn_motif A motif of three consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2). http://purl.obolibrary.org/obo/SO_0001142 st_turn_left_handed_type_one http://purl.obolibrary.org/obo/SO_0001141 serine_threonine_turn The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees. http://purl.obolibrary.org/obo/SO_0001143 st_turn_left_handed_type_two http://purl.obolibrary.org/obo/SO_0001141 serine_threonine_turn The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees. http://purl.obolibrary.org/obo/SO_0001144 st_turn_right_handed_type_one http://purl.obolibrary.org/obo/SO_0001141 serine_threonine_turn The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees. http://purl.obolibrary.org/obo/SO_0001145 st_turn_right_handed_type_two http://purl.obolibrary.org/obo/SO_0001141 serine_threonine_turn The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees. http://purl.obolibrary.org/obo/SO_0001146 polypeptide_variation_site http://purl.obolibrary.org/obo/SO_0000839 polypeptide_region A site of sequence variation (alteration). Alternative sequence due to naturally occurring events such as polymorphisms and alternative splicing or experimental methods such as site directed mutagenesis. http://purl.obolibrary.org/obo/SO_0001147 natural_variant_site http://purl.obolibrary.org/obo/SO_0001146 polypeptide_variation_site Describes the natural sequence variants due to polymorphisms, disease-associated mutations, RNA editing and variations between strains, isolates or cultivars. http://purl.obolibrary.org/obo/SO_0001148 mutated_variant_site http://purl.obolibrary.org/obo/SO_0001146 polypeptide_variation_site Site which has been experimentally altered. http://purl.obolibrary.org/obo/SO_0001149 alternate_sequence_site http://purl.obolibrary.org/obo/SO_0001146 polypeptide_variation_site Description of sequence variants produced by alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting. http://purl.obolibrary.org/obo/SO_0001150 beta_turn_type_six http://purl.obolibrary.org/obo/SO_0001133 beta_turn A motif of four consecutive peptide resides of type VIa or type VIb and where the i+2 residue is cis-proline. http://purl.obolibrary.org/obo/SO_0001151 beta_turn_type_six_a http://purl.obolibrary.org/obo/SO_0001150 beta_turn_type_six A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -90 degrees, psi ~ 0 degrees. http://purl.obolibrary.org/obo/SO_0001152 beta_turn_type_six_a_one http://purl.obolibrary.org/obo/SO_0001151 beta_turn_type_six_a A type VIa beta turn with the following phi and psi sngles on amino acid residues 2 and 3: phi-2 = -60 degrees, psi-2 = 120 degrees, phi-3 = -90 degrees, psi-3 = 0 degrees. http://purl.obolibrary.org/obo/SO_0001153 beta_turn_type_six_a_two http://purl.obolibrary.org/obo/SO_0001151 beta_turn_type_six_a A type VIa beta turn with the following phi and psi sngles on amino acid residues 2 and 3: phi-2 = -120 degrees, psi-2 = 120 degrees, phi-3 = -60 degrees, psi-3 = 0 degrees. http://purl.obolibrary.org/obo/SO_0001154 beta_turn_type_six_b http://purl.obolibrary.org/obo/SO_0001150 beta_turn_type_six A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -120 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -60 degrees, psi ~ 0 degrees. http://purl.obolibrary.org/obo/SO_0001155 beta_turn_type_eight http://purl.obolibrary.org/obo/SO_0001133 beta_turn A motif of four consecutive peptide residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ -30 degrees. Residue(i+2): phi ~ -120 degrees, psi ~ 120 degrees. http://purl.obolibrary.org/obo/SO_0001156 DRE_motif http://purl.obolibrary.org/obo/SO_0000713 DNA_motif A sequence element characteristic of some RNA polymerase II promoters, usually located between -10 and -60 relative to the TSS. Consensus sequence is WATCGATW. http://purl.obolibrary.org/obo/SO_0001157 DMv4_motif http://purl.obolibrary.org/obo/SO_0001659 promoter_element A sequence element characteristic of some RNA polymerase II promoters, located immediately upstream of some TATA box elements with respect to the TSS (+1). Consensus sequence is YGGTCACACTR. Marked spatial preference within core promoter; tend to occur near the TSS, although not as tightly as INR (SO:0000014). http://purl.obolibrary.org/obo/SO_0001158 E_box_motif http://purl.obolibrary.org/obo/SO_0000713 DNA_motif A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and +1 relative to the TSS. Consensus sequence is AWCAGCTGWT. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015). http://purl.obolibrary.org/obo/SO_0001159 DMv5_motif http://purl.obolibrary.org/obo/SO_0001659 promoter_element A sequence element characteristic of some RNA polymerase II promoters, usually located between -50 and -10 relative to the TSS. Consensus sequence is KTYRGTATWTTT. Tends to co-occur with DMv4 (SO:0001157) . Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162). http://purl.obolibrary.org/obo/SO_0001160 DMv3_motif http://purl.obolibrary.org/obo/SO_0001659 promoter_element A sequence element characteristic of some RNA polymerase II promoters, usually located between -30 and +15 relative to the TSS. Consensus sequence is KNNCAKCNCTRNY. Tends to co-occur with DMv2 (SO:0001161). Tends to not occur with DPE motif (SO:0000015) or MTE (0001162). http://purl.obolibrary.org/obo/SO_0001161 DMv2_motif http://purl.obolibrary.org/obo/SO_0001659 promoter_element A sequence element characteristic of some RNA polymerase II promoters, usually located between -60 and -45 relative to the TSS. Consensus sequence is MKSYGGCARCGSYSS. Tends to co-occur with DMv3 (SO:0001160). Tends to not occur with DPE motif (SO:0000015) or MTE (SO:0001162). http://purl.obolibrary.org/obo/SO_0001162 MTE http://purl.obolibrary.org/obo/SO_0001660 core_eukaryotic_promoter_element A sequence element characteristic of some RNA polymerase II promoters, usually located between +20 and +30 relative to the TSS. Consensus sequence is CSARCSSAACGS. Tends to co-occur with INR motif (SO:0000014). Tends to not occur with DPE motif (SO:0000015) or DMv5 (SO:0001159). http://purl.obolibrary.org/obo/SO_0001163 INR1_motif http://purl.obolibrary.org/obo/SO_0000713 DNA_motif A promoter motif with consensus sequence TCATTCG. http://purl.obolibrary.org/obo/SO_0001164 DPE1_motif http://purl.obolibrary.org/obo/SO_0001659 promoter_element A promoter motif with consensus sequence CGGACGT. http://purl.obolibrary.org/obo/SO_0001165 DMv1_motif http://purl.obolibrary.org/obo/SO_0001659 promoter_element A promoter motif with consensus sequence CARCCCT. http://purl.obolibrary.org/obo/SO_0001166 GAGA_motif http://purl.obolibrary.org/obo/SO_0000713 DNA_motif A non directional promoter motif with consensus sequence GAGAGCG. http://purl.obolibrary.org/obo/SO_0001167 NDM2_motif http://purl.obolibrary.org/obo/SO_0001659 promoter_element A non directional promoter motif with consensus CGMYGYCR. http://purl.obolibrary.org/obo/SO_0001168 NDM3_motif http://purl.obolibrary.org/obo/SO_0001659 promoter_element A non directional promoter motif with consensus sequence GAAAGCT. http://purl.obolibrary.org/obo/SO_0001169 ds_RNA_viral_sequence http://purl.obolibrary.org/obo/SO_0001041 viral_sequence A ds_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded RNA. http://purl.obolibrary.org/obo/SO_0001170 polinton http://purl.obolibrary.org/obo/SO_0000208 terminal_inverted_repeat_element A kind of DNA transposon that populates the genomes of protists, fungi, and animals, characterized by a unique set of proteins necessary for their transposition, including a protein-primed DNA polymerase B, retroviral integrase, cysteine protease, and ATPase. Polintons are characterized by 6-bp target site duplications, terminal-inverted repeats that are several hundred nucleotides long, and 5'-AG and TC-3' termini. Polintons exist as autonomous and nonautonomous elements. http://purl.obolibrary.org/obo/SO_0001172 tRNA_region http://purl.obolibrary.org/obo/SO_0000834 mature_transcript_region A region of a tRNA. http://purl.obolibrary.org/obo/SO_0001173 anticodon_loop http://purl.obolibrary.org/obo/SO_0001172 tRNA_region A sequence of seven nucleotide bases in tRNA which contains the anticodon. It has the sequence 5'-pyrimidine-purine-anticodon-modified purine-any base-3. http://purl.obolibrary.org/obo/SO_0001174 anticodon http://purl.obolibrary.org/obo/SO_0001172 tRNA_region A sequence of three nucleotide bases in tRNA which recognizes a codon in mRNA. http://purl.obolibrary.org/obo/SO_0001175 CCA_tail http://purl.obolibrary.org/obo/SO_0001172 tRNA_region Base sequence at the 3' end of a tRNA. The 3'-hydroxyl group on the terminal adenosine is the attachment point for the amino acid. http://purl.obolibrary.org/obo/SO_0001176 DHU_loop http://purl.obolibrary.org/obo/SO_0001172 tRNA_region Non-base-paired sequence of nucleotide bases in tRNA. It contains several dihydrouracil residues. http://purl.obolibrary.org/obo/SO_0001177 T_loop http://purl.obolibrary.org/obo/SO_0001172 tRNA_region Non-base-paired sequence of three nucleotide bases in tRNA. It has sequence T-Psi-C. http://purl.obolibrary.org/obo/SO_0001178 pyrrolysine_tRNA_primary_transcript http://purl.obolibrary.org/obo/SO_0000210 tRNA_primary_transcript A primary transcript encoding pyrrolysyl tRNA (SO:0000766). http://purl.obolibrary.org/obo/SO_0001179 U3_snoRNA http://purl.obolibrary.org/obo/SO_0000593 C_D_box_snoRNA U3 snoRNA is a member of the box C/D class of small nucleolar RNAs. The U3 snoRNA secondary structure is characterised by a small 5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C, C', and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localization, stability and hypermethylation of U3 snoRNA. Both box B/C and C'/D motifs are involved in specific protein interactions and are necessary for the rRNA processing functions of U3 snoRNA. http://purl.obolibrary.org/obo/SO_0001180 AU_rich_element http://purl.obolibrary.org/obo/SO_0000837 UTR_region A cis-acting element found in the 3' UTR of some mRNA which is rich in AUUUA pentamers. Messenger RNAs bearing multiple AU-rich elements are often unstable. http://purl.obolibrary.org/obo/SO_0001181 Bruno_response_element http://purl.obolibrary.org/obo/SO_0000837 UTR_region A cis-acting element found in the 3' UTR of some mRNA which is bound by the Drosophila Bruno protein and its homologs. http://purl.obolibrary.org/obo/SO_0001182 iron_responsive_element http://purl.obolibrary.org/obo/SO_0000837 UTR_region A regulatory sequence found in the 5' and 3' UTRs of many mRNAs which encode iron-binding proteins. It has a hairpin structure and is recognized by trans-acting proteins known as iron-regulatory proteins. http://purl.obolibrary.org/obo/SO_0001183 morpholino_backbone http://purl.obolibrary.org/obo/SO_0000348 nucleic_acid An attribute describing a sequence composed of nucleobases bound to a morpholino backbone. A morpholino backbone consists of morpholine (CHEBI:34856) rings connected by phosphorodiamidate linkages. http://purl.obolibrary.org/obo/SO_0001184 PNA http://purl.obolibrary.org/obo/SO_0000348 nucleic_acid An attribute describing a sequence composed of peptide nucleic acid (CHEBI:48021), a chemical consisting of nucleobases bound to a backbone composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The purine and pyrimidine bases are linked to the backbone by methylene carbonyl bonds. http://purl.obolibrary.org/obo/SO_0001185 enzymatic http://purl.obolibrary.org/obo/SO_0000733 feature_attribute An attribute describing the sequence of a transcript that has catalytic activity with or without an associated ribonucleoprotein. http://purl.obolibrary.org/obo/SO_0001186 ribozymic http://purl.obolibrary.org/obo/SO_0001185 enzymatic An attribute describing the sequence of a transcript that has catalytic activity even without an associated ribonucleoprotein. http://purl.obolibrary.org/obo/SO_0001187 pseudouridylation_guide_snoRNA http://purl.obolibrary.org/obo/SO_0000594 H_ACA_box_snoRNA A snoRNA that specifies the site of pseudouridylation in an RNA molecule by base pairing with a short sequence around the target residue. http://purl.obolibrary.org/obo/SO_0001188 LNA http://purl.obolibrary.org/obo/SO_0000348 nucleic_acid An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of 'locked' deoxyribose rings connected to a phosphate backbone. The deoxyribose unit's conformation is 'locked' by a 2'-C,4'-C-oxymethylene link. http://purl.obolibrary.org/obo/SO_0001189 LNA_oligo http://purl.obolibrary.org/obo/SO_0001247 synthetic_oligo An oligo composed of LNA residues. http://purl.obolibrary.org/obo/SO_0001190 TNA http://purl.obolibrary.org/obo/SO_0000348 nucleic_acid An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of threose rings connected to a phosphate backbone. http://purl.obolibrary.org/obo/SO_0001191 TNA_oligo http://purl.obolibrary.org/obo/SO_0001247 synthetic_oligo An oligo composed of TNA residues. http://purl.obolibrary.org/obo/SO_0001192 GNA http://purl.obolibrary.org/obo/SO_0000348 nucleic_acid An attribute describing a sequence consisting of nucleobases attached to a repeating unit made of an acyclic three-carbon propylene glycol connected to a phosphate backbone. It has two enantiomeric forms, (R)-GNA and (S)-GNA. http://purl.obolibrary.org/obo/SO_0001193 GNA_oligo http://purl.obolibrary.org/obo/SO_0001247 synthetic_oligo An oligo composed of GNA residues. http://purl.obolibrary.org/obo/SO_0001194 R_GNA http://purl.obolibrary.org/obo/SO_0001192 GNA An attribute describing a GNA sequence in the (R)-GNA enantiomer. http://purl.obolibrary.org/obo/SO_0001195 R_GNA_oligo http://purl.obolibrary.org/obo/SO_0001193 GNA_oligo An oligo composed of (R)-GNA residues. http://purl.obolibrary.org/obo/SO_0001196 S_GNA http://purl.obolibrary.org/obo/SO_0001192 GNA An attribute describing a GNA sequence in the (S)-GNA enantiomer. http://purl.obolibrary.org/obo/SO_0001197 S_GNA_oligo http://purl.obolibrary.org/obo/SO_0001193 GNA_oligo An oligo composed of (S)-GNA residues. http://purl.obolibrary.org/obo/SO_0001198 ds_DNA_viral_sequence http://purl.obolibrary.org/obo/SO_0001041 viral_sequence A ds_DNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as double stranded DNA. http://purl.obolibrary.org/obo/SO_0001199 ss_RNA_viral_sequence http://purl.obolibrary.org/obo/SO_0001041 viral_sequence A ss_RNA_viral_sequence is a viral_sequence that is the sequence of a virus that exists as single stranded RNA. http://purl.obolibrary.org/obo/SO_0001200 negative_sense_ssRNA_viral_sequence http://purl.obolibrary.org/obo/SO_0001199 ss_RNA_viral_sequence A negative_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that is complementary to mRNA and must be converted to positive sense RNA by RNA polymerase before translation. http://purl.obolibrary.org/obo/SO_0001201 positive_sense_ssRNA_viral_sequence http://purl.obolibrary.org/obo/SO_0001199 ss_RNA_viral_sequence A positive_sense_RNA_viral_sequence is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus that can be immediately translated by the host. http://purl.obolibrary.org/obo/SO_0001202 ambisense_ssRNA_viral_sequence http://purl.obolibrary.org/obo/SO_0001199 ss_RNA_viral_sequence A ambisense_RNA_virus is a ss_RNA_viral_sequence that is the sequence of a single stranded RNA virus with both messenger and anti messenger polarity. http://purl.obolibrary.org/obo/SO_0001208 five_prime_EST http://purl.obolibrary.org/obo/SO_0000345 EST An EST read from the 5' end of a transcript that usually codes for a protein. These regions tend to be conserved across species and do not change much within a gene family. http://purl.obolibrary.org/obo/SO_0001209 three_prime_EST http://purl.obolibrary.org/obo/SO_0000345 EST An EST read from the 3' end of a transcript. They are more likely to fall within non-coding, or untranslated regions(UTRs). http://purl.obolibrary.org/obo/SO_0001210 translational_frameshift http://purl.obolibrary.org/obo/SO_0000836 mRNA_region The region of mRNA (not divisible by 3 bases) that is skipped or added during the process of translational frameshifting (GO:0006452), causing the reading frame to be different. http://purl.obolibrary.org/obo/SO_0001211 plus_1_translational_frameshift http://purl.obolibrary.org/obo/SO_0001210 translational_frameshift The region of mRNA 1 base long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different. http://purl.obolibrary.org/obo/SO_0001212 plus_2_translational_frameshift http://purl.obolibrary.org/obo/SO_0001210 translational_frameshift The region of mRNA 2 bases long that is skipped during the process of translational frameshifting (GO:0006452), causing the reading frame to be different. http://purl.obolibrary.org/obo/SO_0001213 group_III_intron http://purl.obolibrary.org/obo/SO_0000588 autocatalytically_spliced_intron Group III introns are introns found in the mRNA of the plastids of euglenoid protists. They are spliced by a two step transesterification with bulged adenosine as initiating nucleophile. http://purl.obolibrary.org/obo/SO_0001214 noncoding_region_of_exon http://purl.obolibrary.org/obo/SO_0000852 exon_region The maximal intersection of exon and UTR. http://purl.obolibrary.org/obo/SO_0001215 coding_region_of_exon http://purl.obolibrary.org/obo/SO_0000852 exon_region The region of an exon that encodes for protein sequence. http://purl.obolibrary.org/obo/SO_0001216 endonuclease_spliced_intron http://purl.obolibrary.org/obo/SO_0000188 intron An intron that spliced via endonucleolytic cleavage and ligation rather than transesterification. http://purl.obolibrary.org/obo/SO_0001220 silenced_by_RNA_interference http://purl.obolibrary.org/obo/SO_0000893 silenced An attribute describing an epigenetic process where a gene is inactivated by RNA interference. http://purl.obolibrary.org/obo/SO_0001221 silenced_by_histone_modification http://purl.obolibrary.org/obo/SO_0000893 silenced An attribute describing an epigenetic process where a gene is inactivated by histone modification. http://purl.obolibrary.org/obo/SO_0001222 silenced_by_histone_methylation http://purl.obolibrary.org/obo/SO_0001221 silenced_by_histone_modification An attribute describing an epigenetic process where a gene is inactivated by histone methylation. http://purl.obolibrary.org/obo/SO_0001223 silenced_by_histone_deacetylation http://purl.obolibrary.org/obo/SO_0001221 silenced_by_histone_modification An attribute describing an epigenetic process where a gene is inactivated by histone deacetylation. http://purl.obolibrary.org/obo/SO_0001228 dihydrouridine http://purl.obolibrary.org/obo/SO_0001277 modified_uridine A modified RNA base in which the 5,6-dihydrouracil is bound to the ribose ring. http://purl.obolibrary.org/obo/SO_0001229 pseudouridine http://purl.obolibrary.org/obo/SO_0001277 modified_uridine A modified RNA base in which the 5- position of the uracil is bound to the ribose ring instead of the 4- position. http://purl.obolibrary.org/obo/SO_0001230 inosine http://purl.obolibrary.org/obo/SO_0000250 modified_RNA_base_feature A modified RNA base in which hypoxanthine is bound to the ribose ring. http://purl.obolibrary.org/obo/SO_0001231 seven_methylguanine http://purl.obolibrary.org/obo/SO_0000250 modified_RNA_base_feature A modified RNA base in which guanine is methylated at the 7- position. http://purl.obolibrary.org/obo/SO_0001232 ribothymidine http://purl.obolibrary.org/obo/SO_0000250 modified_RNA_base_feature A modified RNA base in which thymine is bound to the ribose ring. http://purl.obolibrary.org/obo/SO_0001233 methylinosine http://purl.obolibrary.org/obo/SO_0001274 modified_inosine A modified RNA base in which methylhypoxanthine is bound to the ribose ring. http://purl.obolibrary.org/obo/SO_0001238 major_TSS http://purl.obolibrary.org/obo/SO_0000315 TSS The tanscription start site that is most frequently used for transcription of a gene. http://purl.obolibrary.org/obo/SO_0001239 minor_TSS http://purl.obolibrary.org/obo/SO_0000315 TSS A tanscription start site that is not the most frequently used for transcription of a gene. http://purl.obolibrary.org/obo/SO_0001241 encodes_alternate_transcription_start_sites http://purl.obolibrary.org/obo/SO_0000401 gene_attribute A gene that has multiple possible transcription start sites. http://purl.obolibrary.org/obo/SO_0001243 miRNA_primary_transcript_region http://purl.obolibrary.org/obo/SO_0000835 primary_transcript_region A part of an miRNA primary_transcript. http://purl.obolibrary.org/obo/SO_0001244 pre_miRNA http://purl.obolibrary.org/obo/SO_0001243 miRNA_primary_transcript_region The 60-70 nucleotide region remain after Drosha processing of the primary transcript, that folds back upon itself to form a hairpin structure. http://purl.obolibrary.org/obo/SO_0001245 miRNA_stem http://purl.obolibrary.org/obo/SO_0001243 miRNA_primary_transcript_region The stem of the hairpin loop formed by folding of the pre-miRNA. http://purl.obolibrary.org/obo/SO_0001246 miRNA_loop http://purl.obolibrary.org/obo/SO_0001243 miRNA_primary_transcript_region The loop of the hairpin loop formed by folding of the pre-miRNA. http://purl.obolibrary.org/obo/SO_0001247 synthetic_oligo http://purl.obolibrary.org/obo/SO_0000696 oligo An oligo composed of synthetic nucleotides. http://purl.obolibrary.org/obo/SO_0001249 fragment_assembly http://purl.obolibrary.org/obo/SO_0001248 assembly A fragment assembly is a genome assembly that orders overlapping fragments of the genome based on landmark sequences. The base pair distance between the landmarks is known allowing additivity of lengths. http://purl.obolibrary.org/obo/SO_0001250 fingerprint_map http://purl.obolibrary.org/obo/SO_0001249 fragment_assembly A fingerprint_map is a physical map composed of restriction fragments. http://purl.obolibrary.org/obo/SO_0001251 STS_map http://purl.obolibrary.org/obo/SO_0001249 fragment_assembly An STS map is a physical map organized by the unique STS landmarks. http://purl.obolibrary.org/obo/SO_0001252 RH_map http://purl.obolibrary.org/obo/SO_0001249 fragment_assembly A radiation hybrid map is a physical map. http://purl.obolibrary.org/obo/SO_0001253 sonicate_fragment http://purl.obolibrary.org/obo/SO_0000143 assembly_component A DNA fragment generated by sonication. Sonication is a technique used to sheer DNA into smaller fragments. http://purl.obolibrary.org/obo/SO_0001254 polyploid http://purl.obolibrary.org/obo/SO_1000182 chromosome_number_variation A kind of chromosome variation where the chromosome complement is an exact multiple of the haploid number and is greater than the diploid number. http://purl.obolibrary.org/obo/SO_0001255 autopolyploid http://purl.obolibrary.org/obo/SO_0001254 polyploid A polyploid where the multiple chromosome set was derived from the same organism. http://purl.obolibrary.org/obo/SO_0001256 allopolyploid http://purl.obolibrary.org/obo/SO_0001254 polyploid A polyploid where the multiple chromosome set was derived from a different organism. http://purl.obolibrary.org/obo/SO_0001257 homing_endonuclease_binding_site http://purl.obolibrary.org/obo/SO_0000059 nuclease_binding_site The binding site (recognition site) of a homing endonuclease. The binding site is typically large. http://purl.obolibrary.org/obo/SO_0001258 octamer_motif http://purl.obolibrary.org/obo/SO_0000713 DNA_motif A sequence element characteristic of some RNA polymerase II promoters with sequence ATTGCAT that binds Pou-domain transcription factors. http://purl.obolibrary.org/obo/SO_0001259 apicoplast_chromosome http://purl.obolibrary.org/obo/SO_0000340 chromosome A chromosome originating in an apicoplast. http://purl.obolibrary.org/obo/SO_0001261 overlapping_feature_set http://purl.obolibrary.org/obo/SO_0000703 experimental_result_region A continuous region of sequence composed of the overlapping of multiple sequence_features, which ultimately provides evidence for another sequence_feature. http://purl.obolibrary.org/obo/SO_0001262 overlapping_EST_set http://purl.obolibrary.org/obo/SO_0001261 overlapping_feature_set A continous experimental result region extending the length of multiple overlapping EST's. http://purl.obolibrary.org/obo/SO_0001273 modified_adenosine http://purl.obolibrary.org/obo/SO_0000250 modified_RNA_base_feature A modified adenine is an adenine base feature that has been altered. http://purl.obolibrary.org/obo/SO_0001274 modified_inosine http://purl.obolibrary.org/obo/SO_0001230 inosine A modified inosine is an inosine base feature that has been altered. http://purl.obolibrary.org/obo/SO_0001275 modified_cytidine http://purl.obolibrary.org/obo/SO_0000250 modified_RNA_base_feature A modified cytidine is a cytidine base feature which has been altered. http://purl.obolibrary.org/obo/SO_0001276 modified_guanosine http://purl.obolibrary.org/obo/SO_0000250 modified_RNA_base_feature A guanosine base that has been modified. http://purl.obolibrary.org/obo/SO_0001277 modified_uridine http://purl.obolibrary.org/obo/SO_0000250 modified_RNA_base_feature A uridine base that has been modified. http://purl.obolibrary.org/obo/SO_0001278 one_methylinosine http://purl.obolibrary.org/obo/SO_0001274 modified_inosine 1-methylinosine is a modified inosine. http://purl.obolibrary.org/obo/SO_0001279 one_two_prime_O_dimethylinosine http://purl.obolibrary.org/obo/SO_0001274 modified_inosine 1,2'-O-dimethylinosine is a modified inosine. http://purl.obolibrary.org/obo/SO_0001280 two_prime_O_methylinosine http://purl.obolibrary.org/obo/SO_0001274 modified_inosine 2'-O-methylinosine is a modified inosine. http://purl.obolibrary.org/obo/SO_0001281 three_methylcytidine http://purl.obolibrary.org/obo/SO_0001275 modified_cytidine 3-methylcytidine is a modified cytidine. http://purl.obolibrary.org/obo/SO_0001282 five_methylcytidine http://purl.obolibrary.org/obo/SO_0001275 modified_cytidine 5-methylcytidine is a modified cytidine. http://purl.obolibrary.org/obo/SO_0001283 two_prime_O_methylcytidine http://purl.obolibrary.org/obo/SO_0001275 modified_cytidine 2'-O-methylcytidine is a modified cytidine. http://purl.obolibrary.org/obo/SO_0001284 two_thiocytidine http://purl.obolibrary.org/obo/SO_0001275 modified_cytidine 2-thiocytidine is a modified cytidine. http://purl.obolibrary.org/obo/SO_0001285 N4_acetylcytidine http://purl.obolibrary.org/obo/SO_0001275 modified_cytidine N4-acetylcytidine is a modified cytidine. http://purl.obolibrary.org/obo/SO_0001286 five_formylcytidine http://purl.obolibrary.org/obo/SO_0001275 modified_cytidine 5-formylcytidine is a modified cytidine. http://purl.obolibrary.org/obo/SO_0001287 five_two_prime_O_dimethylcytidine http://purl.obolibrary.org/obo/SO_0001275 modified_cytidine 5,2'-O-dimethylcytidine is a modified cytidine. http://purl.obolibrary.org/obo/SO_0001288 N4_acetyl_2_prime_O_methylcytidine http://purl.obolibrary.org/obo/SO_0001275 modified_cytidine N4-acetyl-2'-O-methylcytidine is a modified cytidine. http://purl.obolibrary.org/obo/SO_0001289 lysidine http://purl.obolibrary.org/obo/SO_0001275 modified_cytidine Lysidine is a modified cytidine. http://purl.obolibrary.org/obo/SO_0001290 N4_methylcytidine http://purl.obolibrary.org/obo/SO_0001275 modified_cytidine N4-methylcytidine is a modified cytidine. http://purl.obolibrary.org/obo/SO_0001291 N4_2_prime_O_dimethylcytidine http://purl.obolibrary.org/obo/SO_0001275 modified_cytidine N4,2'-O-dimethylcytidine is a modified cytidine. http://purl.obolibrary.org/obo/SO_0001292 five_hydroxymethylcytidine http://purl.obolibrary.org/obo/SO_0001275 modified_cytidine 5-hydroxymethylcytidine is a modified cytidine. http://purl.obolibrary.org/obo/SO_0001293 five_formyl_two_prime_O_methylcytidine http://purl.obolibrary.org/obo/SO_0001275 modified_cytidine 5-formyl-2'-O-methylcytidine is a modified cytidine. http://purl.obolibrary.org/obo/SO_0001294 N4_N4_2_prime_O_trimethylcytidine http://purl.obolibrary.org/obo/SO_0001275 modified_cytidine N4_N4_2_prime_O_trimethylcytidine is a modified cytidine. http://purl.obolibrary.org/obo/SO_0001295 one_methyladenosine http://purl.obolibrary.org/obo/SO_0001273 modified_adenosine 1_methyladenosine is a modified adenosine. http://purl.obolibrary.org/obo/SO_0001296 two_methyladenosine http://purl.obolibrary.org/obo/SO_0001273 modified_adenosine 2_methyladenosine is a modified adenosine. http://purl.obolibrary.org/obo/SO_0001297 N6_methyladenosine http://purl.obolibrary.org/obo/SO_0001273 modified_adenosine N6_methyladenosine is a modified adenosine. http://purl.obolibrary.org/obo/SO_0001298 two_prime_O_methyladenosine http://purl.obolibrary.org/obo/SO_0001273 modified_adenosine 2prime_O_methyladenosine is a modified adenosine. http://purl.obolibrary.org/obo/SO_0001299 two_methylthio_N6_methyladenosine http://purl.obolibrary.org/obo/SO_0001273 modified_adenosine 2_methylthio_N6_methyladenosine is a modified adenosine. http://purl.obolibrary.org/obo/SO_0001300 N6_isopentenyladenosine http://purl.obolibrary.org/obo/SO_0001273 modified_adenosine N6_isopentenyladenosine is a modified adenosine. http://purl.obolibrary.org/obo/SO_0001301 two_methylthio_N6_isopentenyladenosine http://purl.obolibrary.org/obo/SO_0001273 modified_adenosine 2_methylthio_N6_isopentenyladenosine is a modified adenosine. http://purl.obolibrary.org/obo/SO_0001302 N6_cis_hydroxyisopentenyl_adenosine http://purl.obolibrary.org/obo/SO_0001273 modified_adenosine N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine. http://purl.obolibrary.org/obo/SO_0001303 two_methylthio_N6_cis_hydroxyisopentenyl_adenosine http://purl.obolibrary.org/obo/SO_0001273 modified_adenosine 2_methylthio_N6_cis_hydroxyisopentenyl_adenosine is a modified adenosine. http://purl.obolibrary.org/obo/SO_0001304 N6_glycinylcarbamoyladenosine http://purl.obolibrary.org/obo/SO_0001273 modified_adenosine N6_glycinylcarbamoyladenosine is a modified adenosine. http://purl.obolibrary.org/obo/SO_0001305 N6_threonylcarbamoyladenosine http://purl.obolibrary.org/obo/SO_0001273 modified_adenosine N6_threonylcarbamoyladenosine is a modified adenosine. http://purl.obolibrary.org/obo/SO_0001306 two_methylthio_N6_threonyl_carbamoyladenosine http://purl.obolibrary.org/obo/SO_0001273 modified_adenosine 2_methylthio_N6_threonyl_carbamoyladenosine is a modified adenosine. http://purl.obolibrary.org/obo/SO_0001307 N6_methyl_N6_threonylcarbamoyladenosine http://purl.obolibrary.org/obo/SO_0001273 modified_adenosine N6_methyl_N6_threonylcarbamoyladenosine is a modified adenosine. http://purl.obolibrary.org/obo/SO_0001308 N6_hydroxynorvalylcarbamoyladenosine http://purl.obolibrary.org/obo/SO_0001273 modified_adenosine N6_hydroxynorvalylcarbamoyladenosine is a modified adenosine. http://purl.obolibrary.org/obo/SO_0001309 two_methylthio_N6_hydroxynorvalyl_carbamoyladenosine http://purl.obolibrary.org/obo/SO_0001273 modified_adenosine 2_methylthio_N6_hydroxynorvalyl_carbamoyladenosine is a modified adenosine. http://purl.obolibrary.org/obo/SO_0001310 two_prime_O_ribosyladenosine_phosphate http://purl.obolibrary.org/obo/SO_0001273 modified_adenosine 2prime_O_ribosyladenosine_phosphate is a modified adenosine. http://purl.obolibrary.org/obo/SO_0001311 N6_N6_dimethyladenosine http://purl.obolibrary.org/obo/SO_0001273 modified_adenosine N6_N6_dimethyladenosine is a modified adenosine. http://purl.obolibrary.org/obo/SO_0001312 N6_2_prime_O_dimethyladenosine http://purl.obolibrary.org/obo/SO_0001273 modified_adenosine N6_2prime_O_dimethyladenosine is a modified adenosine. http://purl.obolibrary.org/obo/SO_0001313 N6_N6_2_prime_O_trimethyladenosine http://purl.obolibrary.org/obo/SO_0001273 modified_adenosine N6_N6_2prime_O_trimethyladenosine is a modified adenosine. http://purl.obolibrary.org/obo/SO_0001314 one_two_prime_O_dimethyladenosine http://purl.obolibrary.org/obo/SO_0001273 modified_adenosine 1,2'-O-dimethyladenosine is a modified adenosine. http://purl.obolibrary.org/obo/SO_0001315 N6_acetyladenosine http://purl.obolibrary.org/obo/SO_0001273 modified_adenosine N6_acetyladenosine is a modified adenosine. http://purl.obolibrary.org/obo/SO_0001316 seven_deazaguanosine http://purl.obolibrary.org/obo/SO_0001276 modified_guanosine 7-deazaguanosine is a modified guanosine. http://purl.obolibrary.org/obo/SO_0001317 queuosine http://purl.obolibrary.org/obo/SO_0001316 seven_deazaguanosine Queuosine is a modified 7-deazoguanosine. http://purl.obolibrary.org/obo/SO_0001318 epoxyqueuosine http://purl.obolibrary.org/obo/SO_0001316 seven_deazaguanosine Epoxyqueuosine is a modified 7-deazoguanosine. http://purl.obolibrary.org/obo/SO_0001319 galactosyl_queuosine http://purl.obolibrary.org/obo/SO_0001316 seven_deazaguanosine Galactosyl_queuosine is a modified 7-deazoguanosine. http://purl.obolibrary.org/obo/SO_0001320 mannosyl_queuosine http://purl.obolibrary.org/obo/SO_0001316 seven_deazaguanosine Mannosyl_queuosine is a modified 7-deazoguanosine. http://purl.obolibrary.org/obo/SO_0001321 seven_cyano_seven_deazaguanosine http://purl.obolibrary.org/obo/SO_0001316 seven_deazaguanosine 7_cyano_7_deazaguanosine is a modified 7-deazoguanosine. http://purl.obolibrary.org/obo/SO_0001322 seven_aminomethyl_seven_deazaguanosine http://purl.obolibrary.org/obo/SO_0001316 seven_deazaguanosine 7_aminomethyl_7_deazaguanosine is a modified 7-deazoguanosine. http://purl.obolibrary.org/obo/SO_0001323 archaeosine http://purl.obolibrary.org/obo/SO_0001316 seven_deazaguanosine Archaeosine is a modified 7-deazoguanosine. http://purl.obolibrary.org/obo/SO_0001324 one_methylguanosine http://purl.obolibrary.org/obo/SO_0001276 modified_guanosine 1_methylguanosine is a modified guanosine base feature. http://purl.obolibrary.org/obo/SO_0001325 N2_methylguanosine http://purl.obolibrary.org/obo/SO_0001276 modified_guanosine N2_methylguanosine is a modified guanosine base feature. http://purl.obolibrary.org/obo/SO_0001326 seven_methylguanosine http://purl.obolibrary.org/obo/SO_0001276 modified_guanosine 7_methylguanosine is a modified guanosine base feature. http://purl.obolibrary.org/obo/SO_0001327 two_prime_O_methylguanosine http://purl.obolibrary.org/obo/SO_0001276 modified_guanosine 2prime_O_methylguanosine is a modified guanosine base feature. http://purl.obolibrary.org/obo/SO_0001328 N2_N2_dimethylguanosine http://purl.obolibrary.org/obo/SO_0001276 modified_guanosine N2_N2_dimethylguanosine is a modified guanosine base feature. http://purl.obolibrary.org/obo/SO_0001329 N2_2_prime_O_dimethylguanosine http://purl.obolibrary.org/obo/SO_0001276 modified_guanosine N2_2prime_O_dimethylguanosine is a modified guanosine base feature. http://purl.obolibrary.org/obo/SO_0001330 N2_N2_2_prime_O_trimethylguanosine http://purl.obolibrary.org/obo/SO_0001276 modified_guanosine N2_N2_2prime_O_trimethylguanosine is a modified guanosine base feature. http://purl.obolibrary.org/obo/SO_0001331 two_prime_O_ribosylguanosine_phosphate http://purl.obolibrary.org/obo/SO_0001276 modified_guanosine 2prime_O_ribosylguanosine_phosphate is a modified guanosine base feature. http://purl.obolibrary.org/obo/SO_0001332 wybutosine http://purl.obolibrary.org/obo/SO_0001276 modified_guanosine Wybutosine is a modified guanosine base feature. http://purl.obolibrary.org/obo/SO_0001333 peroxywybutosine http://purl.obolibrary.org/obo/SO_0001276 modified_guanosine Peroxywybutosine is a modified guanosine base feature. http://purl.obolibrary.org/obo/SO_0001334 hydroxywybutosine http://purl.obolibrary.org/obo/SO_0001276 modified_guanosine Hydroxywybutosine is a modified guanosine base feature. http://purl.obolibrary.org/obo/SO_0001335 undermodified_hydroxywybutosine http://purl.obolibrary.org/obo/SO_0001276 modified_guanosine Undermodified_hydroxywybutosine is a modified guanosine base feature. http://purl.obolibrary.org/obo/SO_0001336 wyosine http://purl.obolibrary.org/obo/SO_0001276 modified_guanosine Wyosine is a modified guanosine base feature. http://purl.obolibrary.org/obo/SO_0001337 methylwyosine http://purl.obolibrary.org/obo/SO_0001276 modified_guanosine Methylwyosine is a modified guanosine base feature. http://purl.obolibrary.org/obo/SO_0001338 N2_7_dimethylguanosine http://purl.obolibrary.org/obo/SO_0001276 modified_guanosine N2_7_dimethylguanosine is a modified guanosine base feature. http://purl.obolibrary.org/obo/SO_0001339 N2_N2_7_trimethylguanosine http://purl.obolibrary.org/obo/SO_0001276 modified_guanosine N2_N2_7_trimethylguanosine is a modified guanosine base feature. http://purl.obolibrary.org/obo/SO_0001340 one_two_prime_O_dimethylguanosine http://purl.obolibrary.org/obo/SO_0001276 modified_guanosine 1_2prime_O_dimethylguanosine is a modified guanosine base feature. http://purl.obolibrary.org/obo/SO_0001341 four_demethylwyosine http://purl.obolibrary.org/obo/SO_0001276 modified_guanosine 4_demethylwyosine is a modified guanosine base feature. http://purl.obolibrary.org/obo/SO_0001342 isowyosine http://purl.obolibrary.org/obo/SO_0001276 modified_guanosine Isowyosine is a modified guanosine base feature. http://purl.obolibrary.org/obo/SO_0001343 N2_7_2prirme_O_trimethylguanosine http://purl.obolibrary.org/obo/SO_0001276 modified_guanosine N2_7_2prirme_O_trimethylguanosine is a modified guanosine base feature. http://purl.obolibrary.org/obo/SO_0001344 five_methyluridine http://purl.obolibrary.org/obo/SO_0001277 modified_uridine 5_methyluridine is a modified uridine base feature. http://purl.obolibrary.org/obo/SO_0001345 two_prime_O_methyluridine http://purl.obolibrary.org/obo/SO_0001277 modified_uridine 2prime_O_methyluridine is a modified uridine base feature. http://purl.obolibrary.org/obo/SO_0001346 five_two_prime_O_dimethyluridine http://purl.obolibrary.org/obo/SO_0001277 modified_uridine 5_2_prime_O_dimethyluridine is a modified uridine base feature. http://purl.obolibrary.org/obo/SO_0001347 one_methylpseudouridine http://purl.obolibrary.org/obo/SO_0001277 modified_uridine 1_methylpseudouridine is a modified uridine base feature. http://purl.obolibrary.org/obo/SO_0001348 two_prime_O_methylpseudouridine http://purl.obolibrary.org/obo/SO_0001277 modified_uridine 2prime_O_methylpseudouridine is a modified uridine base feature. http://purl.obolibrary.org/obo/SO_0001349 two_thiouridine http://purl.obolibrary.org/obo/SO_0001277 modified_uridine 2_thiouridine is a modified uridine base feature. http://purl.obolibrary.org/obo/SO_0001350 four_thiouridine http://purl.obolibrary.org/obo/SO_0001277 modified_uridine 4_thiouridine is a modified uridine base feature. http://purl.obolibrary.org/obo/SO_0001351 five_methyl_2_thiouridine http://purl.obolibrary.org/obo/SO_0001277 modified_uridine 5_methyl_2_thiouridine is a modified uridine base feature. http://purl.obolibrary.org/obo/SO_0001352 two_thio_two_prime_O_methyluridine http://purl.obolibrary.org/obo/SO_0001277 modified_uridine 2_thio_2prime_O_methyluridine is a modified uridine base feature. http://purl.obolibrary.org/obo/SO_0001353 three_three_amino_three_carboxypropyl_uridine http://purl.obolibrary.org/obo/SO_0001277 modified_uridine 3_3_amino_3_carboxypropyl_uridine is a modified uridine base feature. http://purl.obolibrary.org/obo/SO_0001354 five_hydroxyuridine http://purl.obolibrary.org/obo/SO_0001277 modified_uridine 5_hydroxyuridine is a modified uridine base feature. http://purl.obolibrary.org/obo/SO_0001355 five_methoxyuridine http://purl.obolibrary.org/obo/SO_0001277 modified_uridine 5_methoxyuridine is a modified uridine base feature. http://purl.obolibrary.org/obo/SO_0001356 uridine_five_oxyacetic_acid http://purl.obolibrary.org/obo/SO_0001277 modified_uridine Uridine_5_oxyacetic_acid is a modified uridine base feature. http://purl.obolibrary.org/obo/SO_0001357 uridine_five_oxyacetic_acid_methyl_ester http://purl.obolibrary.org/obo/SO_0001277 modified_uridine Uridine_5_oxyacetic_acid_methyl_ester is a modified uridine base feature. http://purl.obolibrary.org/obo/SO_0001358 five_carboxyhydroxymethyl_uridine http://purl.obolibrary.org/obo/SO_0001277 modified_uridine 5_carboxyhydroxymethyl_uridine is a modified uridine base feature. http://purl.obolibrary.org/obo/SO_0001359 five_carboxyhydroxymethyl_uridine_methyl_ester http://purl.obolibrary.org/obo/SO_0001277 modified_uridine 5_carboxyhydroxymethyl_uridine_methyl_ester is a modified uridine base feature. http://purl.obolibrary.org/obo/SO_0001360 five_methoxycarbonylmethyluridine http://purl.obolibrary.org/obo/SO_0001277 modified_uridine Five_methoxycarbonylmethyluridine is a modified uridine base feature. http://purl.obolibrary.org/obo/SO_0001361 five_methoxycarbonylmethyl_two_prime_O_methyluridine http://purl.obolibrary.org/obo/SO_0001277 modified_uridine Five_methoxycarbonylmethyl_2_prime_O_methyluridine is a modified uridine base feature. http://purl.obolibrary.org/obo/SO_0001362 five_methoxycarbonylmethyl_two_thiouridine http://purl.obolibrary.org/obo/SO_0001277 modified_uridine 5_methoxycarbonylmethyl_2_thiouridine is a modified uridine base feature. http://purl.obolibrary.org/obo/SO_0001363 five_aminomethyl_two_thiouridine http://purl.obolibrary.org/obo/SO_0001277 modified_uridine 5_aminomethyl_2_thiouridine is a modified uridine base feature. http://purl.obolibrary.org/obo/SO_0001364 five_methylaminomethyluridine http://purl.obolibrary.org/obo/SO_0001277 modified_uridine 5_methylaminomethyluridine is a modified uridine base feature. http://purl.obolibrary.org/obo/SO_0001365 five_methylaminomethyl_two_thiouridine http://purl.obolibrary.org/obo/SO_0001277 modified_uridine 5_methylaminomethyl_2_thiouridine is a modified uridine base feature. http://purl.obolibrary.org/obo/SO_0001366 five_methylaminomethyl_two_selenouridine http://purl.obolibrary.org/obo/SO_0001277 modified_uridine 5_methylaminomethyl_2_selenouridine is a modified uridine base feature. http://purl.obolibrary.org/obo/SO_0001367 five_carbamoylmethyluridine http://purl.obolibrary.org/obo/SO_0001277 modified_uridine 5_carbamoylmethyluridine is a modified uridine base feature. http://purl.obolibrary.org/obo/SO_0001368 five_carbamoylmethyl_two_prime_O_methyluridine http://purl.obolibrary.org/obo/SO_0001277 modified_uridine 5_carbamoylmethyl_2_prime_O_methyluridine is a modified uridine base feature. http://purl.obolibrary.org/obo/SO_0001369 five_carboxymethylaminomethyluridine http://purl.obolibrary.org/obo/SO_0001277 modified_uridine 5_carboxymethylaminomethyluridine is a modified uridine base feature. http://purl.obolibrary.org/obo/SO_0001370 five_carboxymethylaminomethyl_two_prime_O_methyluridine http://purl.obolibrary.org/obo/SO_0001277 modified_uridine 5_carboxymethylaminomethyl_2_prime_O_methyluridine is a modified uridine base feature. http://purl.obolibrary.org/obo/SO_0001371 five_carboxymethylaminomethyl_two_thiouridine http://purl.obolibrary.org/obo/SO_0001277 modified_uridine 5_carboxymethylaminomethyl_2_thiouridine is a modified uridine base feature. http://purl.obolibrary.org/obo/SO_0001372 three_methyluridine http://purl.obolibrary.org/obo/SO_0001277 modified_uridine 3_methyluridine is a modified uridine base feature. http://purl.obolibrary.org/obo/SO_0001373 one_methyl_three_three_amino_three_carboxypropyl_pseudouridine http://purl.obolibrary.org/obo/SO_0001277 modified_uridine 1_methyl_3_3_amino_3_carboxypropyl_pseudouridine is a modified uridine base feature. http://purl.obolibrary.org/obo/SO_0001374 five_carboxymethyluridine http://purl.obolibrary.org/obo/SO_0001277 modified_uridine 5_carboxymethyluridine is a modified uridine base feature. http://purl.obolibrary.org/obo/SO_0001375 three_two_prime_O_dimethyluridine http://purl.obolibrary.org/obo/SO_0001277 modified_uridine 3_2prime_O_dimethyluridine is a modified uridine base feature. http://purl.obolibrary.org/obo/SO_0001376 five_methyldihydrouridine http://purl.obolibrary.org/obo/SO_0001277 modified_uridine 5_methyldihydrouridine is a modified uridine base feature. http://purl.obolibrary.org/obo/SO_0001377 three_methylpseudouridine http://purl.obolibrary.org/obo/SO_0001277 modified_uridine 3_methylpseudouridine is a modified uridine base feature. http://purl.obolibrary.org/obo/SO_0001378 five_taurinomethyluridine http://purl.obolibrary.org/obo/SO_0001277 modified_uridine 5_taurinomethyluridine is a modified uridine base feature. http://purl.obolibrary.org/obo/SO_0001379 five_taurinomethyl_two_thiouridine http://purl.obolibrary.org/obo/SO_0001277 modified_uridine 5_taurinomethyl_2_thiouridineis a modified uridine base feature. http://purl.obolibrary.org/obo/SO_0001380 five_isopentenylaminomethyl_uridine http://purl.obolibrary.org/obo/SO_0001277 modified_uridine 5_isopentenylaminomethyl_uridine is a modified uridine base feature. http://purl.obolibrary.org/obo/SO_0001381 five_isopentenylaminomethyl_two_thiouridine http://purl.obolibrary.org/obo/SO_0001277 modified_uridine 5_isopentenylaminomethyl_2_thiouridine is a modified uridine base feature. http://purl.obolibrary.org/obo/SO_0001382 five_isopentenylaminomethyl_two_prime_O_methyluridine http://purl.obolibrary.org/obo/SO_0001277 modified_uridine 5_isopentenylaminomethyl_2prime_O_methyluridine is a modified uridine base feature. http://purl.obolibrary.org/obo/SO_0001383 histone_binding_site http://purl.obolibrary.org/obo/SO_0001654 nucleotide_to_protein_binding_site A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues of a histone. http://purl.obolibrary.org/obo/SO_0001384 CDS_fragment http://purl.obolibrary.org/obo/SO_0000316 CDS A portion of a CDS that is not the complete CDS. http://purl.obolibrary.org/obo/SO_0001385 modified_amino_acid_feature http://purl.obolibrary.org/obo/SO_0001237 amino_acid A post translationally modified amino acid feature. http://purl.obolibrary.org/obo/SO_0001386 modified_glycine http://purl.obolibrary.org/obo/SO_0001385 modified_amino_acid_feature A post translationally modified glycine amino acid feature. http://purl.obolibrary.org/obo/SO_0001387 modified_L_alanine http://purl.obolibrary.org/obo/SO_0001385 modified_amino_acid_feature A post translationally modified alanine amino acid feature. http://purl.obolibrary.org/obo/SO_0001388 modified_L_asparagine http://purl.obolibrary.org/obo/SO_0001385 modified_amino_acid_feature A post translationally modified asparagine amino acid feature. http://purl.obolibrary.org/obo/SO_0001389 modified_L_aspartic_acid http://purl.obolibrary.org/obo/SO_0001385 modified_amino_acid_feature A post translationally modified aspartic acid amino acid feature. http://purl.obolibrary.org/obo/SO_0001390 modified_L_cysteine http://purl.obolibrary.org/obo/SO_0001385 modified_amino_acid_feature A post translationally modified cysteine amino acid feature. http://purl.obolibrary.org/obo/SO_0001391 modified_L_glutamic_acid http://purl.obolibrary.org/obo/SO_0001385 modified_amino_acid_feature A post translationally modified glutamic acid. http://purl.obolibrary.org/obo/SO_0001392 modified_L_threonine http://purl.obolibrary.org/obo/SO_0001385 modified_amino_acid_feature A post translationally modified threonine amino acid feature. http://purl.obolibrary.org/obo/SO_0001393 modified_L_tryptophan http://purl.obolibrary.org/obo/SO_0001385 modified_amino_acid_feature A post translationally modified tryptophan amino acid feature. http://purl.obolibrary.org/obo/SO_0001394 modified_L_glutamine http://purl.obolibrary.org/obo/SO_0001385 modified_amino_acid_feature A post translationally modified glutamine amino acid feature. http://purl.obolibrary.org/obo/SO_0001395 modified_L_methionine http://purl.obolibrary.org/obo/SO_0001385 modified_amino_acid_feature A post translationally modified methionine amino acid feature. http://purl.obolibrary.org/obo/SO_0001396 modified_L_isoleucine http://purl.obolibrary.org/obo/SO_0001385 modified_amino_acid_feature A post translationally modified isoleucine amino acid feature. http://purl.obolibrary.org/obo/SO_0001397 modified_L_phenylalanine http://purl.obolibrary.org/obo/SO_0001385 modified_amino_acid_feature A post translationally modified phenylalanine amino acid feature. http://purl.obolibrary.org/obo/SO_0001398 modified_L_histidine http://purl.obolibrary.org/obo/SO_0001385 modified_amino_acid_feature A post translationally modified histidine amino acid feature. http://purl.obolibrary.org/obo/SO_0001399 modified_L_serine http://purl.obolibrary.org/obo/SO_0001385 modified_amino_acid_feature A post translationally modified serine amino acid feature. http://purl.obolibrary.org/obo/SO_0001400 modified_L_lysine http://purl.obolibrary.org/obo/SO_0001385 modified_amino_acid_feature A post translationally modified lysine amino acid feature. http://purl.obolibrary.org/obo/SO_0001401 modified_L_leucine http://purl.obolibrary.org/obo/SO_0001385 modified_amino_acid_feature A post translationally modified leucine amino acid feature. http://purl.obolibrary.org/obo/SO_0001402 modified_L_selenocysteine http://purl.obolibrary.org/obo/SO_0001385 modified_amino_acid_feature A post translationally modified selenocysteine amino acid feature. http://purl.obolibrary.org/obo/SO_0001403 modified_L_valine http://purl.obolibrary.org/obo/SO_0001385 modified_amino_acid_feature A post translationally modified valine amino acid feature. http://purl.obolibrary.org/obo/SO_0001404 modified_L_proline http://purl.obolibrary.org/obo/SO_0001385 modified_amino_acid_feature A post translationally modified proline amino acid feature. http://purl.obolibrary.org/obo/SO_0001405 modified_L_tyrosine http://purl.obolibrary.org/obo/SO_0001385 modified_amino_acid_feature A post translationally modified tyrosine amino acid feature. http://purl.obolibrary.org/obo/SO_0001406 modified_L_arginine http://purl.obolibrary.org/obo/SO_0001385 modified_amino_acid_feature A post translationally modified arginine amino acid feature. http://purl.obolibrary.org/obo/SO_0001407 peptidyl http://purl.obolibrary.org/obo/SO_0000443 polymer_attribute An attribute describing the nature of a proteinaceous polymer, where by the amino acid units are joined by peptide bonds. http://purl.obolibrary.org/obo/SO_0001408 cleaved_for_gpi_anchor_region http://purl.obolibrary.org/obo/SO_0100011 cleaved_peptide_region The C-terminal residues of a polypeptide which are exchanged for a GPI-anchor. http://purl.obolibrary.org/obo/SO_0001409 biomaterial_region http://purl.obolibrary.org/obo/SO_0000001 region A region which is intended for use in an experiment. http://purl.obolibrary.org/obo/SO_0001413 translocation_breakpoint http://purl.obolibrary.org/obo/SO_0001021 chromosome_breakpoint The point within a chromosome where a translocation begins or ends. http://purl.obolibrary.org/obo/SO_0001414 insertion_breakpoint http://purl.obolibrary.org/obo/SO_0001021 chromosome_breakpoint The point within a chromosome where a insertion begins or ends. http://purl.obolibrary.org/obo/SO_0001415 deletion_breakpoint http://purl.obolibrary.org/obo/SO_0001021 chromosome_breakpoint The point within a chromosome where a deletion begins or ends. http://purl.obolibrary.org/obo/SO_0001416 five_prime_flanking_region http://purl.obolibrary.org/obo/SO_0000239 flanking_region A flanking region located five prime of a specific region. http://purl.obolibrary.org/obo/SO_0001417 three_prime_flanking_region http://purl.obolibrary.org/obo/SO_0000239 flanking_region A flanking region located three prime of a specific region. http://purl.obolibrary.org/obo/SO_0001418 transcribed_fragment http://purl.obolibrary.org/obo/SO_0001410 experimental_feature An experimental region, defined by a tiling array experiment to be transcribed at some level. http://purl.obolibrary.org/obo/SO_0001419 cis_splice_site http://purl.obolibrary.org/obo/SO_0000162 splice_site Intronic 2 bp region bordering exon. A splice_site that adjacent_to exon and overlaps intron. http://purl.obolibrary.org/obo/SO_0001420 trans_splice_site http://purl.obolibrary.org/obo/SO_0000162 splice_site Primary transcript region bordering trans-splice junction. http://purl.obolibrary.org/obo/SO_0001421 splice_junction http://purl.obolibrary.org/obo/SO_0000699 junction The boundary between an intron and an exon. http://purl.obolibrary.org/obo/SO_0001422 conformational_switch http://purl.obolibrary.org/obo/SO_0100001 biochemical_region_of_peptide A region of a polypeptide, involved in the transition from one conformational state to another. http://purl.obolibrary.org/obo/SO_0001423 dye_terminator_read http://purl.obolibrary.org/obo/SO_0000150 read A read produced by the dye terminator method of sequencing. http://purl.obolibrary.org/obo/SO_0001424 pyrosequenced_read http://purl.obolibrary.org/obo/SO_0000150 read A read produced by pyrosequencing technology. http://purl.obolibrary.org/obo/SO_0001425 ligation_based_read http://purl.obolibrary.org/obo/SO_0000150 read A read produced by ligation based sequencing technologies. http://purl.obolibrary.org/obo/SO_0001426 polymerase_synthesis_read http://purl.obolibrary.org/obo/SO_0000150 read A read produced by the polymerase based sequence by synthesis method. http://purl.obolibrary.org/obo/SO_0001427 cis_regulatory_frameshift_element http://purl.obolibrary.org/obo/SO_0001055 transcriptional_cis_regulatory_region A structural region in an RNA molecule which promotes ribosomal frameshifting of cis coding sequence. http://purl.obolibrary.org/obo/SO_0001428 expressed_sequence_assembly http://purl.obolibrary.org/obo/SO_0000353 sequence_assembly A sequence assembly derived from expressed sequences. http://purl.obolibrary.org/obo/SO_0001429 DNA_binding_site http://purl.obolibrary.org/obo/SO_0001655 nucleotide_binding_site A binding site that, in the molecule, interacts selectively and non-covalently with DNA. http://purl.obolibrary.org/obo/SO_0001433 three_prime_RACE_clone http://purl.obolibrary.org/obo/SO_0000317 cDNA_clone A three prime RACE (Rapid Amplification of cDNA Ends) clone is a cDNA clone copied from the 3' end of an mRNA (using a poly-dT primer to capture the polyA tail and a gene-specific or randomly primed 5' primer), and spliced into a vector for propagation in a suitable host. http://purl.obolibrary.org/obo/SO_0001434 cassette_pseudogene http://purl.obolibrary.org/obo/SO_0001760 non_processed_pseudogene A cassette pseudogene is a kind of gene in an inactive form which may recombine at a telomeric locus to form a functional copy. http://purl.obolibrary.org/obo/SO_0001435 alanine http://purl.obolibrary.org/obo/SO_0001237 amino_acid A non-polar, hydorophobic amino acid encoded by the codons GCN (GCT, GCC, GCA and GCG). http://purl.obolibrary.org/obo/SO_0001436 valine http://purl.obolibrary.org/obo/SO_0001237 amino_acid A non-polar, hydorophobic amino acid encoded by the codons GTN (GTT, GTC, GTA and GTG). http://purl.obolibrary.org/obo/SO_0001437 leucine http://purl.obolibrary.org/obo/SO_0001237 amino_acid A non-polar, hydorophobic amino acid encoded by the codons CTN (CTT, CTC, CTA and CTG), TTA and TTG. http://purl.obolibrary.org/obo/SO_0001438 isoleucine http://purl.obolibrary.org/obo/SO_0001237 amino_acid A non-polar, hydorophobic amino acid encoded by the codons ATH (ATT, ATC and ATA). http://purl.obolibrary.org/obo/SO_0001439 proline http://purl.obolibrary.org/obo/SO_0001237 amino_acid A non-polar, hydorophobic amino acid encoded by the codons CCN (CCT, CCC, CCA and CCG). http://purl.obolibrary.org/obo/SO_0001440 tryptophan http://purl.obolibrary.org/obo/SO_0001237 amino_acid A non-polar, hydorophobic amino acid encoded by the codon TGG. http://purl.obolibrary.org/obo/SO_0001441 phenylalanine http://purl.obolibrary.org/obo/SO_0001237 amino_acid A non-polar, hydorophobic amino acid encoded by the codons TTT and TTC. http://purl.obolibrary.org/obo/SO_0001442 methionine http://purl.obolibrary.org/obo/SO_0001237 amino_acid A non-polar, hydorophobic amino acid encoded by the codon ATG. http://purl.obolibrary.org/obo/SO_0001443 glycine http://purl.obolibrary.org/obo/SO_0001237 amino_acid A non-polar, hydorophilic amino acid encoded by the codons GGN (GGT, GGC, GGA and GGG). http://purl.obolibrary.org/obo/SO_0001444 serine http://purl.obolibrary.org/obo/SO_0001237 amino_acid A polar, hydorophilic amino acid encoded by the codons TCN (TCT, TCC, TCA, TCG), AGT and AGC. http://purl.obolibrary.org/obo/SO_0001445 threonine http://purl.obolibrary.org/obo/SO_0001237 amino_acid A polar, hydorophilic amino acid encoded by the codons ACN (ACT, ACC, ACA and ACG). http://purl.obolibrary.org/obo/SO_0001446 tyrosine http://purl.obolibrary.org/obo/SO_0001237 amino_acid A polar, hydorophilic amino acid encoded by the codons TAT and TAC. http://purl.obolibrary.org/obo/SO_0001447 cysteine http://purl.obolibrary.org/obo/SO_0001237 amino_acid A polar amino acid encoded by the codons TGT and TGC. http://purl.obolibrary.org/obo/SO_0001448 glutamine http://purl.obolibrary.org/obo/SO_0001237 amino_acid A polar, hydorophilic amino acid encoded by the codons CAA and CAG. http://purl.obolibrary.org/obo/SO_0001449 asparagine http://purl.obolibrary.org/obo/SO_0001237 amino_acid A polar, hydorophilic amino acid encoded by the codons AAT and AAC. http://purl.obolibrary.org/obo/SO_0001450 lysine http://purl.obolibrary.org/obo/SO_0001237 amino_acid A positively charged, hydorophilic amino acid encoded by the codons AAA and AAG. http://purl.obolibrary.org/obo/SO_0001451 arginine http://purl.obolibrary.org/obo/SO_0001237 amino_acid A positively charged, hydorophilic amino acid encoded by the codons CGN (CGT, CGC, CGA and CGG), AGA and AGG. http://purl.obolibrary.org/obo/SO_0001452 histidine http://purl.obolibrary.org/obo/SO_0001237 amino_acid A positively charged, hydorophilic amino acid encoded by the codons CAT and CAC. http://purl.obolibrary.org/obo/SO_0001453 aspartic_acid http://purl.obolibrary.org/obo/SO_0001237 amino_acid A negatively charged, hydorophilic amino acid encoded by the codons GAT and GAC. http://purl.obolibrary.org/obo/SO_0001454 glutamic_acid http://purl.obolibrary.org/obo/SO_0001237 amino_acid A negatively charged, hydorophilic amino acid encoded by the codons GAA and GAG. http://purl.obolibrary.org/obo/SO_0001455 selenocysteine http://purl.obolibrary.org/obo/SO_0001237 amino_acid A relatively rare amino acid encoded by the codon UGA in some contexts, whereas UGA is a termination codon in other contexts. http://purl.obolibrary.org/obo/SO_0001456 pyrrolysine http://purl.obolibrary.org/obo/SO_0001237 amino_acid A relatively rare amino acid encoded by the codon UAG in some contexts, whereas UAG is a termination codon in other contexts. http://purl.obolibrary.org/obo/SO_0001457 transcribed_cluster http://purl.obolibrary.org/obo/SO_0001410 experimental_feature A region defined by a set of transcribed sequences from the same gene or expressed pseudogene. http://purl.obolibrary.org/obo/SO_0001458 unigene_cluster http://purl.obolibrary.org/obo/SO_0001457 transcribed_cluster A kind of transcribed_cluster defined by a set of transcribed sequences from the a unique gene. http://purl.obolibrary.org/obo/SO_0001459 CRISPR http://purl.obolibrary.org/obo/SO_0000314 direct_repeat Clustered Palindromic Repeats interspersed with bacteriophage derived spacer sequences. http://purl.obolibrary.org/obo/SO_0001460 insulator_binding_site http://purl.obolibrary.org/obo/SO_0001654 nucleotide_to_protein_binding_site A binding site that, in an insulator region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues. http://purl.obolibrary.org/obo/SO_0001461 enhancer_binding_site http://purl.obolibrary.org/obo/SO_0001654 nucleotide_to_protein_binding_site A binding site that, in the enhancer region of a nucleotide molecule, interacts selectively and non-covalently with polypeptide residues. http://purl.obolibrary.org/obo/SO_0001463 lincRNA http://purl.obolibrary.org/obo/SO_0001877 lncRNA Long, intervening non-coding RNA. A transcript that does not overlap within the start or end genomic coordinates of a coding gene or pseudogene on either strand. http://purl.obolibrary.org/obo/SO_0001464 UST http://purl.obolibrary.org/obo/SO_0000345 EST An EST spanning part or all of the untranslated regions of a protein-coding transcript. http://purl.obolibrary.org/obo/SO_0001465 three_prime_UST http://purl.obolibrary.org/obo/SO_0001464 UST A UST located in the 3'UTR of a protein-coding transcript. http://purl.obolibrary.org/obo/SO_0001466 five_prime_UST http://purl.obolibrary.org/obo/SO_0001464 UST An UST located in the 5'UTR of a protein-coding transcript. http://purl.obolibrary.org/obo/SO_0001467 RST http://purl.obolibrary.org/obo/SO_0000345 EST A tag produced from a single sequencing read from a RACE product; typically a few hundred base pairs long. http://purl.obolibrary.org/obo/SO_0001468 three_prime_RST http://purl.obolibrary.org/obo/SO_0001467 RST A tag produced from a single sequencing read from a 3'-RACE product; typically a few hundred base pairs long. http://purl.obolibrary.org/obo/SO_0001469 five_prime_RST http://purl.obolibrary.org/obo/SO_0001467 RST A tag produced from a single sequencing read from a 5'-RACE product; typically a few hundred base pairs long. http://purl.obolibrary.org/obo/SO_0001470 UST_match http://purl.obolibrary.org/obo/SO_0000102 expressed_sequence_match A match against an UST sequence. http://purl.obolibrary.org/obo/SO_0001471 RST_match http://purl.obolibrary.org/obo/SO_0000102 expressed_sequence_match A match against an RST sequence. http://purl.obolibrary.org/obo/SO_0001472 primer_match http://purl.obolibrary.org/obo/SO_0000347 nucleotide_match A nucleotide match to a primer sequence. http://purl.obolibrary.org/obo/SO_0001473 miRNA_antiguide http://purl.obolibrary.org/obo/SO_0001243 miRNA_primary_transcript_region A region of the pri miRNA that base pairs with the guide to form the hairpin. http://purl.obolibrary.org/obo/SO_0001474 trans_splice_junction http://purl.obolibrary.org/obo/SO_0000699 junction The boundary between the spliced leader and the first exon of the mRNA. http://purl.obolibrary.org/obo/SO_0001475 outron http://purl.obolibrary.org/obo/SO_0000835 primary_transcript_region A region of a primary transcript, that is removed via trans splicing. http://purl.obolibrary.org/obo/SO_0001476 natural_plasmid http://purl.obolibrary.org/obo/SO_0001038 extrachromosomal_mobile_genetic_element A plasmid that occurs naturally. http://purl.obolibrary.org/obo/SO_0001480 PAC_end http://purl.obolibrary.org/obo/SO_0000150 read A region of sequence from the end of a PAC clone that may provide a highly specific marker. http://purl.obolibrary.org/obo/SO_0001481 RAPD http://purl.obolibrary.org/obo/SO_0000006 PCR_product RAPD is a 'PCR product' where a sequence variant is identified through the use of PCR with random primers. http://purl.obolibrary.org/obo/SO_0001482 shadow_enhancer http://purl.obolibrary.org/obo/SO_0000165 enhancer An enhancer that drives the pattern of transcription and binds to the same TF as the primary enhancer, but is located in the intron of or on the far side of a neighboring gene. http://purl.obolibrary.org/obo/SO_0001484 X_element_combinatorial_repeat http://purl.obolibrary.org/obo/SO_0000657 repeat_region An X element combinatorial repeat is a repeat region located between the X element and the telomere or adjacent Y' element. http://purl.obolibrary.org/obo/SO_0001485 Y_prime_element http://purl.obolibrary.org/obo/SO_0000657 repeat_region A Y' element is a repeat region (SO:0000657) located adjacent to telomeric repeats or X element combinatorial repeats, either as a single copy or tandem repeat of two to four copies. http://purl.obolibrary.org/obo/SO_0001486 standard_draft http://purl.obolibrary.org/obo/SO_0001499 whole_genome_sequence_status The status of a whole genome sequence, where the data is minimally filtered or un-filtered, from any number of sequencing platforms, and is assembled into contigs. Genome sequence of this quality may harbour regions of poor quality and can be relatively incomplete. http://purl.obolibrary.org/obo/SO_0001487 high_quality_draft http://purl.obolibrary.org/obo/SO_0001499 whole_genome_sequence_status The status of a whole genome sequence, where overall coverage represents at least 90 percent of the genome. http://purl.obolibrary.org/obo/SO_0001488 improved_high_quality_draft http://purl.obolibrary.org/obo/SO_0001499 whole_genome_sequence_status The status of a whole genome sequence, where additional work has been performed, using either manual or automated methods, such as gap resolution. http://purl.obolibrary.org/obo/SO_0001489 annotation_directed_improved_draft http://purl.obolibrary.org/obo/SO_0001499 whole_genome_sequence_status The status of a whole genome sequence,where annotation, and verification of coding regions has occurred. http://purl.obolibrary.org/obo/SO_0001490 noncontiguous_finished http://purl.obolibrary.org/obo/SO_0001499 whole_genome_sequence_status The status of a whole genome sequence, where the assembly is high quality, closure approaches have been successful for most gaps, misassemblies and low quality regions. http://purl.obolibrary.org/obo/SO_0001491 finished_genome http://purl.obolibrary.org/obo/SO_0001499 whole_genome_sequence_status The status of a whole genome sequence, with less than 1 error per 100,000 base pairs. http://purl.obolibrary.org/obo/SO_0001492 intronic_regulatory_region http://purl.obolibrary.org/obo/SO_0001055 transcriptional_cis_regulatory_region A regulatory region that is part of an intron. http://purl.obolibrary.org/obo/SO_0001493 centromere_DNA_Element_I http://purl.obolibrary.org/obo/SO_0000330 conserved_region A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region composed of 8-11bp which enables binding by the centromere binding factor 1(Cbf1p). http://purl.obolibrary.org/obo/SO_0001494 centromere_DNA_Element_II http://purl.obolibrary.org/obo/SO_0000330 conserved_region A centromere DNA Element II (CDEII) is part a conserved region of the centromere, consisting of a consensus region that is AT-rich and ~ 75-100 bp in length. http://purl.obolibrary.org/obo/SO_0001495 centromere_DNA_Element_III http://purl.obolibrary.org/obo/SO_0000330 conserved_region A centromere DNA Element I (CDEI) is a conserved region, part of the centromere, consisting of a consensus region that consists of a 25-bp which enables binding by the centromere DNA binding factor 3 (CBF3) complex. http://purl.obolibrary.org/obo/SO_0001496 telomeric_repeat http://purl.obolibrary.org/obo/SO_0000657 repeat_region The telomeric repeat is a repeat region, part of the chromosome, which in yeast, is a G-rich terminal sequence of the form (TG(1-3))n or more precisely ((TG)(1-6)TG(2-3))n. http://purl.obolibrary.org/obo/SO_0001497 X_element http://purl.obolibrary.org/obo/SO_0000330 conserved_region The X element is a conserved region, of the telomere, of ~475 bp that contains an ARS sequence and in most cases an Abf1p binding site. http://purl.obolibrary.org/obo/SO_0001499 whole_genome_sequence_status http://purl.obolibrary.org/obo/SO_0000905 status The status of whole genome sequence. http://purl.obolibrary.org/obo/SO_0001501 peptide_collection http://purl.obolibrary.org/obo/SO_0001260 sequence_collection A collection of peptide sequences. http://purl.obolibrary.org/obo/SO_0001502 high_identity_region http://purl.obolibrary.org/obo/SO_0001410 experimental_feature An experimental feature with high sequence identity to another sequence. http://purl.obolibrary.org/obo/SO_0001503 processed_transcript http://purl.obolibrary.org/obo/SO_0000673 transcript A transcript for which no open reading frame has been identified and for which no other function has been determined. http://purl.obolibrary.org/obo/SO_0001504 assortment_derived_variation http://purl.obolibrary.org/obo/SO_0000240 chromosome_variation A chromosome variation derived from an event during meiosis. http://purl.obolibrary.org/obo/SO_0001506 variant_genome http://purl.obolibrary.org/obo/SO_0001026 genome A collection of sequences (often chromosomes) of an individual. http://purl.obolibrary.org/obo/SO_0001507 variant_collection http://purl.obolibrary.org/obo/SO_0001260 sequence_collection A collection of one or more sequences of an individual. http://purl.obolibrary.org/obo/SO_0001508 alteration_attribute http://purl.obolibrary.org/obo/SO_0000733 feature_attribute An attribute of alteration of one or more chromosomes. http://purl.obolibrary.org/obo/SO_0001509 chromosomal_variation_attribute http://purl.obolibrary.org/obo/SO_0001508 alteration_attribute An attribute of a change in the structure or number of a chromosomes. http://purl.obolibrary.org/obo/SO_0001510 intrachromosomal http://purl.obolibrary.org/obo/SO_0001509 chromosomal_variation_attribute A change in chromosomes that occurs between two separate chromosomes. http://purl.obolibrary.org/obo/SO_0001511 interchromosomal http://purl.obolibrary.org/obo/SO_0001509 chromosomal_variation_attribute A change in chromosomes that occurs between two sections of the same chromosome or between homologous chromosomes. http://purl.obolibrary.org/obo/SO_0001512 insertion_attribute http://purl.obolibrary.org/obo/SO_0001508 alteration_attribute A quality of a chromosomal insertion,. http://purl.obolibrary.org/obo/SO_0001513 tandem http://purl.obolibrary.org/obo/SO_0001512 insertion_attribute An insertion of extension of a tandem repeat. http://purl.obolibrary.org/obo/SO_0001514 direct http://purl.obolibrary.org/obo/SO_0001512 insertion_attribute A quality of an insertion where the insert is not in a cytologically inverted orientation. http://purl.obolibrary.org/obo/SO_0001515 inverted http://purl.obolibrary.org/obo/SO_0001512 insertion_attribute A quality of an insertion where the insert is in a cytologically inverted orientation. http://purl.obolibrary.org/obo/SO_0001516 free http://purl.obolibrary.org/obo/SO_0001523 duplication_attribute The quality of a duplication where the new region exists independently of the original. http://purl.obolibrary.org/obo/SO_0001517 inversion_attribute http://purl.obolibrary.org/obo/SO_0001508 alteration_attribute When a region of a chromosome is changed to the reverse order without duplication or deletion. http://purl.obolibrary.org/obo/SO_0001518 pericentric http://purl.obolibrary.org/obo/SO_0001517 inversion_attribute An inversion event that includes the centromere. http://purl.obolibrary.org/obo/SO_0001519 paracentric http://purl.obolibrary.org/obo/SO_0001517 inversion_attribute An inversion event that does not include the centromere. http://purl.obolibrary.org/obo/SO_0001520 translocaton_attribute http://purl.obolibrary.org/obo/SO_0001508 alteration_attribute An attribute of a translocation, which is then a region of nucleotide sequence that has translocated to a new position. The observed adjacency of two previously separated regions. http://purl.obolibrary.org/obo/SO_0001521 reciprocal http://purl.obolibrary.org/obo/SO_0001520 translocaton_attribute When translocation occurs between nonhomologous chromosomes and involved an equal exchange of genetic materials. http://purl.obolibrary.org/obo/SO_0001522 insertional http://purl.obolibrary.org/obo/SO_0001520 translocaton_attribute When a translocation is simply moving genetic material from one chromosome to another. http://purl.obolibrary.org/obo/SO_0001523 duplication_attribute http://purl.obolibrary.org/obo/SO_0001508 alteration_attribute An attribute of a duplication, which is an insertion which derives from, or is identical in sequence to, nucleotides present at a known location in the genome. http://purl.obolibrary.org/obo/SO_0001524 chromosomally_aberrant_genome http://purl.obolibrary.org/obo/SO_0001506 variant_genome When a genome contains an abnormal amount of chromosomes. http://purl.obolibrary.org/obo/SO_0001525 assembly_error_correction http://purl.obolibrary.org/obo/SO_0000413 sequence_difference A region of sequence where the final nucleotide assignment differs from the original assembly due to an improvement that replaces a mistake. http://purl.obolibrary.org/obo/SO_0001526 base_call_error_correction http://purl.obolibrary.org/obo/SO_0000413 sequence_difference A region of sequence where the final nucleotide assignment is different from that given by the base caller due to an improvement that replaces a mistake. http://purl.obolibrary.org/obo/SO_0001527 peptide_localization_signal http://purl.obolibrary.org/obo/SO_0000839 polypeptide_region A region of peptide sequence used to target the polypeptide molecule to a specific organelle. http://purl.obolibrary.org/obo/SO_0001528 nuclear_localization_signal http://purl.obolibrary.org/obo/SO_0001527 peptide_localization_signal A polypeptide region that targets a polypeptide to the nucleus. http://purl.obolibrary.org/obo/SO_0001529 endosomal_localization_signal http://purl.obolibrary.org/obo/SO_0001527 peptide_localization_signal A polypeptide region that targets a polypeptide to the endosome. http://purl.obolibrary.org/obo/SO_0001530 lysosomal_localization_signal http://purl.obolibrary.org/obo/SO_0001527 peptide_localization_signal A polypeptide region that targets a polypeptide to the lysosome. http://purl.obolibrary.org/obo/SO_0001531 nuclear_export_signal http://purl.obolibrary.org/obo/SO_0001527 peptide_localization_signal A polypeptide region that targets a polypeptide to he cytoplasm. http://purl.obolibrary.org/obo/SO_0001532 recombination_signal_sequence http://purl.obolibrary.org/obo/SO_0000299 specific_recombination_site A region recognized by a recombinase. http://purl.obolibrary.org/obo/SO_0001534 nuclear_rim_localization_signal http://purl.obolibrary.org/obo/SO_0001527 peptide_localization_signal A polypeptide region that targets a polypeptide to the nuclear rim. http://purl.obolibrary.org/obo/SO_0001535 P_TIR_transposon http://purl.obolibrary.org/obo/SO_0000208 terminal_inverted_repeat_element A P-element is a DNA transposon responsible for hybrid dysgenesis. P elements in this terminal inverted repeat (TIR) transposon superfamily have 31 bp perfect TIR and upon insertion duplicate an 8 bp sequence. It contains transposase that may lack the DDE domain. http://purl.obolibrary.org/obo/SO_0001536 functional_effect_variant http://purl.obolibrary.org/obo/SO_0001060 sequence_variant A variant whereby the effect is evaluated with respect to a reference. http://purl.obolibrary.org/obo/SO_0001537 structural_variant http://purl.obolibrary.org/obo/SO_0001060 sequence_variant A sequence variant that changes one or more structural features. http://purl.obolibrary.org/obo/SO_0001538 transcript_function_variant http://purl.obolibrary.org/obo/SO_0002218 functionally_abnormal A sequence variant which alters the functioning of a transcript with respect to a reference sequence. http://purl.obolibrary.org/obo/SO_0001539 translational_product_function_variant http://purl.obolibrary.org/obo/SO_0002218 functionally_abnormal A sequence variant that affects the functioning of a translational product with respect to a reference sequence. http://purl.obolibrary.org/obo/SO_0001540 level_of_transcript_variant http://purl.obolibrary.org/obo/SO_0001538 transcript_function_variant A sequence variant which alters the level of a transcript. http://purl.obolibrary.org/obo/SO_0001541 decreased_transcript_level_variant http://purl.obolibrary.org/obo/SO_0001540 level_of_transcript_variant A sequence variant that decreases the level of mature, spliced and processed RNA with respect to a reference sequence. http://purl.obolibrary.org/obo/SO_0001542 increased_transcript_level_variant http://purl.obolibrary.org/obo/SO_0001540 level_of_transcript_variant A sequence variant that increases the level of mature, spliced and processed RNA with respect to a reference sequence. http://purl.obolibrary.org/obo/SO_0001543 transcript_processing_variant http://purl.obolibrary.org/obo/SO_0001538 transcript_function_variant A sequence variant that affects the post transcriptional processing of a transcript with respect to a reference sequence. http://purl.obolibrary.org/obo/SO_0001544 editing_variant http://purl.obolibrary.org/obo/SO_0001543 transcript_processing_variant A transcript processing variant whereby the process of editing is disrupted with respect to the reference. http://purl.obolibrary.org/obo/SO_0001545 polyadenylation_variant http://purl.obolibrary.org/obo/SO_0001543 transcript_processing_variant A sequence variant that changes polyadenylation with respect to a reference sequence. http://purl.obolibrary.org/obo/SO_0001546 transcript_stability_variant http://purl.obolibrary.org/obo/SO_0001538 transcript_function_variant A variant that changes the stability of a transcript with respect to a reference sequence. http://purl.obolibrary.org/obo/SO_0001547 decreased_transcript_stability_variant http://purl.obolibrary.org/obo/SO_0001546 transcript_stability_variant A sequence variant that decreases transcript stability with respect to a reference sequence. http://purl.obolibrary.org/obo/SO_0001548 increased_transcript_stability_variant http://purl.obolibrary.org/obo/SO_0001546 transcript_stability_variant A sequence variant that increases transcript stability with respect to a reference sequence. http://purl.obolibrary.org/obo/SO_0001549 transcription_variant http://purl.obolibrary.org/obo/SO_0001538 transcript_function_variant A variant that changes alters the transcription of a transcript with respect to a reference sequence. http://purl.obolibrary.org/obo/SO_0001550 rate_of_transcription_variant http://purl.obolibrary.org/obo/SO_0001549 transcription_variant A sequence variant that changes the rate of transcription with respect to a reference sequence. http://purl.obolibrary.org/obo/SO_0001551 increased_transcription_rate_variant http://purl.obolibrary.org/obo/SO_0001550 rate_of_transcription_variant A sequence variant that increases the rate of transcription with respect to a reference sequence. http://purl.obolibrary.org/obo/SO_0001552 decreased_transcription_rate_variant http://purl.obolibrary.org/obo/SO_0001550 rate_of_transcription_variant A sequence variant that decreases the rate of transcription with respect to a reference sequence. http://purl.obolibrary.org/obo/SO_0001553 translational_product_level_variant http://purl.obolibrary.org/obo/SO_0001539 translational_product_function_variant A functional variant that changes the translational product level with respect to a reference sequence. http://purl.obolibrary.org/obo/SO_0001554 polypeptide_function_variant http://purl.obolibrary.org/obo/SO_0001539 translational_product_function_variant A sequence variant which changes polypeptide functioning with respect to a reference sequence. http://purl.obolibrary.org/obo/SO_0001555 decreased_translational_product_level http://purl.obolibrary.org/obo/SO_0001553 translational_product_level_variant A sequence variant which decreases the translational product level with respect to a reference sequence. http://purl.obolibrary.org/obo/SO_0001556 increased_translational_product_level http://purl.obolibrary.org/obo/SO_0001553 translational_product_level_variant A sequence variant which increases the translational product level with respect to a reference sequence. http://purl.obolibrary.org/obo/SO_0001557 polypeptide_gain_of_function_variant http://purl.obolibrary.org/obo/SO_0001554 polypeptide_function_variant A sequence variant which causes gain of polypeptide function with respect to a reference sequence. http://purl.obolibrary.org/obo/SO_0001558 polypeptide_localization_variant http://purl.obolibrary.org/obo/SO_0001554 polypeptide_function_variant A sequence variant which changes the localization of a polypeptide with respect to a reference sequence. http://purl.obolibrary.org/obo/SO_0001559 polypeptide_loss_of_function_variant http://purl.obolibrary.org/obo/SO_0001554 polypeptide_function_variant A sequence variant that causes the loss of a polypeptide function with respect to a reference sequence. http://purl.obolibrary.org/obo/SO_0001560 inactive_ligand_binding_site http://purl.obolibrary.org/obo/SO_0001559 polypeptide_loss_of_function_variant A sequence variant that causes the inactivation of a ligand binding site with respect to a reference sequence. http://purl.obolibrary.org/obo/SO_0001561 polypeptide_partial_loss_of_function http://purl.obolibrary.org/obo/SO_0001559 polypeptide_loss_of_function_variant A sequence variant that causes some but not all loss of polypeptide function with respect to a reference sequence. http://purl.obolibrary.org/obo/SO_0001562 polypeptide_post_translational_processing_variant http://purl.obolibrary.org/obo/SO_0001554 polypeptide_function_variant A sequence variant that causes a change in post translational processing of the peptide with respect to a reference sequence. http://purl.obolibrary.org/obo/SO_0001563 copy_number_change http://purl.obolibrary.org/obo/SO_0002160 sequence_length_variant A sequence variant where copies of a feature (CNV) are either increased or decreased. http://purl.obolibrary.org/obo/SO_0001564 gene_variant http://purl.obolibrary.org/obo/SO_0001878 feature_variant A sequence variant where the structure of the gene is changed. http://purl.obolibrary.org/obo/SO_0001565 gene_fusion http://purl.obolibrary.org/obo/SO_0001882 feature_fusion A sequence variant whereby a two genes have become joined. http://purl.obolibrary.org/obo/SO_0001566 regulatory_region_variant http://purl.obolibrary.org/obo/SO_0001878 feature_variant A sequence variant located within a regulatory region. http://purl.obolibrary.org/obo/SO_0001567 stop_retained_variant http://purl.obolibrary.org/obo/SO_0001819 synonymous_variant A sequence variant where at least one base in the terminator codon is changed, but the terminator remains. http://purl.obolibrary.org/obo/SO_0001568 splicing_variant http://purl.obolibrary.org/obo/SO_0001576 transcript_variant A sequence variant that changes the process of splicing. http://purl.obolibrary.org/obo/SO_0001569 cryptic_splice_site_variant http://purl.obolibrary.org/obo/SO_0001568 splicing_variant A sequence variant causing a new (functional) splice site. http://purl.obolibrary.org/obo/SO_0001570 cryptic_splice_acceptor http://purl.obolibrary.org/obo/SO_0001569 cryptic_splice_site_variant A sequence variant whereby a new splice site is created due to the activation of a new acceptor. http://purl.obolibrary.org/obo/SO_0001571 cryptic_splice_donor http://purl.obolibrary.org/obo/SO_0001569 cryptic_splice_site_variant A sequence variant whereby a new splice site is created due to the activation of a new donor. http://purl.obolibrary.org/obo/SO_0001572 exon_loss_variant http://purl.obolibrary.org/obo/SO_0001568 splicing_variant A sequence variant whereby an exon is lost from the transcript. http://purl.obolibrary.org/obo/SO_0001573 intron_gain_variant http://purl.obolibrary.org/obo/SO_0001568 splicing_variant A sequence variant whereby an intron is gained by the processed transcript; usually a result of an alteration of the donor or acceptor. http://purl.obolibrary.org/obo/SO_0001574 splice_acceptor_variant http://purl.obolibrary.org/obo/SO_0001629 splice_site_variant A splice variant that changes the 2 base region at the 3' end of an intron. http://purl.obolibrary.org/obo/SO_0001575 splice_donor_variant http://purl.obolibrary.org/obo/SO_0001629 splice_site_variant A splice variant that changes the 2 base pair region at the 5' end of an intron. http://purl.obolibrary.org/obo/SO_0001576 transcript_variant http://purl.obolibrary.org/obo/SO_0001564 gene_variant A sequence variant that changes the structure of the transcript. http://purl.obolibrary.org/obo/SO_0001577 complex_transcript_variant http://purl.obolibrary.org/obo/SO_0001576 transcript_variant A transcript variant with a complex INDEL- Insertion or deletion that spans an exon/intron border or a coding sequence/UTR border. http://purl.obolibrary.org/obo/SO_0001578 stop_lost http://purl.obolibrary.org/obo/SO_0001992 nonsynonymous_variant A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript. http://purl.obolibrary.org/obo/SO_0001580 coding_sequence_variant http://purl.obolibrary.org/obo/SO_0001968 coding_transcript_variant A sequence variant that changes the coding sequence. http://purl.obolibrary.org/obo/SO_0001582 initiator_codon_variant http://purl.obolibrary.org/obo/SO_0001580 coding_sequence_variant A codon variant that changes at least one base of the first codon of a transcript. http://purl.obolibrary.org/obo/SO_0001583 missense_variant http://purl.obolibrary.org/obo/SO_0001992 nonsynonymous_variant A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved. http://purl.obolibrary.org/obo/SO_0001585 conservative_missense_variant http://purl.obolibrary.org/obo/SO_0001583 missense_variant A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for a different but similar amino acid. These variants may or may not be deleterious. http://purl.obolibrary.org/obo/SO_0001586 non_conservative_missense_variant http://purl.obolibrary.org/obo/SO_0001583 missense_variant A sequence variant whereby at least one base of a codon is changed resulting in a codon that encodes for an amino acid with different biochemical properties. http://purl.obolibrary.org/obo/SO_0001587 stop_gained http://purl.obolibrary.org/obo/SO_0001992 nonsynonymous_variant A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened polypeptide. http://purl.obolibrary.org/obo/SO_0001589 frameshift_variant http://purl.obolibrary.org/obo/SO_0001818 protein_altering_variant A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three. http://purl.obolibrary.org/obo/SO_0001590 terminator_codon_variant http://purl.obolibrary.org/obo/SO_0001580 coding_sequence_variant A sequence variant whereby at least one of the bases in the terminator codon is changed. http://purl.obolibrary.org/obo/SO_0001591 frame_restoring_variant http://purl.obolibrary.org/obo/SO_0001589 frameshift_variant A sequence variant that reverts the sequence of a previous frameshift mutation back to the initial frame. http://purl.obolibrary.org/obo/SO_0001592 minus_1_frameshift_variant http://purl.obolibrary.org/obo/SO_0001589 frameshift_variant A sequence variant which causes a disruption of the translational reading frame, by shifting one base ahead. http://purl.obolibrary.org/obo/SO_0001593 minus_2_frameshift_variant http://purl.obolibrary.org/obo/SO_0001589 frameshift_variant A sequence variant which causes a disruption of the translational reading frame, by shifting two bases forward. http://purl.obolibrary.org/obo/SO_0001594 plus_1_frameshift_variant http://purl.obolibrary.org/obo/SO_0001589 frameshift_variant A sequence variant which causes a disruption of the translational reading frame, by shifting one base backward. http://purl.obolibrary.org/obo/SO_0001595 plus_2_frameshift_variant http://purl.obolibrary.org/obo/SO_0001589 frameshift_variant A sequence variant which causes a disruption of the translational reading frame, by shifting two bases backward. http://purl.obolibrary.org/obo/SO_0001596 transcript_secondary_structure_variant http://purl.obolibrary.org/obo/SO_0001576 transcript_variant A sequence variant within a transcript that changes the secondary structure of the RNA product. http://purl.obolibrary.org/obo/SO_0001597 compensatory_transcript_secondary_structure_variant http://purl.obolibrary.org/obo/SO_0001596 transcript_secondary_structure_variant A secondary structure variant that compensate for the change made by a previous variant. http://purl.obolibrary.org/obo/SO_0001598 translational_product_structure_variant http://purl.obolibrary.org/obo/SO_0001564 gene_variant A sequence variant within the transcript that changes the structure of the translational product. http://purl.obolibrary.org/obo/SO_0001599 3D_polypeptide_structure_variant http://purl.obolibrary.org/obo/SO_0001539 translational_product_function_variant A sequence variant that changes the resulting polypeptide structure. http://purl.obolibrary.org/obo/SO_0001600 complex_3D_structural_variant http://purl.obolibrary.org/obo/SO_0001599 3D_polypeptide_structure_variant A sequence variant that changes the resulting polypeptide structure. http://purl.obolibrary.org/obo/SO_0001601 conformational_change_variant http://purl.obolibrary.org/obo/SO_0001599 3D_polypeptide_structure_variant A sequence variant in the CDS region that causes a conformational change in the resulting polypeptide sequence. http://purl.obolibrary.org/obo/SO_0001602 complex_change_of_translational_product_variant http://purl.obolibrary.org/obo/SO_0001539 translational_product_function_variant A variant that changes the translational product with respect to the reference. http://purl.obolibrary.org/obo/SO_0001603 polypeptide_sequence_variant http://purl.obolibrary.org/obo/SO_0001598 translational_product_structure_variant A sequence variant with in the CDS that causes a change in the resulting polypeptide sequence. http://purl.obolibrary.org/obo/SO_0001604 amino_acid_deletion http://purl.obolibrary.org/obo/SO_0001603 polypeptide_sequence_variant A sequence variant within a CDS resulting in the loss of an amino acid from the resulting polypeptide. http://purl.obolibrary.org/obo/SO_0001605 amino_acid_insertion http://purl.obolibrary.org/obo/SO_0001603 polypeptide_sequence_variant A sequence variant within a CDS resulting in the gain of an amino acid to the resulting polypeptide. http://purl.obolibrary.org/obo/SO_0001606 amino_acid_substitution http://purl.obolibrary.org/obo/SO_0001603 polypeptide_sequence_variant A sequence variant of a codon resulting in the substitution of one amino acid for another in the resulting polypeptide. http://purl.obolibrary.org/obo/SO_0001607 conservative_amino_acid_substitution http://purl.obolibrary.org/obo/SO_0001606 amino_acid_substitution A sequence variant of a codon causing the substitution of a similar amino acid for another in the resulting polypeptide. http://purl.obolibrary.org/obo/SO_0001608 non_conservative_amino_acid_substitution http://purl.obolibrary.org/obo/SO_0001606 amino_acid_substitution A sequence variant of a codon causing the substitution of a non conservative amino acid for another in the resulting polypeptide. http://purl.obolibrary.org/obo/SO_0001609 elongated_polypeptide http://purl.obolibrary.org/obo/SO_0001603 polypeptide_sequence_variant An elongation of a polypeptide sequence deriving from a sequence variant extending the CDS. http://purl.obolibrary.org/obo/SO_0001610 elongated_polypeptide_C_terminal http://purl.obolibrary.org/obo/SO_0001609 elongated_polypeptide An elongation of a polypeptide sequence at the C terminus deriving from a sequence variant extending the CDS. http://purl.obolibrary.org/obo/SO_0001611 elongated_polypeptide_N_terminal http://purl.obolibrary.org/obo/SO_0001609 elongated_polypeptide An elongation of a polypeptide sequence at the N terminus deriving from a sequence variant extending the CDS. http://purl.obolibrary.org/obo/SO_0001612 elongated_in_frame_polypeptide_C_terminal http://purl.obolibrary.org/obo/SO_0001610 elongated_polypeptide_C_terminal A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the C terminus. http://purl.obolibrary.org/obo/SO_0001613 elongated_out_of_frame_polypeptide_C_terminal http://purl.obolibrary.org/obo/SO_0001610 elongated_polypeptide_C_terminal A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the C terminus. http://purl.obolibrary.org/obo/SO_0001614 elongated_in_frame_polypeptide_N_terminal_elongation http://purl.obolibrary.org/obo/SO_0001611 elongated_polypeptide_N_terminal A sequence variant with in the CDS that causes in frame elongation of the resulting polypeptide sequence at the N terminus. http://purl.obolibrary.org/obo/SO_0001615 elongated_out_of_frame_polypeptide_N_terminal http://purl.obolibrary.org/obo/SO_0001611 elongated_polypeptide_N_terminal A sequence variant with in the CDS that causes out of frame elongation of the resulting polypeptide sequence at the N terminus. http://purl.obolibrary.org/obo/SO_0001616 polypeptide_fusion http://purl.obolibrary.org/obo/SO_0001603 polypeptide_sequence_variant A sequence variant that causes a fusion of two polypeptide sequences. http://purl.obolibrary.org/obo/SO_0001617 polypeptide_truncation http://purl.obolibrary.org/obo/SO_0001603 polypeptide_sequence_variant A sequence variant of the CD that causes a truncation of the resulting polypeptide. http://purl.obolibrary.org/obo/SO_0001618 inactive_catalytic_site http://purl.obolibrary.org/obo/SO_0001560 inactive_ligand_binding_site A sequence variant that causes the inactivation of a catalytic site with respect to a reference sequence. http://purl.obolibrary.org/obo/SO_0001619 non_coding_transcript_variant http://purl.obolibrary.org/obo/SO_0001576 transcript_variant A transcript variant of a non coding RNA gene. http://purl.obolibrary.org/obo/SO_0001620 mature_miRNA_variant http://purl.obolibrary.org/obo/SO_0001619 non_coding_transcript_variant A transcript variant located with the sequence of the mature miRNA. http://purl.obolibrary.org/obo/SO_0001621 NMD_transcript_variant http://purl.obolibrary.org/obo/SO_0001576 transcript_variant A variant in a transcript that is the target of nonsense-mediated mRNA decay. http://purl.obolibrary.org/obo/SO_0001622 UTR_variant http://purl.obolibrary.org/obo/SO_0001968 coding_transcript_variant A transcript variant that is located within the UTR. http://purl.obolibrary.org/obo/SO_0001623 5_prime_UTR_variant http://purl.obolibrary.org/obo/SO_0001622 UTR_variant A UTR variant of the 5' UTR. http://purl.obolibrary.org/obo/SO_0001624 3_prime_UTR_variant http://purl.obolibrary.org/obo/SO_0001622 UTR_variant A UTR variant of the 3' UTR. http://purl.obolibrary.org/obo/SO_0001626 incomplete_terminal_codon_variant http://purl.obolibrary.org/obo/SO_0001650 inframe_variant A sequence variant where at least one base of the final codon of an incompletely annotated transcript is changed. http://purl.obolibrary.org/obo/SO_0001627 intron_variant http://purl.obolibrary.org/obo/SO_0001576 transcript_variant A transcript variant occurring within an intron. http://purl.obolibrary.org/obo/SO_0001629 splice_site_variant http://purl.obolibrary.org/obo/SO_0001627 intron_variant A sequence variant that changes the first two or last two bases of an intron, or the 5th base from the start of the intron in the orientation of the transcript. http://purl.obolibrary.org/obo/SO_0001630 splice_region_variant http://purl.obolibrary.org/obo/SO_0001568 splicing_variant A sequence variant in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8 bases of the intron. http://purl.obolibrary.org/obo/SO_0001631 upstream_gene_variant http://purl.obolibrary.org/obo/SO_0001628 intergenic_variant A sequence variant located 5' of a gene. http://purl.obolibrary.org/obo/SO_0001632 downstream_gene_variant http://purl.obolibrary.org/obo/SO_0001628 intergenic_variant A sequence variant located 3' of a gene. http://purl.obolibrary.org/obo/SO_0001633 5KB_downstream_variant http://purl.obolibrary.org/obo/SO_0001632 downstream_gene_variant A sequence variant located within 5 KB of the end of a gene. http://purl.obolibrary.org/obo/SO_0001634 500B_downstream_variant http://purl.obolibrary.org/obo/SO_0001632 downstream_gene_variant A sequence variant located within a half KB of the end of a gene. http://purl.obolibrary.org/obo/SO_0001635 5KB_upstream_variant http://purl.obolibrary.org/obo/SO_0001631 upstream_gene_variant A sequence variant located within 5KB 5' of a gene. http://purl.obolibrary.org/obo/SO_0001636 2KB_upstream_variant http://purl.obolibrary.org/obo/SO_0001631 upstream_gene_variant A sequence variant located within 2KB 5' of a gene. http://purl.obolibrary.org/obo/SO_0001642 mathematically_defined_repeat http://purl.obolibrary.org/obo/SO_0001410 experimental_feature A mathematically defined repeat (MDR) is a experimental feature that is determined by querying overlapping oligomers of length k against a database of shotgun sequence data and identifying regions in the query sequence that exceed a statistically determined threshold of repetitiveness. http://purl.obolibrary.org/obo/SO_0001644 targeting_vector http://purl.obolibrary.org/obo/SO_0000440 vector_replicon An engineered vector that is able to take part in homologous recombination in a host with the intent of introducing site specific genomic modifications. http://purl.obolibrary.org/obo/SO_0001646 DArT_marker http://purl.obolibrary.org/obo/SO_0001645 genetic_marker A genetic marker, discovered using Diversity Arrays Technology (DArT) technology. http://purl.obolibrary.org/obo/SO_0001647 kozak_sequence http://purl.obolibrary.org/obo/SO_0000139 ribosome_entry_site A kind of ribosome entry site, specific to Eukaryotic organisms that overlaps part of both 5' UTR and CDS sequence. http://purl.obolibrary.org/obo/SO_0001648 nested_transposon http://purl.obolibrary.org/obo/SO_0000101 transposable_element A transposon that is disrupted by the insertion of another element. http://purl.obolibrary.org/obo/SO_0001649 nested_repeat http://purl.obolibrary.org/obo/SO_0000657 repeat_region A repeat that is disrupted by the insertion of another element. http://purl.obolibrary.org/obo/SO_0001650 inframe_variant http://purl.obolibrary.org/obo/SO_0001818 protein_altering_variant A sequence variant which does not cause a disruption of the translational reading frame. http://purl.obolibrary.org/obo/SO_0001653 retinoic_acid_responsive_element http://purl.obolibrary.org/obo/SO_0000235 TF_binding_site A transcription factor binding site of variable direct repeats of the sequence PuGGTCA spaced by five nucleotides (DR5) found in the promoters of retinoic acid-responsive genes, to which retinoic acid receptors bind. http://purl.obolibrary.org/obo/SO_0001655 nucleotide_binding_site http://purl.obolibrary.org/obo/SO_0000409 binding_site A binding site that, in the molecule, interacts selectively and non-covalently with nucleotide residues. http://purl.obolibrary.org/obo/SO_0001656 metal_binding_site http://purl.obolibrary.org/obo/SO_0000409 binding_site A binding site that, in the molecule, interacts selectively and non-covalently with metal ions. http://purl.obolibrary.org/obo/SO_0001657 ligand_binding_site http://purl.obolibrary.org/obo/SO_0000409 binding_site A binding site that, in the molecule, interacts selectively and non-covalently with a small molecule such as a drug, or hormone. http://purl.obolibrary.org/obo/SO_0001658 nested_tandem_repeat http://purl.obolibrary.org/obo/SO_0001649 nested_repeat An NTR is a nested repeat of two distinct tandem motifs interspersed with each other. http://purl.obolibrary.org/obo/SO_0001660 core_eukaryotic_promoter_element http://purl.obolibrary.org/obo/SO_0002309 core_promoter_element An element that only exists within the promoter region of a eukaryotic gene. http://purl.obolibrary.org/obo/SO_0001661 RNA_polymerase_II_TATA_box http://purl.obolibrary.org/obo/SO_0000174 TATA_box A TATA box core promoter of a gene transcribed by RNA polymerase II. http://purl.obolibrary.org/obo/SO_0001662 RNA_polymerase_III_TATA_box http://purl.obolibrary.org/obo/SO_0000174 TATA_box A TATA box core promoter of a gene transcribed by RNA polymerase III. http://purl.obolibrary.org/obo/SO_0001663 BREd_motif http://purl.obolibrary.org/obo/SO_0001660 core_eukaryotic_promoter_element A core RNA polymerase II promoter element with consensus (G/A)T(T/G/A)(T/A)(G/T)(T/G)(T/G). http://purl.obolibrary.org/obo/SO_0001664 DCE http://purl.obolibrary.org/obo/SO_0001660 core_eukaryotic_promoter_element A discontinuous core element of RNA polymerase II transcribed genes, situated downstream of the TSS. It is composed of three sub elements: SI, SII and SIII. http://purl.obolibrary.org/obo/SO_0001665 DCE_SI http://purl.obolibrary.org/obo/SO_0000713 DNA_motif A sub element of the DCE core promoter element, with consensus sequence CTTC. http://purl.obolibrary.org/obo/SO_0001666 DCE_SII http://purl.obolibrary.org/obo/SO_0000713 DNA_motif A sub element of the DCE core promoter element with consensus sequence CTGT. http://purl.obolibrary.org/obo/SO_0001667 DCE_SIII http://purl.obolibrary.org/obo/SO_0000713 DNA_motif A sub element of the DCE core promoter element with consensus sequence AGC. http://purl.obolibrary.org/obo/SO_0001668 proximal_promoter_element http://purl.obolibrary.org/obo/SO_0001678 regulatory_promoter_element DNA segment that ranges from about -250 to -40 relative to +1 of RNA transcription start site, where sequence specific DNA-binding transcription factors binds, such as Sp1, CTF (CCAAT-binding transcription factor), and CBF (CCAAT-box binding factor). http://purl.obolibrary.org/obo/SO_0001670 distal_promoter_element http://purl.obolibrary.org/obo/SO_0001678 regulatory_promoter_element A regulatory promoter element that is distal from the TSS. http://purl.obolibrary.org/obo/SO_0001673 minus_12_signal http://purl.obolibrary.org/obo/SO_0000713 DNA_motif A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54. http://purl.obolibrary.org/obo/SO_0001674 minus_24_signal http://purl.obolibrary.org/obo/SO_0000713 DNA_motif A conserved region about 24-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54. http://purl.obolibrary.org/obo/SO_0001675 A_box_type_1 http://purl.obolibrary.org/obo/SO_0000619 A_box An A box within an RNA polymerase III type 1 promoter. http://purl.obolibrary.org/obo/SO_0001676 A_box_type_2 http://purl.obolibrary.org/obo/SO_0000619 A_box An A box within an RNA polymerase III type 2 promoter. http://purl.obolibrary.org/obo/SO_0001677 intermediate_element http://purl.obolibrary.org/obo/SO_0001660 core_eukaryotic_promoter_element A core promoter region of RNA polymerase III type 1 promoters. http://purl.obolibrary.org/obo/SO_0001678 regulatory_promoter_element http://purl.obolibrary.org/obo/SO_0001659 promoter_element A promoter element that is not part of the core promoter, but provides the promoter with a specific regulatory region. http://purl.obolibrary.org/obo/SO_0001680 translation_regulatory_region http://purl.obolibrary.org/obo/SO_0005836 regulatory_region A regulatory region that is involved in the control of the process of translation. http://purl.obolibrary.org/obo/SO_0001681 recombination_regulatory_region http://purl.obolibrary.org/obo/SO_0005836 regulatory_region A regulatory region that is involved in the control of the process of recombination. http://purl.obolibrary.org/obo/SO_0001682 replication_regulatory_region http://purl.obolibrary.org/obo/SO_0005836 regulatory_region A regulatory region that is involved in the control of the process of nucleotide replication. http://purl.obolibrary.org/obo/SO_0001684 experimental_feature_attribute http://purl.obolibrary.org/obo/SO_0000733 feature_attribute An attribute of an experimentally derived feature. http://purl.obolibrary.org/obo/SO_0001685 score http://purl.obolibrary.org/obo/SO_0001684 experimental_feature_attribute The score of an experimentally derived feature such as a p-value. http://purl.obolibrary.org/obo/SO_0001688 restriction_enzyme_cleavage_junction http://purl.obolibrary.org/obo/SO_0002204 nucleotide_cleavage_site The boundary at which a restriction enzyme breaks the nucleotide sequence. http://purl.obolibrary.org/obo/SO_0001689 five_prime_restriction_enzyme_junction http://purl.obolibrary.org/obo/SO_0001694 single_strand_restriction_enzyme_cleavage_site The restriction enzyme cleavage junction on the 5' strand of the nucleotide sequence. http://purl.obolibrary.org/obo/SO_0001690 three_prime_restriction_enzyme_junction http://purl.obolibrary.org/obo/SO_0001694 single_strand_restriction_enzyme_cleavage_site The restriction enzyme cleavage junction on the 3' strand of the nucleotide sequence. http://purl.obolibrary.org/obo/SO_0001691 blunt_end_restriction_enzyme_cleavage_site http://purl.obolibrary.org/obo/SO_0001687 restriction_enzyme_recognition_site A restriction enzyme recognition site that, when cleaved, results in no overhangs. http://purl.obolibrary.org/obo/SO_0001692 sticky_end_restriction_enzyme_cleavage_site http://purl.obolibrary.org/obo/SO_0001687 restriction_enzyme_recognition_site A site where restriction enzymes can cleave that will produce an overhang or 'sticky end'. http://purl.obolibrary.org/obo/SO_0001693 blunt_end_restriction_enzyme_cleavage_junction http://purl.obolibrary.org/obo/SO_0001688 restriction_enzyme_cleavage_junction A restriction enzyme cleavage site where both strands are cut at the same position. http://purl.obolibrary.org/obo/SO_0001694 single_strand_restriction_enzyme_cleavage_site http://purl.obolibrary.org/obo/SO_0001688 restriction_enzyme_cleavage_junction A restriction enzyme cleavage site whereby only one strand is cut. http://purl.obolibrary.org/obo/SO_0001696 experimentally_defined_binding_region http://purl.obolibrary.org/obo/SO_0001410 experimental_feature A region that has been implicated in binding although the exact coordinates of binding may be unknown. http://purl.obolibrary.org/obo/SO_0001697 ChIP_seq_region http://purl.obolibrary.org/obo/SO_0001696 experimentally_defined_binding_region A region of sequence identified by CHiP seq technology to contain a protein binding site. http://purl.obolibrary.org/obo/SO_0001698 ASPE_primer http://purl.obolibrary.org/obo/SO_0000112 primer "A primer containing an SNV at the 3' end for accurate genotyping. http://purl.obolibrary.org/obo/SO_0001699 dCAPS_primer http://purl.obolibrary.org/obo/SO_0000112 primer A primer with one or more mismatches to the DNA template corresponding to a position within a restriction enzyme recognition site. http://purl.obolibrary.org/obo/SO_0001700 histone_modification http://purl.obolibrary.org/obo/SO_0001089 post_translationally_modified_region Histone modification is a post translationally modified region whereby residues of the histone protein are modified by methylation, acetylation, phosphorylation, ubiquitination, sumoylation, citrullination, or ADP-ribosylation. http://purl.obolibrary.org/obo/SO_0001701 histone_methylation_site http://purl.obolibrary.org/obo/SO_0001700 histone_modification A histone modification site where the modification is the methylation of the residue. http://purl.obolibrary.org/obo/SO_0001702 histone_acetylation_site http://purl.obolibrary.org/obo/SO_0001700 histone_modification A histone modification where the modification is the acylation of the residue. http://purl.obolibrary.org/obo/SO_0001703 H3K9_acetylation_site http://purl.obolibrary.org/obo/SO_0001973 histone_3_acetylation_site A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is acetylated. http://purl.obolibrary.org/obo/SO_0001704 H3K14_acetylation_site http://purl.obolibrary.org/obo/SO_0001973 histone_3_acetylation_site A kind of histone modification site, whereby the 14th residue (a lysine), from the start of the H3 histone protein is acetylated. http://purl.obolibrary.org/obo/SO_0001705 H3K4_monomethylation_site http://purl.obolibrary.org/obo/SO_0001734 H3K4_methylation_site A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is mono-methylated. http://purl.obolibrary.org/obo/SO_0001706 H3K4_trimethylation http://purl.obolibrary.org/obo/SO_0001734 H3K4_methylation_site A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 protein is tri-methylated. http://purl.obolibrary.org/obo/SO_0001707 H3K9_trimethylation_site http://purl.obolibrary.org/obo/SO_0001736 H3K9_methylation_site A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is tri-methylated. http://purl.obolibrary.org/obo/SO_0001708 H3K27_monomethylation_site http://purl.obolibrary.org/obo/SO_0001732 H3K27_methylation_site A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is mono-methylated. http://purl.obolibrary.org/obo/SO_0001709 H3K27_trimethylation_site http://purl.obolibrary.org/obo/SO_0001732 H3K27_methylation_site A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is tri-methylated. http://purl.obolibrary.org/obo/SO_0001710 H3K79_monomethylation_site http://purl.obolibrary.org/obo/SO_0001735 H3K79_methylation_site A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is mono- methylated. http://purl.obolibrary.org/obo/SO_0001711 H3K79_dimethylation_site http://purl.obolibrary.org/obo/SO_0001735 H3K79_methylation_site A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is di-methylated. http://purl.obolibrary.org/obo/SO_0001712 H3K79_trimethylation_site http://purl.obolibrary.org/obo/SO_0001735 H3K79_methylation_site A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is tri-methylated. http://purl.obolibrary.org/obo/SO_0001713 H4K20_monomethylation_site http://purl.obolibrary.org/obo/SO_0001701 histone_methylation_site A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H4histone protein is mono-methylated. http://purl.obolibrary.org/obo/SO_0001714 H2BK5_monomethylation_site http://purl.obolibrary.org/obo/SO_0001701 histone_methylation_site A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2B protein is methylated. http://purl.obolibrary.org/obo/SO_0001716 histone_ubiqitination_site http://purl.obolibrary.org/obo/SO_0001700 histone_modification A histone modification site where ubiquitin may be added. http://purl.obolibrary.org/obo/SO_0001717 H2B_ubiquitination_site http://purl.obolibrary.org/obo/SO_0001716 histone_ubiqitination_site A histone modification site on H2B where ubiquitin may be added. http://purl.obolibrary.org/obo/SO_0001718 H3K18_acetylation_site http://purl.obolibrary.org/obo/SO_0001973 histone_3_acetylation_site A kind of histone modification site, whereby the 18th residue (a lysine), from the start of the H3 histone protein is acetylated. http://purl.obolibrary.org/obo/SO_0001719 H3K23_acetylation_site http://purl.obolibrary.org/obo/SO_0001973 histone_3_acetylation_site A kind of histone modification, whereby the 23rd residue (a lysine), from the start of the H3 histone protein is acetylated. http://purl.obolibrary.org/obo/SO_0001722 H3K36_monomethylation_site http://purl.obolibrary.org/obo/SO_0001733 H3K36_methylation_site A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is mono-methylated. http://purl.obolibrary.org/obo/SO_0001723 H3K36_dimethylation_site http://purl.obolibrary.org/obo/SO_0001733 H3K36_methylation_site A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is dimethylated. http://purl.obolibrary.org/obo/SO_0001724 H3K36_trimethylation_site http://purl.obolibrary.org/obo/SO_0001733 H3K36_methylation_site A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is tri-methylated. http://purl.obolibrary.org/obo/SO_0001725 H3K4_dimethylation_site http://purl.obolibrary.org/obo/SO_0001734 H3K4_methylation_site A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is di-methylated. http://purl.obolibrary.org/obo/SO_0001726 H3K27_dimethylation_site http://purl.obolibrary.org/obo/SO_0001732 H3K27_methylation_site A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is di-methylated. http://purl.obolibrary.org/obo/SO_0001727 H3K9_monomethylation_site http://purl.obolibrary.org/obo/SO_0001736 H3K9_methylation_site A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is mono-methylated. http://purl.obolibrary.org/obo/SO_0001728 H3K9_dimethylation_site http://purl.obolibrary.org/obo/SO_0001736 H3K9_methylation_site A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein may be dimethylated. http://purl.obolibrary.org/obo/SO_0001729 H4K16_acetylation_site http://purl.obolibrary.org/obo/SO_0001972 histone_4_acetylation_site A kind of histone modification site, whereby the 16th residue (a lysine), from the start of the H4 histone protein is acetylated. http://purl.obolibrary.org/obo/SO_0001730 H4K5_acetylation_site http://purl.obolibrary.org/obo/SO_0001972 histone_4_acetylation_site A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H4 histone protein is acetylated. http://purl.obolibrary.org/obo/SO_0001731 H4K8_acetylation_site http://purl.obolibrary.org/obo/SO_0001972 histone_4_acetylation_site A kind of histone modification site, whereby the 8th residue (a lysine), from the start of the H4 histone protein is acetylated. http://purl.obolibrary.org/obo/SO_0001732 H3K27_methylation_site http://purl.obolibrary.org/obo/SO_0001701 histone_methylation_site A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is methylated. http://purl.obolibrary.org/obo/SO_0001733 H3K36_methylation_site http://purl.obolibrary.org/obo/SO_0001701 histone_methylation_site A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is methylated. http://purl.obolibrary.org/obo/SO_0001734 H3K4_methylation_site http://purl.obolibrary.org/obo/SO_0001701 histone_methylation_site A kind of histone modification, whereby the 4th residue (a lysine), from the start of the H3 protein is methylated. http://purl.obolibrary.org/obo/SO_0001735 H3K79_methylation_site http://purl.obolibrary.org/obo/SO_0001701 histone_methylation_site A kind of histone modification site, whereby the 79th residue (a lysine), from the start of the H3 histone protein is methylated. http://purl.obolibrary.org/obo/SO_0001736 H3K9_methylation_site http://purl.obolibrary.org/obo/SO_0001701 histone_methylation_site A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H3 histone protein is methylated. http://purl.obolibrary.org/obo/SO_0001737 histone_acylation_region http://purl.obolibrary.org/obo/SO_0001700 histone_modification A histone modification, whereby the histone protein is acylated at multiple sites in a region. http://purl.obolibrary.org/obo/SO_0001738 H4K_acylation_region http://purl.obolibrary.org/obo/SO_0001737 histone_acylation_region A region of the H4 histone whereby multiple lysines are acylated. http://purl.obolibrary.org/obo/SO_0001748 SL3_acceptor_site http://purl.obolibrary.org/obo/SO_0000709 SL2_acceptor_site A SL2_acceptor_site which appends the SL3 RNA leader sequence to the 5' end of an mRNA. SL3 acceptor sites occur in genes in internal segments of polycistronic transcripts. http://purl.obolibrary.org/obo/SO_0001749 SL4_acceptor_site http://purl.obolibrary.org/obo/SO_0000709 SL2_acceptor_site A SL2_acceptor_site which appends the SL4 RNA leader sequence to the 5' end of an mRNA. SL4 acceptor sites occur in genes in internal segments of polycistronic transcripts. http://purl.obolibrary.org/obo/SO_0001750 SL5_acceptor_site http://purl.obolibrary.org/obo/SO_0000709 SL2_acceptor_site A SL2_acceptor_site which appends the SL5 RNA leader sequence to the 5' end of an mRNA. SL5 acceptor sites occur in genes in internal segments of polycistronic transcripts. http://purl.obolibrary.org/obo/SO_0001751 SL6_acceptor_site http://purl.obolibrary.org/obo/SO_0000709 SL2_acceptor_site A SL2_acceptor_site which appends the SL6 RNA leader sequence to the 5' end of an mRNA. SL6 acceptor sites occur in genes in internal segments of polycistronic transcripts. http://purl.obolibrary.org/obo/SO_0001752 SL7_acceptor_site http://purl.obolibrary.org/obo/SO_0000709 SL2_acceptor_site A SL2_acceptor_site which appends the SL7 RNA leader sequence to the 5' end of an mRNA. SL7 acceptor sites occur in genes in internal segments of polycistronic transcripts. http://purl.obolibrary.org/obo/SO_0001753 SL8_acceptor_site http://purl.obolibrary.org/obo/SO_0000709 SL2_acceptor_site A SL2_acceptor_site which appends the SL8 RNA leader sequence to the 5' end of an mRNA. SL8 acceptor sites occur in genes in internal segments of polycistronic transcripts. http://purl.obolibrary.org/obo/SO_0001754 SL9_acceptor_site http://purl.obolibrary.org/obo/SO_0000709 SL2_acceptor_site A SL2_acceptor_site which appends the SL9 RNA leader sequence to the 5' end of an mRNA. SL9 acceptor sites occur in genes in internal segments of polycistronic transcripts. http://purl.obolibrary.org/obo/SO_0001755 SL10_acceptor_site http://purl.obolibrary.org/obo/SO_0000709 SL2_acceptor_site A SL2_acceptor_site which appends the SL10 RNA leader sequence to the 5' end of an mRNA. SL10 acceptor sites occur in genes in internal segments of polycistronic transcripts. http://purl.obolibrary.org/obo/SO_0001756 SL11_acceptor_site http://purl.obolibrary.org/obo/SO_0000709 SL2_acceptor_site A SL2_acceptor_site which appends the SL11 RNA leader sequence to the 5' end of an mRNA. SL11 acceptor sites occur in genes in internal segments of polycistronic transcripts. http://purl.obolibrary.org/obo/SO_0001757 SL12_acceptor_site http://purl.obolibrary.org/obo/SO_0000709 SL2_acceptor_site A SL2_acceptor_site which appends the SL12 RNA leader sequence to the 5' end of an mRNA. SL12 acceptor sites occur in genes in internal segments of polycistronic transcripts. http://purl.obolibrary.org/obo/SO_0001758 duplicated_pseudogene http://purl.obolibrary.org/obo/SO_0001760 non_processed_pseudogene A pseudogene that arose via gene duplication. Generally duplicated pseudogenes have the same structure as the original gene, including intron-exon structure and some regulatory sequence. http://purl.obolibrary.org/obo/SO_0001759 unitary_pseudogene http://purl.obolibrary.org/obo/SO_0001760 non_processed_pseudogene A pseudogene, deactivated from original state by mutation, fixed in a population,where the ortholog in a reference species such as mouse remains functional. http://purl.obolibrary.org/obo/SO_0001760 non_processed_pseudogene http://purl.obolibrary.org/obo/SO_0000336 pseudogene A pseudogene that arose from a means other than retrotransposition. A pseudogene created via genomic duplication of a functional protein-coding parent gene followed by accumulation of deleterious mutations. http://purl.obolibrary.org/obo/SO_0001761 variant_quality http://purl.obolibrary.org/obo/SO_0000400 sequence_attribute A dependent entity that inheres in a bearer, a sequence variant. http://purl.obolibrary.org/obo/SO_0001762 variant_origin http://purl.obolibrary.org/obo/SO_0001761 variant_quality A quality inhering in a variant by virtue of its origin. http://purl.obolibrary.org/obo/SO_0001763 variant_frequency http://purl.obolibrary.org/obo/SO_0001761 variant_quality A physical quality which inheres to the variant by virtue of the number instances of the variant within a population. http://purl.obolibrary.org/obo/SO_0001764 unique_variant http://purl.obolibrary.org/obo/SO_0001763 variant_frequency A physical quality which inheres to the variant by virtue of the number instances of the variant within a population. http://purl.obolibrary.org/obo/SO_0001765 rare_variant http://purl.obolibrary.org/obo/SO_0001763 variant_frequency When a variant from the genomic sequence is rarely found in the general population. The threshold for 'rare' varies between studies. http://purl.obolibrary.org/obo/SO_0001766 polymorphic_variant http://purl.obolibrary.org/obo/SO_0001763 variant_frequency A variant that affects one of several possible alleles at that location, such as the major histocompatibility complex (MHC) genes. http://purl.obolibrary.org/obo/SO_0001767 common_variant http://purl.obolibrary.org/obo/SO_0001763 variant_frequency When a variant from the genomic sequence is commonly found in the general population. http://purl.obolibrary.org/obo/SO_0001768 fixed_variant http://purl.obolibrary.org/obo/SO_0001763 variant_frequency When a variant has become fixed in the population so that it is now the only variant. http://purl.obolibrary.org/obo/SO_0001769 variant_phenotype http://purl.obolibrary.org/obo/SO_0001761 variant_quality A quality inhering in a variant by virtue of its phenotype. http://purl.obolibrary.org/obo/SO_0001770 benign_variant http://purl.obolibrary.org/obo/SO_0001769 variant_phenotype A variant that does not affect the function of the gene or cause disease. http://purl.obolibrary.org/obo/SO_0001771 disease_associated_variant http://purl.obolibrary.org/obo/SO_0001769 variant_phenotype A variant that has been found to be associated with disease. http://purl.obolibrary.org/obo/SO_0001772 disease_causing_variant http://purl.obolibrary.org/obo/SO_0001769 variant_phenotype A variant that has been found to cause disease. http://purl.obolibrary.org/obo/SO_0001773 lethal_variant http://purl.obolibrary.org/obo/SO_0002218 functionally_abnormal A sequence variant where the mutated gene product does not allow for one or more basic functions necessary for survival. http://purl.obolibrary.org/obo/SO_0001774 quantitative_variant http://purl.obolibrary.org/obo/SO_0001769 variant_phenotype A variant within a gene that contributes to a quantitative trait such as height or weight. http://purl.obolibrary.org/obo/SO_0001775 maternal_variant http://purl.obolibrary.org/obo/SO_0001762 variant_origin A variant in the genetic material inherited from the mother. http://purl.obolibrary.org/obo/SO_0001776 paternal_variant http://purl.obolibrary.org/obo/SO_0001762 variant_origin A variant in the genetic material inherited from the father. http://purl.obolibrary.org/obo/SO_0001777 somatic_variant http://purl.obolibrary.org/obo/SO_0001762 variant_origin A variant that has arisen after splitting of the embryo, resulting in the variant being found in only some of the tissues or cells of the body. http://purl.obolibrary.org/obo/SO_0001778 germline_variant http://purl.obolibrary.org/obo/SO_0001762 variant_origin A variant present in the embryo that is carried by every cell in the body. http://purl.obolibrary.org/obo/SO_0001779 pedigree_specific_variant http://purl.obolibrary.org/obo/SO_0001762 variant_origin A variant that is found only by individuals that belong to the same pedigree. http://purl.obolibrary.org/obo/SO_0001780 population_specific_variant http://purl.obolibrary.org/obo/SO_0001762 variant_origin A variant found within only speficic populations. http://purl.obolibrary.org/obo/SO_0001781 de_novo_variant http://purl.obolibrary.org/obo/SO_0001762 variant_origin A variant arising in the offspring that is not found in either of the parents. http://purl.obolibrary.org/obo/SO_0001782 TF_binding_site_variant http://purl.obolibrary.org/obo/SO_0001566 regulatory_region_variant A sequence variant located within a transcription factor binding site. http://purl.obolibrary.org/obo/SO_0001786 loss_of_heterozygosity http://purl.obolibrary.org/obo/SO_0002218 functionally_abnormal A functional variant whereby the sequence alteration causes a loss of function of one allele of a gene. http://purl.obolibrary.org/obo/SO_0001787 splice_donor_5th_base_variant http://purl.obolibrary.org/obo/SO_0001629 splice_site_variant A sequence variant that causes a change at the 5th base pair after the start of the intron in the orientation of the transcript. http://purl.obolibrary.org/obo/SO_0001788 U_box http://purl.obolibrary.org/obo/SO_0000330 conserved_region An U-box is a conserved T-rich region upstream of a retroviral polypurine tract that is involved in PPT primer creation during reverse transcription. http://purl.obolibrary.org/obo/SO_0001790 paired_end_fragment http://purl.obolibrary.org/obo/SO_0000143 assembly_component An assembly region that has been sequenced from both ends resulting in a read_pair (mate_pair). http://purl.obolibrary.org/obo/SO_0001791 exon_variant http://purl.obolibrary.org/obo/SO_0001576 transcript_variant A sequence variant that changes exon sequence. http://purl.obolibrary.org/obo/SO_0001792 non_coding_transcript_exon_variant http://purl.obolibrary.org/obo/SO_0001791 exon_variant A sequence variant that changes non-coding exon sequence in a non-coding transcript. http://purl.obolibrary.org/obo/SO_0001793 clone_end http://purl.obolibrary.org/obo/SO_0000150 read A read from an end of the clone sequence. http://purl.obolibrary.org/obo/SO_0001794 point_centromere http://purl.obolibrary.org/obo/SO_0000577 centromere A point centromere is a relatively small centromere (about 125 bp DNA) in discrete sequence, found in some yeast including S. cerevisiae. http://purl.obolibrary.org/obo/SO_0001800 tasiRNA http://purl.obolibrary.org/obo/SO_0000655 ncRNA The sequence of a 21 nucleotide double stranded, polyadenylated non coding RNA, transcribed from the TAS gene. http://purl.obolibrary.org/obo/SO_0001801 tasiRNA_primary_transcript http://purl.obolibrary.org/obo/SO_0000483 nc_primary_transcript A primary transcript encoding a tasiRNA. http://purl.obolibrary.org/obo/SO_0001802 increased_polyadenylation_variant http://purl.obolibrary.org/obo/SO_0001545 polyadenylation_variant A transcript processing variant whereby polyadenylation of the encoded transcript is increased with respect to the reference. http://purl.obolibrary.org/obo/SO_0001803 decreased_polyadenylation_variant http://purl.obolibrary.org/obo/SO_0001545 polyadenylation_variant A transcript processing variant whereby polyadenylation of the encoded transcript is decreased with respect to the reference. http://purl.obolibrary.org/obo/SO_0001804 DDB_box http://purl.obolibrary.org/obo/SO_0001093 protein_protein_contact A conserved polypeptide motif that mediates protein-protein interaction and defines adaptor proteins for DDB1/cullin 4 ubiquitin ligases. http://purl.obolibrary.org/obo/SO_0001805 destruction_box http://purl.obolibrary.org/obo/SO_0100017 polypeptide_conserved_motif A conserved polypeptide motif that can be recognized by both Fizzy/Cdc20- and FZR/Cdh1-activated anaphase-promoting complex/cyclosome (APC/C) and targets a protein for ubiquitination and subsequent degradation by the APC/C. The consensus sequence is RXXLXXXXN. http://purl.obolibrary.org/obo/SO_0001806 ER_retention_signal http://purl.obolibrary.org/obo/SO_0001527 peptide_localization_signal A C-terminal tetrapeptide motif that mediates retention of a protein in (or retrieval to) the endoplasmic reticulum. In mammals the sequence is KDEL, and in fungi HDEL or DDEL. http://purl.obolibrary.org/obo/SO_0001807 KEN_box http://purl.obolibrary.org/obo/SO_0100017 polypeptide_conserved_motif A conserved polypeptide motif that can be recognized by FZR/Cdh1-activated anaphase-promoting complex/cyclosome (APC/C) and targets a protein for ubiquitination and subsequent degradation by the APC/C. The consensus sequence is KENXXXN. http://purl.obolibrary.org/obo/SO_0001808 mitochondrial_targeting_signal http://purl.obolibrary.org/obo/SO_0001527 peptide_localization_signal A polypeptide region that targets a polypeptide to the mitochondrion. http://purl.obolibrary.org/obo/SO_0001809 signal_anchor http://purl.obolibrary.org/obo/SO_0000418 signal_peptide A signal sequence that is not cleaved from the polypeptide. Anchors a Type II membrane protein to the membrane. http://purl.obolibrary.org/obo/SO_0001810 PIP_box http://purl.obolibrary.org/obo/SO_0001093 protein_protein_contact A polypeptide region that mediates binding to PCNA. The consensus sequence is QXX(hh)XX(aa), where (h) denotes residues with moderately hydrophobic side chains and (a) denotes residues with highly hydrophobic aromatic side chains. http://purl.obolibrary.org/obo/SO_0001811 phosphorylation_site http://purl.obolibrary.org/obo/SO_0001089 post_translationally_modified_region A post-translationally modified region in which residues of the protein are modified by phosphorylation. http://purl.obolibrary.org/obo/SO_0001812 transmembrane_helix http://purl.obolibrary.org/obo/SO_0001114 peptide_helix A region that traverses the lipid bilayer and adopts a helical secondary structure. http://purl.obolibrary.org/obo/SO_0001813 vacuolar_sorting_signal http://purl.obolibrary.org/obo/SO_0001527 peptide_localization_signal A polypeptide region that targets a polypeptide to the vacuole. http://purl.obolibrary.org/obo/SO_0001814 coding_variant_quality http://purl.obolibrary.org/obo/SO_0001761 variant_quality An attribute of a coding genomic variant. http://purl.obolibrary.org/obo/SO_0001815 synonymous http://purl.obolibrary.org/obo/SO_0001814 coding_variant_quality A variant that does not lead to any change in the amino acid sequence. http://purl.obolibrary.org/obo/SO_0001816 non_synonymous http://purl.obolibrary.org/obo/SO_0001814 coding_variant_quality A variant that leads to the change of an amino acid within the protein. http://purl.obolibrary.org/obo/SO_0001817 inframe http://purl.obolibrary.org/obo/SO_0000863 mRNA_attribute An attribute describing a sequence that contains a mutation involving the deletion or insertion of one or more bases, where this number is divisible by 3. http://purl.obolibrary.org/obo/SO_0001818 protein_altering_variant http://purl.obolibrary.org/obo/SO_0001580 coding_sequence_variant A sequence_variant which is predicted to change the protein encoded in the coding sequence. http://purl.obolibrary.org/obo/SO_0001819 synonymous_variant http://purl.obolibrary.org/obo/SO_0001580 coding_sequence_variant A sequence variant where there is no resulting change to the encoded amino acid. http://purl.obolibrary.org/obo/SO_0001820 inframe_indel http://purl.obolibrary.org/obo/SO_0001650 inframe_variant A coding sequence variant where the change does not alter the frame of the transcript. http://purl.obolibrary.org/obo/SO_0001821 inframe_insertion http://purl.obolibrary.org/obo/SO_0001908 internal_feature_elongation An inframe non synonymous variant that inserts bases into in the coding sequence. http://purl.obolibrary.org/obo/SO_0001822 inframe_deletion http://purl.obolibrary.org/obo/SO_0001906 feature_truncation An inframe non synonymous variant that deletes bases from the coding sequence. http://purl.obolibrary.org/obo/SO_0001823 conservative_inframe_insertion http://purl.obolibrary.org/obo/SO_0001821 inframe_insertion An inframe increase in cds length that inserts one or more codons into the coding sequence between existing codons. http://purl.obolibrary.org/obo/SO_0001824 disruptive_inframe_insertion http://purl.obolibrary.org/obo/SO_0001821 inframe_insertion An inframe increase in cds length that inserts one or more codons into the coding sequence within an existing codon. http://purl.obolibrary.org/obo/SO_0001825 conservative_inframe_deletion http://purl.obolibrary.org/obo/SO_0001822 inframe_deletion An inframe decrease in cds length that deletes one or more entire codons from the coding sequence but does not change any remaining codons. http://purl.obolibrary.org/obo/SO_0001826 disruptive_inframe_deletion http://purl.obolibrary.org/obo/SO_0001822 inframe_deletion An inframe decrease in cds length that deletes bases from the coding sequence starting within an existing codon. http://purl.obolibrary.org/obo/SO_0001827 mRNA_read http://purl.obolibrary.org/obo/SO_0000150 read A sequencer read of an mRNA substrate. http://purl.obolibrary.org/obo/SO_0001828 genomic_DNA_read http://purl.obolibrary.org/obo/SO_0000150 read A sequencer read of a genomic DNA substrate. http://purl.obolibrary.org/obo/SO_0001829 mRNA_contig http://purl.obolibrary.org/obo/SO_0000149 contig A contig composed of mRNA_reads. http://purl.obolibrary.org/obo/SO_0001830 AFLP_fragment http://purl.obolibrary.org/obo/SO_0000006 PCR_product A PCR product obtained by applying the AFLP technique, based on a restriction enzyme digestion of genomic DNA and an amplification of the resulting fragments. http://purl.obolibrary.org/obo/SO_0001831 protein_hmm_match http://purl.obolibrary.org/obo/SO_0000349 protein_match A match to a protein HMM such as pfam. http://purl.obolibrary.org/obo/SO_0001832 immunoglobulin_region http://purl.obolibrary.org/obo/SO_0000839 polypeptide_region A region of immunoglobulin sequence, either constant or variable. http://purl.obolibrary.org/obo/SO_0001833 V_region http://purl.obolibrary.org/obo/SO_0001832 immunoglobulin_region The variable region of an immunoglobulin polypeptide sequence. http://purl.obolibrary.org/obo/SO_0001834 C_region http://purl.obolibrary.org/obo/SO_0001832 immunoglobulin_region The constant region of an immunoglobulin polypeptide sequence. http://purl.obolibrary.org/obo/SO_0001835 N_region http://purl.obolibrary.org/obo/SO_0000301 vertebrate_immune_system_gene_recombination_feature Extra nucleotides inserted between rearranged immunoglobulin segments. http://purl.obolibrary.org/obo/SO_0001836 S_region http://purl.obolibrary.org/obo/SO_0000301 vertebrate_immune_system_gene_recombination_feature The switch region of immunoglobulin heavy chains; it is involved in the rearrangement of heavy chain DNA leading to the expression of a different immunoglobulin classes from the same B-cell. http://purl.obolibrary.org/obo/SO_0001837 mobile_element_insertion http://purl.obolibrary.org/obo/SO_0000667 insertion A kind of insertion where the inserted sequence is a mobile element. http://purl.obolibrary.org/obo/SO_0001838 novel_sequence_insertion http://purl.obolibrary.org/obo/SO_0000667 insertion An insertion the sequence of which cannot be mapped to the reference genome. http://purl.obolibrary.org/obo/SO_0001839 CSL_response_element http://purl.obolibrary.org/obo/SO_0001659 promoter_element A promoter element with consensus sequence GTGRGAA, bound by CSL (CBF1/RBP-JK/Suppressor of Hairless/LAG-1) transcription factors. http://purl.obolibrary.org/obo/SO_0001840 GATA_box http://purl.obolibrary.org/obo/SO_0000235 TF_binding_site A GATA transcription factor element containing the consensus sequence WGATAR (in which W indicates A/T and R indicates A/G). http://purl.obolibrary.org/obo/SO_0001841 polymorphic_pseudogene http://purl.obolibrary.org/obo/SO_0000336 pseudogene A pseudogene in the reference genome, though known to be intact in the genomes of other individuals of the same species. The annotation process has confirmed that the pseudogenisation event is not a genomic sequencing error. http://purl.obolibrary.org/obo/SO_0001842 AP_1_binding_site http://purl.obolibrary.org/obo/SO_0001659 promoter_element A promoter element with consensus sequence TGACTCA, bound by AP-1 and related transcription factors. http://purl.obolibrary.org/obo/SO_0001844 CuRE http://purl.obolibrary.org/obo/SO_0001659 promoter_element A promoter element bound by copper ion-sensing transcription factors such as S. cerevisiae Mac1p or S. pombe Cuf1; the consensus sequence is HTHNNGCTGD (more specifically TTTGCKCR in budding yeast). http://purl.obolibrary.org/obo/SO_0001845 DRE http://purl.obolibrary.org/obo/SO_0001659 promoter_element A promoter element with consensus sequence CGWGGWNGMM, bound by transcription factors related to RecA and found in promoters of genes expressed following several types of DNA damage or inhibition of DNA synthesis. http://purl.obolibrary.org/obo/SO_0001846 FLEX_element http://purl.obolibrary.org/obo/SO_0001659 promoter_element A promoter element that has consensus sequence GTAAACAAACAAAM and contains a heptameric core GTAAACA, bound by transcription factors with a forkhead DNA-binding domain. http://purl.obolibrary.org/obo/SO_0001847 forkhead_motif http://purl.obolibrary.org/obo/SO_0001659 promoter_element A promoter element with consensus sequence TTTRTTTACA, bound by transcription factors with a forkhead DNA-binding domain. http://purl.obolibrary.org/obo/SO_0001848 homol_D_box http://purl.obolibrary.org/obo/SO_0001660 core_eukaryotic_promoter_element A core promoter element that has the consensus sequence CAGTCACA (or its inverted form TGTGACTG), and plays the role of a TATA box in promoters that do not contain a canonical TATA sequence. http://purl.obolibrary.org/obo/SO_0001849 homol_E_box http://purl.obolibrary.org/obo/SO_0001659 promoter_element A core promoter element that has the consensus sequence ACCCTACCCT (or its inverted form AGGGTAGGGT), and is found near the homol D box in some promoters that use a homol D box instead of a canonical TATA sequence. http://purl.obolibrary.org/obo/SO_0001851 iron_repressed_GATA_element http://purl.obolibrary.org/obo/SO_0001840 GATA_box A GATA promoter element with consensus sequence WGATAA, found in promoters of genes repressed in the presence of iron. http://purl.obolibrary.org/obo/SO_0001852 mating_type_M_box http://purl.obolibrary.org/obo/SO_0001659 promoter_element A promoter element with consensus sequence ACAAT, found in promoters of mating type M-specific genes in fission yeast and bound by the transcription factor Mat1-Mc. http://purl.obolibrary.org/obo/SO_0001853 androgen_response_element http://purl.obolibrary.org/obo/SO_0000713 DNA_motif A non-palindromic sequence found in the promoters of genes whose expression is regulated in response to androgen. http://purl.obolibrary.org/obo/SO_0001854 smFISH_probe http://purl.obolibrary.org/obo/SO_0000051 probe A smFISH is a probe that binds RNA in a single molecule in situ hybridization experiment. http://purl.obolibrary.org/obo/SO_0001856 CCAAT_motif http://purl.obolibrary.org/obo/SO_0001659 promoter_element A promoter element with consensus sequence CCAAT, bound by a protein complex that represses transcription in response to low iron levels. http://purl.obolibrary.org/obo/SO_0001857 Ace2_UAS http://purl.obolibrary.org/obo/SO_0001659 promoter_element A promoter element with consensus sequence CCAGCC, bound by the fungal transcription factor Ace2. http://purl.obolibrary.org/obo/SO_0001859 STREP_motif http://purl.obolibrary.org/obo/SO_0001659 promoter_element A promoter element with consensus sequence CCCCTC, bound by the PKA-responsive zinc finger transcription factor Rst2. http://purl.obolibrary.org/obo/SO_0001860 rDNA_intergenic_spacer_element http://purl.obolibrary.org/obo/SO_0000713 DNA_motif A DNA motif that contains a core consensus sequence AGGTAAGGGTAATGCAC, is found in the intergenic regions of rDNA repeats, and is bound by an RNA polymerase I transcription termination factor (e.g. S. pombe Reb1). The S. pombe telomeric repeat consensus is TTAC(0-1)A(0-1)G(1-8). http://purl.obolibrary.org/obo/SO_0001862 GT_dinucleotide_repeat http://purl.obolibrary.org/obo/SO_0000290 dinucleotide_repeat_microsatellite_feature A dinucleotide repeat region composed of GT repeating elements. http://purl.obolibrary.org/obo/SO_0001863 GTT_trinucleotide_repeat http://purl.obolibrary.org/obo/SO_0000291 trinucleotide_repeat_microsatellite_feature A trinucleotide repeat region composed of GTT repeating elements. http://purl.obolibrary.org/obo/SO_0001864 Sap1_recognition_motif http://purl.obolibrary.org/obo/SO_0000713 DNA_motif A DNA motif to which the S. pombe Sap1 protein binds. The consensus sequence is 5'-TARGCAGNTNYAACGMG-3'; it is found at the mating type locus, where it is important for mating type switching, and at replication fork barriers in rDNA repeats. http://purl.obolibrary.org/obo/SO_0001865 CDRE_motif http://purl.obolibrary.org/obo/SO_0001659 promoter_element An RNA polymerase II promoter element found in the promoters of genes regulated by calcineurin. The consensus sequence is GNGGCKCA. http://purl.obolibrary.org/obo/SO_0001866 BAC_read_contig http://purl.obolibrary.org/obo/SO_0000149 contig A contig of BAC reads. http://purl.obolibrary.org/obo/SO_0001870 enhancerRNA http://purl.obolibrary.org/obo/SO_0000655 ncRNA A short ncRNA that is transcribed from an enhancer. May have a regulatory function. http://purl.obolibrary.org/obo/SO_0001873 interchromosomal_breakpoint http://purl.obolibrary.org/obo/SO_0001021 chromosome_breakpoint A rearrangement breakpoint between two different chromosomes. http://purl.obolibrary.org/obo/SO_0001874 intrachromosomal_breakpoint http://purl.obolibrary.org/obo/SO_0001021 chromosome_breakpoint A rearrangement breakpoint within the same chromosome. http://purl.obolibrary.org/obo/SO_0001875 unassigned_supercontig http://purl.obolibrary.org/obo/SO_0000148 supercontig A supercontig that is not been assigned to any ultracontig during a genome assembly project. http://purl.obolibrary.org/obo/SO_0001876 partial_genomic_sequence_assembly http://purl.obolibrary.org/obo/SO_0000353 sequence_assembly A partial DNA sequence assembly of a chromosome or full genome, which contains gaps that are filled with N's. http://purl.obolibrary.org/obo/SO_0001877 lncRNA http://purl.obolibrary.org/obo/SO_0000655 ncRNA A non-coding RNA generally longer than 200 nucleotides that cannot be classified as any other ncRNA subtype. Similar to mRNAs, lncRNAs are mainly transcribed by RNA polymerase II, are often capped by 7-methyl guanosine at their 5' ends, polyadenylated at their 3' ends and may be spliced. http://purl.obolibrary.org/obo/SO_0001878 feature_variant http://purl.obolibrary.org/obo/SO_0001537 structural_variant A sequence variant that falls entirely or partially within a genomic feature. http://purl.obolibrary.org/obo/SO_0001879 feature_ablation http://purl.obolibrary.org/obo/SO_0001537 structural_variant A sequence variant, caused by an alteration of the genomic sequence, where the deletion, is greater than the extent of the underlying genomic features. http://purl.obolibrary.org/obo/SO_0001880 feature_amplification http://purl.obolibrary.org/obo/SO_0001537 structural_variant A sequence variant, caused by an alteration of the genomic sequence, where the structural change, an amplification of sequence, is greater than the extent of the underlying genomic features. http://purl.obolibrary.org/obo/SO_0001881 feature_translocation http://purl.obolibrary.org/obo/SO_0001537 structural_variant A sequence variant, caused by an alteration of the genomic sequence, where the structural change, a translocation, is greater than the extent of the underlying genomic features. http://purl.obolibrary.org/obo/SO_0001882 feature_fusion http://purl.obolibrary.org/obo/SO_0001537 structural_variant A sequence variant, caused by an alteration of the genomic sequence, where a deletion fuses genomic features. http://purl.obolibrary.org/obo/SO_0001883 transcript_translocation http://purl.obolibrary.org/obo/SO_0001881 feature_translocation A feature translocation where the region contains a transcript. http://purl.obolibrary.org/obo/SO_0001884 regulatory_region_translocation http://purl.obolibrary.org/obo/SO_0001881 feature_translocation A feature translocation where the region contains a regulatory region. http://purl.obolibrary.org/obo/SO_0001885 TFBS_translocation http://purl.obolibrary.org/obo/SO_0001884 regulatory_region_translocation A feature translocation where the region contains a transcription factor binding site. http://purl.obolibrary.org/obo/SO_0001886 transcript_fusion http://purl.obolibrary.org/obo/SO_0001882 feature_fusion A feature fusion where the deletion brings together transcript regions. http://purl.obolibrary.org/obo/SO_0001887 regulatory_region_fusion http://purl.obolibrary.org/obo/SO_0001882 feature_fusion A feature fusion where the deletion brings together regulatory regions. http://purl.obolibrary.org/obo/SO_0001888 TFBS_fusion http://purl.obolibrary.org/obo/SO_0001887 regulatory_region_fusion A fusion where the deletion brings together transcription factor binding sites. http://purl.obolibrary.org/obo/SO_0001889 transcript_amplification http://purl.obolibrary.org/obo/SO_0001880 feature_amplification A feature amplification of a region containing a transcript. http://purl.obolibrary.org/obo/SO_0001890 transcript_regulatory_region_fusion http://purl.obolibrary.org/obo/SO_0001882 feature_fusion A feature fusion where the deletion brings together a regulatory region and a transcript region. http://purl.obolibrary.org/obo/SO_0001891 regulatory_region_amplification http://purl.obolibrary.org/obo/SO_0001880 feature_amplification A feature amplification of a region containing a regulatory region. http://purl.obolibrary.org/obo/SO_0001892 TFBS_amplification http://purl.obolibrary.org/obo/SO_0001891 regulatory_region_amplification A feature amplification of a region containing a transcription factor binding site. http://purl.obolibrary.org/obo/SO_0001893 transcript_ablation http://purl.obolibrary.org/obo/SO_0001879 feature_ablation A feature ablation whereby the deleted region includes a transcript feature. http://purl.obolibrary.org/obo/SO_0001894 regulatory_region_ablation http://purl.obolibrary.org/obo/SO_0001879 feature_ablation A feature ablation whereby the deleted region includes a regulatory region. http://purl.obolibrary.org/obo/SO_0001895 TFBS_ablation http://purl.obolibrary.org/obo/SO_0001894 regulatory_region_ablation A feature ablation whereby the deleted region includes a transcription factor binding site. http://purl.obolibrary.org/obo/SO_0001898 dg_repeat http://purl.obolibrary.org/obo/SO_0001797 centromeric_repeat A repeat region which is part of the regional centromere outer repeat region. http://purl.obolibrary.org/obo/SO_0001899 dh_repeat http://purl.obolibrary.org/obo/SO_0001797 centromeric_repeat A repeat region which is part of the regional centromere outer repeat region. http://purl.obolibrary.org/obo/SO_0001901 AACCCT_box http://purl.obolibrary.org/obo/SO_0001660 core_eukaryotic_promoter_element A conserved 17-bp sequence (5'-ATCA(C/A)AACCCTAACCCT-3') commonly present upstream of the start site of histone transcription units functioning as a transcription factor binding site. http://purl.obolibrary.org/obo/SO_0001902 splice_region http://purl.obolibrary.org/obo/SO_0000835 primary_transcript_region A region surrounding a cis_splice site, either within 1-3 bases of the exon or 3-8 bases of the intron. http://purl.obolibrary.org/obo/SO_0001904 antisense_lncRNA http://purl.obolibrary.org/obo/SO_0001877 lncRNA Non-coding RNA transcribed from the opposite DNA strand compared with other transcripts and overlap in part with sense RNA. http://purl.obolibrary.org/obo/SO_0001906 feature_truncation http://purl.obolibrary.org/obo/SO_0001878 feature_variant A sequence variant that causes the reduction of a genomic feature, with regard to the reference sequence. http://purl.obolibrary.org/obo/SO_0001907 feature_elongation http://purl.obolibrary.org/obo/SO_0001878 feature_variant A sequence variant that causes the extension of a genomic feature, with regard to the reference sequence. http://purl.obolibrary.org/obo/SO_0001908 internal_feature_elongation http://purl.obolibrary.org/obo/SO_0001907 feature_elongation A sequence variant that causes the extension of a genomic feature from within the feature rather than from the terminus of the feature, with regard to the reference sequence. http://purl.obolibrary.org/obo/SO_0001909 frameshift_elongation http://purl.obolibrary.org/obo/SO_0001908 internal_feature_elongation A frameshift variant that causes the translational reading frame to be extended relative to the reference feature. http://purl.obolibrary.org/obo/SO_0001910 frameshift_truncation http://purl.obolibrary.org/obo/SO_0001906 feature_truncation A frameshift variant that causes the translational reading frame to be shortened relative to the reference feature. http://purl.obolibrary.org/obo/SO_0001911 copy_number_increase http://purl.obolibrary.org/obo/SO_0001563 copy_number_change A sequence variant where copies of a feature are increased relative to the reference. http://purl.obolibrary.org/obo/SO_0001912 copy_number_decrease http://purl.obolibrary.org/obo/SO_0001563 copy_number_change A sequence variant where copies of a feature are decreased relative to the reference. http://purl.obolibrary.org/obo/SO_0001915 transcription_start_cluster http://purl.obolibrary.org/obo/SO_0001410 experimental_feature A region defined by a cluster of experimentally determined transcription starting sites. http://purl.obolibrary.org/obo/SO_0001916 CAGE_tag http://purl.obolibrary.org/obo/SO_0000324 tag A CAGE tag is a sequence tag hat corresponds to 5' ends of mRNA at cap sites, produced by cap analysis gene expression and used to identify transcriptional start sites. http://purl.obolibrary.org/obo/SO_0001917 CAGE_cluster http://purl.obolibrary.org/obo/SO_0001915 transcription_start_cluster A kind of transcription_initiation_cluster defined by the clustering of CAGE tags on a sequence region. http://purl.obolibrary.org/obo/SO_0001918 5_methylcytosine http://purl.obolibrary.org/obo/SO_0000114 methylated_cytosine A cytosine methylated at the 5 carbon. http://purl.obolibrary.org/obo/SO_0001919 4_methylcytosine http://purl.obolibrary.org/obo/SO_0000114 methylated_cytosine A cytosine methylated at the 4 nitrogen. http://purl.obolibrary.org/obo/SO_0001920 N6_methyladenine http://purl.obolibrary.org/obo/SO_0000161 methylated_adenine An adenine methylated at the 6 nitrogen. http://purl.obolibrary.org/obo/SO_0001921 mitochondrial_contig http://purl.obolibrary.org/obo/SO_0000149 contig A contig of mitochondria derived sequences. http://purl.obolibrary.org/obo/SO_0001922 mitochondrial_supercontig http://purl.obolibrary.org/obo/SO_0000148 supercontig A scaffold composed of mitochondrial contigs. http://purl.obolibrary.org/obo/SO_0001923 TERRA http://purl.obolibrary.org/obo/SO_0001927 telomeric_transcript A non-coding RNA transcript, derived from the transcription of the telomere. These transcripts contain G rich telomeric RNA repeats and RNA tracts corresponding to adjacent subtelomeric sequences. They are 100-9000 bases long. http://purl.obolibrary.org/obo/SO_0001924 ARRET http://purl.obolibrary.org/obo/SO_0001927 telomeric_transcript A non coding RNA transcript, complementary to subtelomeric tract of TERRA transcript but devoid of the repeats. http://purl.obolibrary.org/obo/SO_0001925 ARIA http://purl.obolibrary.org/obo/SO_0001927 telomeric_transcript A non-coding RNA transcript, derived from the transcription of the telomere. These transcripts consist of C rich repeats. http://purl.obolibrary.org/obo/SO_0001926 anti_ARRET http://purl.obolibrary.org/obo/SO_0001927 telomeric_transcript A non-coding RNA transcript, derived from the transcription of the telomere. These transcripts are antisense of ARRET transcripts. http://purl.obolibrary.org/obo/SO_0001928 distal_duplication http://purl.obolibrary.org/obo/SO_1000035 duplication A duplication of the distal region of a chromosome. http://purl.obolibrary.org/obo/SO_0001929 mitochondrial_DNA_read http://purl.obolibrary.org/obo/SO_0000150 read A sequencer read of a mitochondrial DNA sample. http://purl.obolibrary.org/obo/SO_0001930 chloroplast_DNA_read http://purl.obolibrary.org/obo/SO_0000150 read A sequencer read of a chloroplast DNA sample. http://purl.obolibrary.org/obo/SO_0001931 consensus_gDNA http://purl.obolibrary.org/obo/SO_0000994 consensus_region Genomic DNA sequence produced from some base calling or alignment algorithm which uses aligned or assembled multiple gDNA sequences as input. http://purl.obolibrary.org/obo/SO_0001932 restriction_enzyme_five_prime_single_strand_overhang http://purl.obolibrary.org/obo/SO_0001695 restriction_enzyme_single_strand_overhang A terminal region of DNA sequence where the end of the region is not blunt ended and the exposed single strand terminates at the 5' end. http://purl.obolibrary.org/obo/SO_0001933 restriction_enzyme_three_prime_single_strand_overhang http://purl.obolibrary.org/obo/SO_0001695 restriction_enzyme_single_strand_overhang A terminal region of DNA sequence where the end of the region is not blunt ended and the exposed single strand terminates at the 3' end. http://purl.obolibrary.org/obo/SO_0001934 monomeric_repeat http://purl.obolibrary.org/obo/SO_0000705 tandem_repeat A repeat_region containing repeat_units of 1 bp that is repeated multiple times in tandem. http://purl.obolibrary.org/obo/SO_0001935 H3K20_trimethylation_site http://purl.obolibrary.org/obo/SO_0001701 histone_methylation_site A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H3 protein is tri-methylated. http://purl.obolibrary.org/obo/SO_0001936 H3K36_acetylation_site http://purl.obolibrary.org/obo/SO_0001973 histone_3_acetylation_site A kind of histone modification site, whereby the 36th residue (a lysine), from the start of the H3 histone protein is acetylated. http://purl.obolibrary.org/obo/SO_0001937 H2BK12_acetylation_site http://purl.obolibrary.org/obo/SO_0002143 histone_2B_acetylation_site A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H2B protein is acetylated. http://purl.obolibrary.org/obo/SO_0001938 H2AK5_acetylation_site http://purl.obolibrary.org/obo/SO_0002142 histone_2A_acetylation_site A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2A histone protein is acetylated. http://purl.obolibrary.org/obo/SO_0001939 H4K12_acetylation_site http://purl.obolibrary.org/obo/SO_0001972 histone_4_acetylation_site A kind of histone modification site, whereby the 12th residue (a lysine), from the start of the H4 histone protein is acetylated. http://purl.obolibrary.org/obo/SO_0001940 H2BK120_acetylation_site http://purl.obolibrary.org/obo/SO_0002143 histone_2B_acetylation_site A kind of histone modification site, whereby the 120th residue (a lysine), from the start of the H2B histone protein is acetylated. http://purl.obolibrary.org/obo/SO_0001941 H4K91_acetylation_site http://purl.obolibrary.org/obo/SO_0001972 histone_4_acetylation_site A kind of histone modification site, whereby the 91st residue (a lysine), from the start of the H4 histone protein is acetylated. http://purl.obolibrary.org/obo/SO_0001942 H2BK20_acetylation_site http://purl.obolibrary.org/obo/SO_0002143 histone_2B_acetylation_site A kind of histone modification site, whereby the 20th residue (a lysine), from the start of the H2B histone protein is acetylated. http://purl.obolibrary.org/obo/SO_0001943 H3K4_acetylation_site http://purl.obolibrary.org/obo/SO_0001973 histone_3_acetylation_site A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H3 histone protein is acetylated. http://purl.obolibrary.org/obo/SO_0001944 H2AK9_acetylation_site http://purl.obolibrary.org/obo/SO_0002142 histone_2A_acetylation_site A kind of histone modification site, whereby the 9th residue (a lysine), from the start of the H2A histone protein is acetylated. http://purl.obolibrary.org/obo/SO_0001945 H3K56_acetylation_site http://purl.obolibrary.org/obo/SO_0001973 histone_3_acetylation_site A kind of histone modification site, whereby the 56th residue (a lysine), from the start of the H3 histone protein is acetylated. http://purl.obolibrary.org/obo/SO_0001946 H2BK15_acetylation_site http://purl.obolibrary.org/obo/SO_0002143 histone_2B_acetylation_site A kind of histone modification site, whereby the 15th residue (a lysine), from the start of the H2B histone protein is acetylated. http://purl.obolibrary.org/obo/SO_0001947 H3R2_monomethylation_site http://purl.obolibrary.org/obo/SO_0001701 histone_methylation_site A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is mono-methylated. http://purl.obolibrary.org/obo/SO_0001948 H3R2_dimethylation_site http://purl.obolibrary.org/obo/SO_0001701 histone_methylation_site A kind of histone modification site, whereby the 2nd residue (an arginine), from the start of the H3 protein is di-methylated. http://purl.obolibrary.org/obo/SO_0001949 H4R3_dimethylation_site http://purl.obolibrary.org/obo/SO_0001701 histone_methylation_site A kind of histone modification site, whereby the 3nd residue (an arginine), from the start of the H4 protein is di-methylated. http://purl.obolibrary.org/obo/SO_0001950 H4K4_trimethylation_site http://purl.obolibrary.org/obo/SO_0001701 histone_methylation_site A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H4 protein is tri-methylated. http://purl.obolibrary.org/obo/SO_0001951 H3K23_dimethylation_site http://purl.obolibrary.org/obo/SO_0001701 histone_methylation_site A kind of histone modification site, whereby the 23rd residue (a lysine), from the start of the H3 protein is di-methylated. http://purl.obolibrary.org/obo/SO_0001952 promoter_flanking_region http://purl.obolibrary.org/obo/SO_0001055 transcriptional_cis_regulatory_region A region immediately adjacent to a promoter which may or may not contain transcription factor binding sites. http://purl.obolibrary.org/obo/SO_0001953 restriction_enzyme_assembly_scar http://purl.obolibrary.org/obo/SO_0001954 restriction_enzyme_region A region of DNA sequence formed from the ligation of two sticky ends where the palindrome is broken and no longer comprises the recognition site and thus cannot be re-cut by the restriction enzymes used to create the sticky ends. http://purl.obolibrary.org/obo/SO_0001954 restriction_enzyme_region http://purl.obolibrary.org/obo/SO_0001411 biological_region A region related to restriction enzyme function. http://purl.obolibrary.org/obo/SO_0001955 protein_stability_element http://purl.obolibrary.org/obo/SO_0000839 polypeptide_region A polypeptide region that proves structure in a protein that affects the stability of the protein. http://purl.obolibrary.org/obo/SO_0001956 protease_site http://purl.obolibrary.org/obo/SO_0000839 polypeptide_region A polypeptide_region that codes for a protease cleavage site. http://purl.obolibrary.org/obo/SO_0001959 TCT_motif http://purl.obolibrary.org/obo/SO_0001660 core_eukaryotic_promoter_element A cis-regulatory element, conserved sequence YYC+1TTTYY, and spans -2 to +6 relative to +1 TSS. It is present in most ribosomal protein genes in Drosophila and mammals but not in the yeast Saccharomyces cerevisiae. Resembles the initiator (TCAKTY in Drosophila) but functionally distinct from initiator. http://purl.obolibrary.org/obo/SO_0001960 5_hydroxymethylcytosine http://purl.obolibrary.org/obo/SO_0000114 methylated_cytosine A modified DNA cytosine base feature, modified by a hydroxymethyl group at the 5 carbon. http://purl.obolibrary.org/obo/SO_0001961 5_formylcytosine http://purl.obolibrary.org/obo/SO_0001963 modified_cytosine A modified DNA cytosine base feature, modified by a formyl group at the 5 carbon. http://purl.obolibrary.org/obo/SO_0001962 modified_adenine http://purl.obolibrary.org/obo/SO_0000305 modified_DNA_base A modified adenine DNA base feature. http://purl.obolibrary.org/obo/SO_0001963 modified_cytosine http://purl.obolibrary.org/obo/SO_0000305 modified_DNA_base A modified cytosine DNA base feature. http://purl.obolibrary.org/obo/SO_0001964 modified_guanine http://purl.obolibrary.org/obo/SO_0000305 modified_DNA_base A modified guanine DNA base feature. http://purl.obolibrary.org/obo/SO_0001965 8_oxoguanine http://purl.obolibrary.org/obo/SO_0001964 modified_guanine A modified DNA guanine base,at the 8 carbon, often the product of DNA damage. http://purl.obolibrary.org/obo/SO_0001966 5_carboxylcytosine http://purl.obolibrary.org/obo/SO_0001963 modified_cytosine A modified DNA cytosine base feature, modified by a carboxy group at the 5 carbon. http://purl.obolibrary.org/obo/SO_0001967 8_oxoadenine http://purl.obolibrary.org/obo/SO_0001962 modified_adenine A modified DNA adenine base,at the 8 carbon, often the product of DNA damage. http://purl.obolibrary.org/obo/SO_0001968 coding_transcript_variant http://purl.obolibrary.org/obo/SO_0001576 transcript_variant A transcript variant of a protein coding gene. http://purl.obolibrary.org/obo/SO_0001969 coding_transcript_intron_variant http://purl.obolibrary.org/obo/SO_0001968 coding_transcript_variant A transcript variant occurring within an intron of a coding transcript. http://purl.obolibrary.org/obo/SO_0001970 non_coding_transcript_intron_variant http://purl.obolibrary.org/obo/SO_0001627 intron_variant A transcript variant occurring within an intron of a non coding transcript. http://purl.obolibrary.org/obo/SO_0001971 zinc_finger_binding_site http://purl.obolibrary.org/obo/SO_0001429 DNA_binding_site A binding site to which a polypeptide will bind with a zinc finger motif, which is characterized by requiring one or more Zinc 2+ ions for stabilized folding. http://purl.obolibrary.org/obo/SO_0001972 histone_4_acetylation_site http://purl.obolibrary.org/obo/SO_0001702 histone_acetylation_site A histone 4 modification where the modification is the acetylation of the residue. http://purl.obolibrary.org/obo/SO_0001973 histone_3_acetylation_site http://purl.obolibrary.org/obo/SO_0001702 histone_acetylation_site A histone 3 modification where the modification is the acetylation of the residue. http://purl.obolibrary.org/obo/SO_0001974 CTCF_binding_site http://purl.obolibrary.org/obo/SO_0001659 promoter_element A transcription factor binding site with consensus sequence CCGCGNGGNGGCAG, bound by CCCTF-binding factor. http://purl.obolibrary.org/obo/SO_0001975 five_prime_sticky_end_restriction_enzyme_cleavage_site http://purl.obolibrary.org/obo/SO_0001692 sticky_end_restriction_enzyme_cleavage_site A restriction enzyme recognition site that, when cleaved, results in 5 prime overhangs. http://purl.obolibrary.org/obo/SO_0001976 three_prime_sticky_end_restriction_enzyme_cleavage_site http://purl.obolibrary.org/obo/SO_0001692 sticky_end_restriction_enzyme_cleavage_site A restriction enzyme recognition site that, when cleaved, results in 3 prime overhangs. http://purl.obolibrary.org/obo/SO_0001977 ribonuclease_site http://purl.obolibrary.org/obo/SO_0000833 transcript_region A region of a transcript encoding the cleavage site for a ribonuclease enzyme. http://purl.obolibrary.org/obo/SO_0001978 signature http://purl.obolibrary.org/obo/SO_0000804 engineered_region A region of sequence where developer information is encoded. http://purl.obolibrary.org/obo/SO_0001979 RNA_stability_element http://purl.obolibrary.org/obo/SO_0000715 RNA_motif A motif that affects the stability of RNA. http://purl.obolibrary.org/obo/SO_0001980 G_box http://purl.obolibrary.org/obo/SO_0001678 regulatory_promoter_element A regulatory promoter element identified in mutation experiments, with consensus sequence: CACGTG. Present in promoters, intergenic regions, coding regions, and introns. They are involved in gene expression responses to light and interact with G-box binding factor and I-box binding factor 1a. http://purl.obolibrary.org/obo/SO_0001981 L_box http://purl.obolibrary.org/obo/SO_0001678 regulatory_promoter_element An orientation dependent regulatory promoter element, with consensus sequence of TTGCACAN4TTGCACA, found in plants. http://purl.obolibrary.org/obo/SO_0001982 I-box http://purl.obolibrary.org/obo/SO_0001678 regulatory_promoter_element A plant regulatory promoter motif, composed of a highly conserved hexamer GATAAG (I-box core). http://purl.obolibrary.org/obo/SO_0001983 5_prime_UTR_premature_start_codon_variant http://purl.obolibrary.org/obo/SO_0001623 5_prime_UTR_variant A 5' UTR variant where a premature start codon is introduced, moved or lost. http://purl.obolibrary.org/obo/SO_0001986 upstream_transcript_variant http://purl.obolibrary.org/obo/SO_0001628 intergenic_variant A feature variant, where the alteration occurs upstream of the transcript TSS. http://purl.obolibrary.org/obo/SO_0001987 downstream_transcript_variant http://purl.obolibrary.org/obo/SO_0001628 intergenic_variant A feature variant, where the alteration occurs downstream of the transcript termination site. http://purl.obolibrary.org/obo/SO_0001988 5_prime_UTR_premature_start_codon_gain_variant http://purl.obolibrary.org/obo/SO_0001983 5_prime_UTR_premature_start_codon_variant A 5' UTR variant where a premature start codon is gained. http://purl.obolibrary.org/obo/SO_0001989 5_prime_UTR_premature_start_codon_loss_variant http://purl.obolibrary.org/obo/SO_0001983 5_prime_UTR_premature_start_codon_variant A 5' UTR variant where a premature start codon is lost. http://purl.obolibrary.org/obo/SO_0001990 five_prime_UTR_premature_start_codon_location_variant http://purl.obolibrary.org/obo/SO_0001983 5_prime_UTR_premature_start_codon_variant A 5' UTR variant where a premature start codon is moved. http://purl.obolibrary.org/obo/SO_0001991 consensus_AFLP_fragment http://purl.obolibrary.org/obo/SO_0000994 consensus_region A consensus AFLP fragment is an AFLP sequence produced from any alignment algorithm which uses assembled multiple AFLP sequences as input. http://purl.obolibrary.org/obo/SO_0001992 nonsynonymous_variant http://purl.obolibrary.org/obo/SO_0001650 inframe_variant A non-synonymous variant is an inframe, protein altering variant, resulting in a codon change. http://purl.obolibrary.org/obo/SO_0001993 extended_cis_splice_site http://purl.obolibrary.org/obo/SO_0001419 cis_splice_site Intronic positions associated with cis-splicing. Contains the first and second positions immediately before the exon and the first, second and fifth positions immediately after. http://purl.obolibrary.org/obo/SO_0001994 intron_base_5 http://purl.obolibrary.org/obo/SO_0001014 intron_domain Fifth intronic position after the intron exon boundary, close to the 5' edge of the intron. http://purl.obolibrary.org/obo/SO_0001995 extended_intronic_splice_region_variant http://purl.obolibrary.org/obo/SO_0001568 splicing_variant A sequence variant occurring in the intron, within 10 bases of exon. http://purl.obolibrary.org/obo/SO_0001996 extended_intronic_splice_region http://purl.obolibrary.org/obo/SO_0001014 intron_domain Region of intronic sequence within 10 bases of an exon. http://purl.obolibrary.org/obo/SO_0001998 sgRNA http://purl.obolibrary.org/obo/SO_0000696 oligo A small RNA oligo, typically about 20 bases, that guides the cas nuclease to a target DNA sequence in the CRISPR/cas mutagenesis method. http://purl.obolibrary.org/obo/SO_0001999 mating_type_region_motif http://purl.obolibrary.org/obo/SO_0000713 DNA_motif DNA motif that is a component of a mating type region. http://purl.obolibrary.org/obo/SO_0002001 Y_region http://purl.obolibrary.org/obo/SO_0001999 mating_type_region_motif A segment of non-homology between a and alpha mating alleles, found at all three mating loci (HML, MAT, and HMR), has two forms (Ya and Yalpha). http://purl.obolibrary.org/obo/SO_0002002 Z1_region http://purl.obolibrary.org/obo/SO_0001999 mating_type_region_motif A mating type region motif, one of two segments of homology found at all three mating loci (HML, MAT, and HMR). http://purl.obolibrary.org/obo/SO_0002003 Z2_region http://purl.obolibrary.org/obo/SO_0001999 mating_type_region_motif A mating type region motif, the rightmost segment of homology in the HML and MAT mating loci (not present in HMR). http://purl.obolibrary.org/obo/SO_0002004 ARS_consensus_sequence http://purl.obolibrary.org/obo/SO_0000713 DNA_motif The ACS is an 11-bp sequence of the form 5'-WTTTAYRTTTW-3' which is at the core of every yeast ARS, and is necessary but not sufficient for recognition and binding by the origin recognition complex (ORC). Functional ARSs require an ACS, as well as other cis elements in the 5' (C domain) and 3' (B domain) flanking sequences of the ACS. http://purl.obolibrary.org/obo/SO_0002005 DSR_motif http://purl.obolibrary.org/obo/SO_0000713 DNA_motif The determinant of selective removal (DSR) motif consists of repeats of U(U/C)AAAC. The motif targets meiotic transcripts for removal during mitosis via the exosome. http://purl.obolibrary.org/obo/SO_0002006 zinc_repressed_element http://purl.obolibrary.org/obo/SO_0001659 promoter_element A promoter element that has the consensus sequence GNMGATC, and is found in promoters of genes repressed in the presence of zinc. http://purl.obolibrary.org/obo/SO_0002007 MNV http://purl.obolibrary.org/obo/SO_1000002 substitution An MNV is a multiple nucleotide variant (substitution) in which the inserted sequence is the same length as the replaced sequence. http://purl.obolibrary.org/obo/SO_0002008 rare_amino_acid_variant http://purl.obolibrary.org/obo/SO_0001586 non_conservative_missense_variant A sequence variant whereby at least one base of a codon encoding a rare amino acid is changed, resulting in a different encoded amino acid. http://purl.obolibrary.org/obo/SO_0002009 selenocysteine_loss http://purl.obolibrary.org/obo/SO_0002008 rare_amino_acid_variant A sequence variant whereby at least one base of a codon encoding selenocysteine is changed, resulting in a different encoded amino acid. http://purl.obolibrary.org/obo/SO_0002010 pyrrolysine_loss http://purl.obolibrary.org/obo/SO_0002008 rare_amino_acid_variant A sequence variant whereby at least one base of a codon encoding pyrrolysine is changed, resulting in a different encoded amino acid. http://purl.obolibrary.org/obo/SO_0002011 intragenic_variant http://purl.obolibrary.org/obo/SO_0001576 transcript_variant A variant that occurs within a gene but falls outside of all transcript features. This occurs when alternate transcripts of a gene do not share overlapping sequence. http://purl.obolibrary.org/obo/SO_0002012 start_lost http://purl.obolibrary.org/obo/SO_0001992 nonsynonymous_variant A codon variant that changes at least one base of the canonical start codon. http://purl.obolibrary.org/obo/SO_0002013 5_prime_UTR_truncation http://purl.obolibrary.org/obo/SO_0001623 5_prime_UTR_variant A sequence variant that causes the reduction of a the 5'UTR with regard to the reference sequence. http://purl.obolibrary.org/obo/SO_0002014 5_prime_UTR_elongation http://purl.obolibrary.org/obo/SO_0001623 5_prime_UTR_variant A sequence variant that causes the extension of 5' UTR, with regard to the reference sequence. http://purl.obolibrary.org/obo/SO_0002015 3_prime_UTR_truncation http://purl.obolibrary.org/obo/SO_0001624 3_prime_UTR_variant A sequence variant that causes the reduction of a the 3' UTR with regard to the reference sequence. http://purl.obolibrary.org/obo/SO_0002016 3_prime_UTR_elongation http://purl.obolibrary.org/obo/SO_0001624 3_prime_UTR_variant A sequence variant that causes the extension of 3' UTR, with regard to the reference sequence. http://purl.obolibrary.org/obo/SO_0002017 conserved_intergenic_variant http://purl.obolibrary.org/obo/SO_0001628 intergenic_variant A sequence variant located in a conserved intergenic region, between genes. http://purl.obolibrary.org/obo/SO_0002018 conserved_intron_variant http://purl.obolibrary.org/obo/SO_0001627 intron_variant A transcript variant occurring within a conserved region of an intron. http://purl.obolibrary.org/obo/SO_0002019 start_retained_variant http://purl.obolibrary.org/obo/SO_0001819 synonymous_variant A sequence variant where at least one base in the start codon is changed, but the start remains. http://purl.obolibrary.org/obo/SO_0002020 boundary_element http://purl.obolibrary.org/obo/SO_0000627 insulator Boundary elements are DNA motifs that prevent heterochromatin from spreading into neighboring euchromatic regions. http://purl.obolibrary.org/obo/SO_0002022 priRNA http://purl.obolibrary.org/obo/SO_0000655 ncRNA A small RNA molecule, 22-23 nt in size, that is the product of a longer RNA. The production of priRNAs is independent of dicer and involves binding of RNA by argonaute and trimming by triman. In fission yeast, priRNAs trigger the establishment of heterochromatin. PriRNAs are primarily generated from centromeric transcripts (dg and dh repeats), but may also be produced from degradation products of primary transcripts. http://purl.obolibrary.org/obo/SO_0002023 multiplexing_sequence_identifier http://purl.obolibrary.org/obo/SO_0000324 tag A nucleic tag which is used in a ligation step of library preparation process to allow pooling of samples while maintaining ability to identify individual source material and creation of a multiplexed library. http://purl.obolibrary.org/obo/SO_0002024 W_region http://purl.obolibrary.org/obo/SO_0001999 mating_type_region_motif The leftmost segment of homology in the HML and MAT mating loci, but not present in HMR. http://purl.obolibrary.org/obo/SO_0002026 intein_encoding_region http://purl.obolibrary.org/obo/SO_0000842 gene_component_region The nucleotide sequence which encodes the intein portion of the precursor gene. http://purl.obolibrary.org/obo/SO_0002027 uORF http://purl.obolibrary.org/obo/SO_0000236 ORF A short open reading frame that is found in the 5' untranslated region of an mRNA and plays a role in translational regulation. http://purl.obolibrary.org/obo/SO_0002028 sORF http://purl.obolibrary.org/obo/SO_0000236 ORF An open reading frame that encodes a peptide of less than 100 amino acids. http://purl.obolibrary.org/obo/SO_0002029 tnaORF http://purl.obolibrary.org/obo/SO_0000236 ORF A translated ORF encoded entirely within the antisense strand of a known protein coding gene. http://purl.obolibrary.org/obo/SO_0002030 X_region http://purl.obolibrary.org/obo/SO_0001999 mating_type_region_motif One of two segments of homology found at all three mating loci (HML, MAT and HMR). http://purl.obolibrary.org/obo/SO_0002031 shRNA http://purl.obolibrary.org/obo/SO_0000655 ncRNA A short hairpin RNA (shRNA) is an RNA transcript that makes a tight hairpin turn that can be used to silence target gene expression via RNA interference. http://purl.obolibrary.org/obo/SO_0002032 moR http://purl.obolibrary.org/obo/SO_0000370 small_regulatory_ncRNA A non-coding transcript encoded by sequences adjacent to the ends of the 5' and 3' miR-encoding sequences that abut the loop in precursor miRNA. http://purl.obolibrary.org/obo/SO_0002033 loR http://purl.obolibrary.org/obo/SO_0000370 small_regulatory_ncRNA A short, non coding transcript of loop-derived sequences encoded in precursor miRNA. http://purl.obolibrary.org/obo/SO_0002034 miR_encoding_snoRNA_primary_transcript http://purl.obolibrary.org/obo/SO_0000232 snoRNA_primary_transcript A snoRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA. http://purl.obolibrary.org/obo/SO_0002035 lncRNA_primary_transcript http://purl.obolibrary.org/obo/SO_0000483 nc_primary_transcript A primary transcript encoding a lncRNA. http://purl.obolibrary.org/obo/SO_0002036 miR_encoding_lncRNA_primary_transcript http://purl.obolibrary.org/obo/SO_0002035 lncRNA_primary_transcript A lncRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA. http://purl.obolibrary.org/obo/SO_0002037 miR_encoding_tRNA_primary_transcript http://purl.obolibrary.org/obo/SO_0000210 tRNA_primary_transcript A tRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA. http://purl.obolibrary.org/obo/SO_0002038 shRNA_primary_transcript http://purl.obolibrary.org/obo/SO_0000483 nc_primary_transcript A primary transcript encoding an shRNA. http://purl.obolibrary.org/obo/SO_0002039 miR_encoding_shRNA_primary_transcript http://purl.obolibrary.org/obo/SO_0002038 shRNA_primary_transcript A shRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA. http://purl.obolibrary.org/obo/SO_0002040 vaultRNA_primary_transcript http://purl.obolibrary.org/obo/SO_0000483 nc_primary_transcript A primary transcript encoding a vaultRNA. http://purl.obolibrary.org/obo/SO_0002041 miR_encoding_vaultRNA_primary_transcript http://purl.obolibrary.org/obo/SO_0002040 vaultRNA_primary_transcript A vaultRNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA. http://purl.obolibrary.org/obo/SO_0002042 Y_RNA_primary_transcript http://purl.obolibrary.org/obo/SO_0000483 nc_primary_transcript A primary transcript encoding a Y-RNA. http://purl.obolibrary.org/obo/SO_0002043 miR_encoding_Y_RNA_primary_transcript http://purl.obolibrary.org/obo/SO_0002042 Y_RNA_primary_transcript A Y-RNA primary transcript that also encodes pre-miR sequence that is processed to form functionally active miRNA. http://purl.obolibrary.org/obo/SO_0002044 TCS_element http://purl.obolibrary.org/obo/SO_0001659 promoter_element A TCS element is a (yeast) transcription factor binding site, bound by the TEA DNA binding domain (DBD) of transcription factors. The consensus site is CATTCC or CATTCT. http://purl.obolibrary.org/obo/SO_0002045 pheromone_response_element http://purl.obolibrary.org/obo/SO_0001659 promoter_element A PRE is a (yeast) TFBS with consensus site [TGAAAC(A/G)]. http://purl.obolibrary.org/obo/SO_0002046 FRE http://purl.obolibrary.org/obo/SO_0001461 enhancer_binding_site A FRE is an enhancer element necessary and sufficient to confer filamentation associated expression in S. cerevisiae. http://purl.obolibrary.org/obo/SO_0002047 transcription_pause_site http://purl.obolibrary.org/obo/SO_0001055 transcriptional_cis_regulatory_region Transcription pause sites are regions of a gene where RNA polymerase may pause during transcription. The functional role of pausing may be to facilitate factor recruitment, RNA folding, and synchronization with translation. Consensus transcription pause site have been observed in E. coli. http://purl.obolibrary.org/obo/SO_0002048 disabled_reading_frame http://purl.obolibrary.org/obo/SO_0000717 reading_frame A reading frame that could encode a full-length protein but which contains obvious mid-sequence disablements (frameshifts or premature stop codons). http://purl.obolibrary.org/obo/SO_0002049 H3K27_acetylation_site http://purl.obolibrary.org/obo/SO_0001973 histone_3_acetylation_site A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is acetylated. http://purl.obolibrary.org/obo/SO_0002050 constitutive_promoter http://purl.obolibrary.org/obo/SO_0000167 promoter A promoter that allows for continual transcription of gene. http://purl.obolibrary.org/obo/SO_0002051 inducible_promoter http://purl.obolibrary.org/obo/SO_0000167 promoter A promoter whereby activity is induced by the presence or absence of biotic or abiotic factors. http://purl.obolibrary.org/obo/SO_0002052 dominant_negative_variant http://purl.obolibrary.org/obo/SO_0002218 functionally_abnormal A variant where the mutated gene product adversely affects the other (wild type) gene product. http://purl.obolibrary.org/obo/SO_0002053 gain_of_function_variant http://purl.obolibrary.org/obo/SO_0002218 functionally_abnormal A sequence variant whereby new or enhanced function is conferred on the gene product. http://purl.obolibrary.org/obo/SO_0002054 loss_of_function_variant http://purl.obolibrary.org/obo/SO_0002218 functionally_abnormal A sequence variant whereby the gene product has diminished or abolished function. http://purl.obolibrary.org/obo/SO_0002055 null_mutation http://purl.obolibrary.org/obo/SO_0002218 functionally_abnormal A variant whereby the gene product is not functional or the gene product is not produced. http://purl.obolibrary.org/obo/SO_0002056 intronic_splicing_silencer http://purl.obolibrary.org/obo/SO_0000625 silencer An intronic splicing regulatory element that functions to recruit trans acting splicing factors suppress the transcription of the gene or genes they control. http://purl.obolibrary.org/obo/SO_0002058 exonic_splicing_silencer http://purl.obolibrary.org/obo/SO_0000852 exon_region An exonic splicing regulatory element that functions to recruit trans acting splicing factors suppress the transcription of the gene or genes they control. http://purl.obolibrary.org/obo/SO_0002059 recombination_enhancer http://purl.obolibrary.org/obo/SO_0001681 recombination_regulatory_region A regulatory_region that promotes or induces the process of recombination. http://purl.obolibrary.org/obo/SO_0002060 interchromosomal_translocation http://purl.obolibrary.org/obo/SO_1000044 chromosomal_translocation A translocation where the regions involved are from different chromosomes. http://purl.obolibrary.org/obo/SO_0002061 intrachromosomal_translocation http://purl.obolibrary.org/obo/SO_1000044 chromosomal_translocation A translocation where the regions involved are from the same chromosome. http://purl.obolibrary.org/obo/SO_0002062 complex_chromosomal_rearrangement http://purl.obolibrary.org/obo/SO_0001784 complex_structural_alteration A contiguous cluster of translocations, usually the result of a single catastrophic event such as chromothripsis or chromoanasynthesis. http://purl.obolibrary.org/obo/SO_0002063 Alu_insertion http://purl.obolibrary.org/obo/SO_0001837 mobile_element_insertion An insertion of sequence from the Alu family of mobile elements. http://purl.obolibrary.org/obo/SO_0002064 LINE1_insertion http://purl.obolibrary.org/obo/SO_0001837 mobile_element_insertion An insertion from the Line1 family of mobile elements. http://purl.obolibrary.org/obo/SO_0002065 SVA_insertion http://purl.obolibrary.org/obo/SO_0001837 mobile_element_insertion An insertion of sequence from the SVA family of mobile elements. http://purl.obolibrary.org/obo/SO_0002066 mobile_element_deletion http://purl.obolibrary.org/obo/SO_0000159 deletion A deletion of a mobile element when comparing a reference sequence (has mobile element) to a individual sequence (does not have mobile element). http://purl.obolibrary.org/obo/SO_0002067 HERV_deletion http://purl.obolibrary.org/obo/SO_0002066 mobile_element_deletion A deletion of the HERV mobile element with respect to a reference. http://purl.obolibrary.org/obo/SO_0002068 SVA_deletion http://purl.obolibrary.org/obo/SO_0002066 mobile_element_deletion A deletion of an SVA mobile element. http://purl.obolibrary.org/obo/SO_0002069 LINE1_deletion http://purl.obolibrary.org/obo/SO_0002066 mobile_element_deletion A deletion of a LINE1 mobile element with respect to a reference. http://purl.obolibrary.org/obo/SO_0002070 Alu_deletion http://purl.obolibrary.org/obo/SO_0002066 mobile_element_deletion A deletion of an Alu mobile element with respect to a reference. http://purl.obolibrary.org/obo/SO_0002071 CDS_supported_by_peptide_spectrum_match http://purl.obolibrary.org/obo/SO_1001251 CDS_supported_by_sequence_similarity_data A CDS that is supported by proteomics data. http://purl.obolibrary.org/obo/SO_0002073 no_sequence_alteration http://purl.obolibrary.org/obo/SO_0002072 sequence_comparison A position or feature within a sequence that is identical to the comparable position or feature of a specified reference sequence. http://purl.obolibrary.org/obo/SO_0002074 intergenic_1kb_variant http://purl.obolibrary.org/obo/SO_0001628 intergenic_variant A variant that falls in an intergenic region that is 1 kb or less between 2 genes. http://purl.obolibrary.org/obo/SO_0002075 incomplete_transcript_variant http://purl.obolibrary.org/obo/SO_0001576 transcript_variant A sequence variant that intersects an incompletely annotated transcript. http://purl.obolibrary.org/obo/SO_0002076 incomplete_transcript_3UTR_variant http://purl.obolibrary.org/obo/SO_0002075 incomplete_transcript_variant A sequence variant that intersects the 3' UTR of an incompletely annotated transcript. http://purl.obolibrary.org/obo/SO_0002077 incomplete_transcript_5UTR_variant http://purl.obolibrary.org/obo/SO_0002075 incomplete_transcript_variant A sequence variant that intersects the 5' UTR of an incompletely annotated transcript. http://purl.obolibrary.org/obo/SO_0002078 incomplete_transcript_intronic_variant http://purl.obolibrary.org/obo/SO_0002075 incomplete_transcript_variant A sequence variant that intersects the intron of an incompletely annotated transcript. http://purl.obolibrary.org/obo/SO_0002079 incomplete_transcript_splice_region_variant http://purl.obolibrary.org/obo/SO_0002075 incomplete_transcript_variant A sequence variant that intersects the splice region of an incompletely annotated transcript. http://purl.obolibrary.org/obo/SO_0002080 incomplete_transcript_exonic_variant http://purl.obolibrary.org/obo/SO_0002075 incomplete_transcript_variant A sequence variant that intersects the exon of an incompletely annotated transcript. http://purl.obolibrary.org/obo/SO_0002081 incomplete_transcript_CDS http://purl.obolibrary.org/obo/SO_0002075 incomplete_transcript_variant A sequence variant that intersects the coding regions of an incompletely annotated transcript. http://purl.obolibrary.org/obo/SO_0002082 incomplete_transcript_coding_splice_variant http://purl.obolibrary.org/obo/SO_0002079 incomplete_transcript_splice_region_variant A sequence variant that intersects the coding sequence near a splice region of an incompletely annotated transcript. http://purl.obolibrary.org/obo/SO_0002083 2KB_downstream_variant http://purl.obolibrary.org/obo/SO_0001632 downstream_gene_variant A sequence variant located within 2KB 3' of a gene. http://purl.obolibrary.org/obo/SO_0002084 exonic_splice_region_variant http://purl.obolibrary.org/obo/SO_0001630 splice_region_variant A sequence variant in which a change has occurred within the exonic region of the splice site, 1-2 bases from boundary. http://purl.obolibrary.org/obo/SO_0002085 unidirectional_gene_fusion http://purl.obolibrary.org/obo/SO_0001565 gene_fusion A sequence variant whereby two genes, on the same strand have become joined. http://purl.obolibrary.org/obo/SO_0002086 bidirectional_gene_fusion http://purl.obolibrary.org/obo/SO_0001565 gene_fusion A sequence variant whereby two genes, on alternate strands have become joined. http://purl.obolibrary.org/obo/SO_0002087 pseudogenic_CDS http://purl.obolibrary.org/obo/SO_0000462 pseudogenic_region A non functional descendant of the coding portion of a coding transcript, part of a pseudogene. http://purl.obolibrary.org/obo/SO_0002088 non_coding_transcript_splice_region_variant http://purl.obolibrary.org/obo/SO_0001630 splice_region_variant A transcript variant occurring within the splice region (1-3 bases of the exon or 3-8 bases of the intron) of a non coding transcript. http://purl.obolibrary.org/obo/SO_0002089 3_prime_UTR_exon_variant http://purl.obolibrary.org/obo/SO_0001624 3_prime_UTR_variant A UTR variant of exonic sequence of the 3' UTR. http://purl.obolibrary.org/obo/SO_0002090 3_prime_UTR_intron_variant http://purl.obolibrary.org/obo/SO_0001969 coding_transcript_intron_variant A UTR variant of intronic sequence of the 3' UTR. http://purl.obolibrary.org/obo/SO_0002091 5_prime_UTR_intron_variant http://purl.obolibrary.org/obo/SO_0001969 coding_transcript_intron_variant A UTR variant of intronic sequence of the 5' UTR. http://purl.obolibrary.org/obo/SO_0002092 5_prime_UTR_exon_variant http://purl.obolibrary.org/obo/SO_0001623 5_prime_UTR_variant A UTR variant of exonic sequence of the 5' UTR. http://purl.obolibrary.org/obo/SO_0002093 structural_interaction_variant http://purl.obolibrary.org/obo/SO_0001599 3D_polypeptide_structure_variant A variant that impacts the internal interactions of the resulting polypeptide structure. http://purl.obolibrary.org/obo/SO_0002094 non_allelic_homologous_recombination_region http://purl.obolibrary.org/obo/SO_0000339 recombination_hotspot A genomic region at a non-allelic position where exchange of genetic material happens as a result of homologous recombination. http://purl.obolibrary.org/obo/SO_0002095 scaRNA http://purl.obolibrary.org/obo/SO_0000275 snoRNA A ncRNA, specific to the Cajal body, that has been demonstrated to function as a guide RNA in the site-specific synthesis of 2'-O-ribose-methylated nucleotides and pseudouridines in the RNA polymerase II-transcribed U1, U2, U4 and U5 spliceosomal small nuclear RNAs (snRNAs). http://purl.obolibrary.org/obo/SO_0002096 short_tandem_repeat_variation http://purl.obolibrary.org/obo/SO_0000248 sequence_length_alteration A variation that expands or contracts a tandem repeat with regard to a reference. http://purl.obolibrary.org/obo/SO_0002097 vertebrate_immune_system_pseudogene http://purl.obolibrary.org/obo/SO_0000336 pseudogene A pseudogene derived from a vertebrate immune system gene. http://purl.obolibrary.org/obo/SO_0002098 immunoglobulin_pseudogene http://purl.obolibrary.org/obo/SO_0002097 vertebrate_immune_system_pseudogene A pseudogene derived from an immunoglobulin gene. http://purl.obolibrary.org/obo/SO_0002099 T_cell_receptor_pseudogene http://purl.obolibrary.org/obo/SO_0002097 vertebrate_immune_system_pseudogene A pseudogene derived from a T-cell receptor gene. http://purl.obolibrary.org/obo/SO_0002100 IG_C_pseudogene http://purl.obolibrary.org/obo/SO_0002098 immunoglobulin_pseudogene A pseudogenic constant region of an immunoglobulin gene which closely resembles a known functional Imunoglobulin constant gene but in which the coding region has stop codons, frameshift mutations or a mutation that effects the initiation codon. http://purl.obolibrary.org/obo/SO_0002101 IG_J_pseudogene http://purl.obolibrary.org/obo/SO_0002098 immunoglobulin_pseudogene A pseudogenic joining region which closely resembles a known functional imunoglobulin joining gene but in which the coding region has stop codons, frameshift mutations or a mutation that effects the initiation codon that rearranges at the DNA level and codes the joining region of the variable domain of an immunoglobulin chain. http://purl.obolibrary.org/obo/SO_0002102 IG_V_pseudogene http://purl.obolibrary.org/obo/SO_0002098 immunoglobulin_pseudogene A pseudogenic variable region which closely resembles a known functional imunoglobulin variable gene but in which the coding region has stop codons, frameshift mutations or a mutation that effects the initiation codon that rearranges at the DNA level and codes the variable region of an immunoglobulin chain. http://purl.obolibrary.org/obo/SO_0002103 TR_V_pseudogene http://purl.obolibrary.org/obo/SO_0002099 T_cell_receptor_pseudogene A pseudogenic variable region which closely resembles a known functional T receptor variable gene but in which the coding region has stop codons, frameshift mutations or a mutation that effects the initiation codon that rearranges at the DNA level and codes the variable region of an immunoglobulin chain. http://purl.obolibrary.org/obo/SO_0002104 TR_J_pseudogene http://purl.obolibrary.org/obo/SO_0002099 T_cell_receptor_pseudogene A pseudogenic joining region which closely resembles a known functional T receptor (TR) joining gene but in which the coding region has stop codons, frameshift mutations or a mutation that effects the initiation codon that rearranges at the DNA level and codes the joining region of the variable domain of an immunoglobulin chain. http://purl.obolibrary.org/obo/SO_0002105 translated_processed_pseudogene http://purl.obolibrary.org/obo/SO_0000043 processed_pseudogene A processed pseudogene where there is evidence, (mass spec data) suggesting that it is also translated. http://purl.obolibrary.org/obo/SO_0002106 translated_unprocessed_pseudogene http://purl.obolibrary.org/obo/SO_0001760 non_processed_pseudogene A non-processed pseudogene where there is evidence, (mass spec data) suggesting that it is also translated. http://purl.obolibrary.org/obo/SO_0002107 transcribed_unprocessed_pseudogene http://purl.obolibrary.org/obo/SO_0001760 non_processed_pseudogene A unprocessed pseudogene supported by locus-specific evidence of transcription. http://purl.obolibrary.org/obo/SO_0002108 transcribed_unitary_pseudogene http://purl.obolibrary.org/obo/SO_0001759 unitary_pseudogene A species specific unprocessed pseudogene without a parent gene, as it has an active orthologue in another species. http://purl.obolibrary.org/obo/SO_0002109 transcribed_processed_pseudogene http://purl.obolibrary.org/obo/SO_0000043 processed_pseudogene A processed_pseudogene overlapped by locus-specific evidence of transcription. http://purl.obolibrary.org/obo/SO_0002110 polymorphic_pseudogene_with_retained_intron http://purl.obolibrary.org/obo/SO_0001841 polymorphic_pseudogene A polymorphic pseudogene in the reference genome, containing a retained intron, known to be intact in the genomes of other individuals of the same species. The annotation process has confirmed that the pseudogenisation event is not a genomic sequencing error. http://purl.obolibrary.org/obo/SO_0002111 pseudogene_processed_transcript http://purl.obolibrary.org/obo/SO_0001503 processed_transcript A processed_transcript supported by EST and/or mRNA evidence that aligns unambiguously to a pseudogene locus (i.e. alignment to the pseudogene locus clearly better than alignment to parent locus). http://purl.obolibrary.org/obo/SO_0002112 coding_transcript_with_retained_intron http://purl.obolibrary.org/obo/SO_0000120 protein_coding_primary_transcript A protein coding transcript containing a retained intron. http://purl.obolibrary.org/obo/SO_0002113 lncRNA_with_retained_intron http://purl.obolibrary.org/obo/SO_0002035 lncRNA_primary_transcript A lncRNA transcript containing a retained intron. http://purl.obolibrary.org/obo/SO_0002114 NMD_transcript http://purl.obolibrary.org/obo/SO_0000120 protein_coding_primary_transcript A protein coding transcript that contains a CDS but has one or more splice junctions >50bp downstream of stop codon, making it susceptible to nonsense mediated decay. http://purl.obolibrary.org/obo/SO_0002115 pseudogenic_transcript_with_retained_intron http://purl.obolibrary.org/obo/SO_0000185 primary_transcript A transcript supported by EST and/or mRNA evidence that aligns unambiguously to the pseudogene locus; has retained intronic sequence compared to a reference transcript sequence. http://purl.obolibrary.org/obo/SO_0002116 polymorphic_pseudogene_processed_transcript http://purl.obolibrary.org/obo/SO_0002111 pseudogene_processed_transcript A processed transcript that does not contain a CDS that fullfills annotation criteria and not necessarily functionally non-coding. http://purl.obolibrary.org/obo/SO_0002118 NMD_polymorphic_pseudogene_transcript http://purl.obolibrary.org/obo/SO_0002114 NMD_transcript A polymorphic pseudogene transcript that contains a CDS but has one or more splice junctions >50bp downstream of stop codon. Premature stop codon is not introduced, directly or indirectly, as a result of the variation i.e. must be present in both protein_coding and pseudogenic alleles. http://purl.obolibrary.org/obo/SO_0002119 allelic_frequency http://purl.obolibrary.org/obo/SO_0001763 variant_frequency A physical quality which inheres to the allele by virtue of the number instances of the allele within a population. This is the relative frequency of the allele at a given locus in a population. http://purl.obolibrary.org/obo/SO_0002120 three_prime_overlapping_ncrna http://purl.obolibrary.org/obo/SO_0000655 ncRNA Transcript where ditag (digital gene expression profiling)and/or published experimental data strongly supports the existence of short non-coding transcripts transcribed from the 3'UTR. http://purl.obolibrary.org/obo/SO_0002121 vertebrate_immune_system_gene http://purl.obolibrary.org/obo/SO_0000704 gene The configuration of the IG and TR variable (V), diversity (D) and joining (J) germline genes before DNA rearrangements (with or without constant (C) genes in undefined configuration. (germline, non rearranged regions of the IG DNA loci). http://purl.obolibrary.org/obo/SO_0002122 immunoglobulin_gene http://purl.obolibrary.org/obo/SO_0002121 vertebrate_immune_system_gene A germline immunoglobulin gene. http://purl.obolibrary.org/obo/SO_0002123 IG_C_gene http://purl.obolibrary.org/obo/SO_0002122 immunoglobulin_gene A constant (C) gene, a gene that codes the constant region of an immunoglobulin chain. http://purl.obolibrary.org/obo/SO_0002124 IG_D_gene http://purl.obolibrary.org/obo/SO_0002122 immunoglobulin_gene A gene that rearranges at the DNA level and codes the diversity region of the variable domain of an immunoglobuin (IG) gene. http://purl.obolibrary.org/obo/SO_0002125 IG_J_gene http://purl.obolibrary.org/obo/SO_0002122 immunoglobulin_gene A joining gene that rearranges at the DNA level and codes the joining region of the variable domain of an immunoglobulin chain. http://purl.obolibrary.org/obo/SO_0002126 IG_V_gene http://purl.obolibrary.org/obo/SO_0002122 immunoglobulin_gene A variable gene that rearranges at the DNA level and codes the variable region of the variable domain of an Immunoglobulin chain. http://purl.obolibrary.org/obo/SO_0002127 lncRNA_gene http://purl.obolibrary.org/obo/SO_0001263 ncRNA_gene A gene that encodes a long non-coding RNA. http://purl.obolibrary.org/obo/SO_0002128 mt_rRNA http://purl.obolibrary.org/obo/SO_0000252 rRNA Mitochondrial rRNA is an RNA component of the small or large subunits of mitochondrial ribosomes. http://purl.obolibrary.org/obo/SO_0002129 mt_tRNA http://purl.obolibrary.org/obo/SO_0000253 tRNA Mitochondrial transfer RNA. http://purl.obolibrary.org/obo/SO_0002130 NSD_transcript http://purl.obolibrary.org/obo/SO_0000234 mRNA A transcript that contains a CDS but has no stop codon before the polyA site is reached. http://purl.obolibrary.org/obo/SO_0002131 sense_intronic_lncRNA http://purl.obolibrary.org/obo/SO_0001877 lncRNA A long non-coding transcript found within an intron of a coding or non-coding gene, with no overlap of exonic sequence. http://purl.obolibrary.org/obo/SO_0002132 sense_overlap_lncRNA http://purl.obolibrary.org/obo/SO_0001877 lncRNA A long non-coding transcript that contains a protein coding gene within its intronic sequence on the same strand, with no overlap of exonic sequence. http://purl.obolibrary.org/obo/SO_0002133 T_cell_receptor_gene http://purl.obolibrary.org/obo/SO_0002121 vertebrate_immune_system_gene A T-cell receptor germline gene. http://purl.obolibrary.org/obo/SO_0002134 TR_C_Gene http://purl.obolibrary.org/obo/SO_0002133 T_cell_receptor_gene A constant (C) gene, a gene that codes the constant region of a T-cell receptor chain. http://purl.obolibrary.org/obo/SO_0002135 TR_D_Gene http://purl.obolibrary.org/obo/SO_0002133 T_cell_receptor_gene A gene that rearranges at the DNA level and codes the diversity region of the variable domain of aT-cell receptor gene. http://purl.obolibrary.org/obo/SO_0002136 TR_J_Gene http://purl.obolibrary.org/obo/SO_0002133 T_cell_receptor_gene A joining gene that rearranges at the DNA level and codes the joining region of the variable domain of aT-cell receptor chain. http://purl.obolibrary.org/obo/SO_0002137 TR_V_Gene http://purl.obolibrary.org/obo/SO_0002133 T_cell_receptor_gene A variable gene that rearranges at the DNA level and codes the variable region of the variable domain of aT-cell receptor chain. http://purl.obolibrary.org/obo/SO_0002138 predicted_transcript http://purl.obolibrary.org/obo/SO_0000673 transcript A transcript feature that has been predicted but is not yet validated. http://purl.obolibrary.org/obo/SO_0002139 unconfirmed_transcript http://purl.obolibrary.org/obo/SO_0002138 predicted_transcript This is used for non-spliced EST clusters that have polyA features. This category has been specifically created for the ENCODE project to highlight regions that could indicate the presence of protein coding genes that require experimental validation, either by 5' RACE or RT-PCR to extend the transcripts, or by confirming expression of the putatively-encoded peptide with specific antibodies. http://purl.obolibrary.org/obo/SO_0002140 early_origin_of_replication http://purl.obolibrary.org/obo/SO_0000296 origin_of_replication An origin of replication that initiates early in S phase. http://purl.obolibrary.org/obo/SO_0002142 histone_2A_acetylation_site http://purl.obolibrary.org/obo/SO_0001702 histone_acetylation_site A histone 2A modification where the modification is the acetylation of the residue. http://purl.obolibrary.org/obo/SO_0002143 histone_2B_acetylation_site http://purl.obolibrary.org/obo/SO_0001702 histone_acetylation_site A histone 2B modification where the modification is the acetylation of the residue. http://purl.obolibrary.org/obo/SO_0002144 histone_2AZ_acetylation_site http://purl.obolibrary.org/obo/SO_0002142 histone_2A_acetylation_site A histone 2AZ modification where the modification is the acetylation of the residue. http://purl.obolibrary.org/obo/SO_0002145 H2AZK4_acetylation_site http://purl.obolibrary.org/obo/SO_0002144 histone_2AZ_acetylation_site A kind of histone modification site, whereby the 4th residue (a lysine), from the start of the H2AZ histone protein is acetylated. http://purl.obolibrary.org/obo/SO_0002146 H2AZK7_acetylation_site http://purl.obolibrary.org/obo/SO_0002144 histone_2AZ_acetylation_site A kind of histone modification site, whereby the 7th residue (a lysine), from the start of the H2AZ histone protein is acetylated. http://purl.obolibrary.org/obo/SO_0002147 H2AZK11_acetylation_site http://purl.obolibrary.org/obo/SO_0002144 histone_2AZ_acetylation_site A kind of histone modification site, whereby the 11th residue (a lysine), from the start of the H2AZ histone protein is acetylated. http://purl.obolibrary.org/obo/SO_0002148 H2AZK13_acetylation_site http://purl.obolibrary.org/obo/SO_0002144 histone_2AZ_acetylation_site A kind of histone modification site, whereby the 13th residue (a lysine), from the start of the H2AZ histone protein is acetylated. http://purl.obolibrary.org/obo/SO_0002149 H2AZK15_acetylation_site http://purl.obolibrary.org/obo/SO_0002144 histone_2AZ_acetylation_site A kind of histone modification site, whereby the 15th residue (a lysine), from the start of the H2AZ histone protein is acetylated. http://purl.obolibrary.org/obo/SO_0002150 AUG_initiated_uORF http://purl.obolibrary.org/obo/SO_0002027 uORF A uORF beginning with the canonical start codon AUG. http://purl.obolibrary.org/obo/SO_0002151 non_AUG_initiated_uORF http://purl.obolibrary.org/obo/SO_0002027 uORF A uORF beginning with a codon other than AUG. http://purl.obolibrary.org/obo/SO_0002152 genic_downstream_transcript_variant http://purl.obolibrary.org/obo/SO_0001564 gene_variant A variant that falls downstream of a transcript, but within the genic region of the gene due to alternately transcribed isoforms. http://purl.obolibrary.org/obo/SO_0002153 genic_upstream_transcript_variant http://purl.obolibrary.org/obo/SO_0001564 gene_variant A variant that falls upstream of a transcript, but within the genic region of the gene due to alternately transcribed isoforms. http://purl.obolibrary.org/obo/SO_0002154 mitotic_recombination_region http://purl.obolibrary.org/obo/SO_0000298 recombination_feature A genomic region where there is an exchange of genetic material with another genomic region, occurring in somatic cells. http://purl.obolibrary.org/obo/SO_0002155 meiotic_recombination_region http://purl.obolibrary.org/obo/SO_0000298 recombination_feature A genomic region in which there is an exchange of genetic material as a result of the repair of meiosis-specific double strand breaks that occur during meiotic prophase. http://purl.obolibrary.org/obo/SO_0002156 CArG_box http://purl.obolibrary.org/obo/SO_0001659 promoter_element A promoter element bound by the MADS family of transcription factors with consensus 5'-(C/T)TA(T/A)4TA(G/A)-3'. http://purl.obolibrary.org/obo/SO_0002157 Mat2P http://purl.obolibrary.org/obo/SO_0001984 silent_mating_type_cassette_array A gene cassette array containing H+ mating type specific information. http://purl.obolibrary.org/obo/SO_0002158 Mat3M http://purl.obolibrary.org/obo/SO_0001984 silent_mating_type_cassette_array A gene cassette array containing H- mating type specific information. http://purl.obolibrary.org/obo/SO_0002159 SHP_box http://purl.obolibrary.org/obo/SO_0100017 polypeptide_conserved_motif A conserved Cdc48/p97 interaction motif with strict consensus sequence F[PI]GKG[TK][RK]LG[GT] and relaxed consensus sequence FXGKGX[RK]LG. http://purl.obolibrary.org/obo/SO_0005837 U14_snoRNA_primary_transcript http://purl.obolibrary.org/obo/SO_0000232 snoRNA_primary_transcript The primary transcript of an evolutionarily conserved eukaryotic low molecular weight RNA capable of intermolecular hybridization with both homologous and heterologous 18S rRNA. http://purl.obolibrary.org/obo/SO_0005841 methylation_guide_snoRNA http://purl.obolibrary.org/obo/SO_0000593 C_D_box_snoRNA A snoRNA that specifies the site of 2'-O-ribose methylation in an RNA molecule by base pairing with a short sequence around the target residue. http://purl.obolibrary.org/obo/SO_0005843 rRNA_cleavage_RNA http://purl.obolibrary.org/obo/SO_0000655 ncRNA An ncRNA that is part of a ribonucleoprotein that cleaves the primary pre-rRNA transcript in the process of producing mature rRNA molecules. http://purl.obolibrary.org/obo/SO_0005845 exon_of_single_exon_gene http://purl.obolibrary.org/obo/SO_0000147 exon An exon that is the only exon in a gene. http://purl.obolibrary.org/obo/SO_0005847 cassette_array_member http://purl.obolibrary.org/obo/SO_0005848 gene_cassette_member A gene that is a member of a gene cassette, which is a mobile genetic element. http://purl.obolibrary.org/obo/SO_0005848 gene_cassette_member http://purl.obolibrary.org/obo/SO_0000081 gene_array_member A gene that is a member of a gene cassette, which is a mobile genetic element. http://purl.obolibrary.org/obo/SO_0005849 gene_subarray_member http://purl.obolibrary.org/obo/SO_0000081 gene_array_member A gene that is a member of a group of genes that are either regulated or transcribed together within a larger group of genes that are regulated or transcribed together. http://purl.obolibrary.org/obo/SO_0005850 primer_binding_site http://purl.obolibrary.org/obo/SO_0001655 nucleotide_binding_site Non-covalent primer binding site for initiation of replication, transcription, or reverse transcription. http://purl.obolibrary.org/obo/SO_0005851 gene_array http://purl.obolibrary.org/obo/SO_0005855 gene_group An array includes two or more genes, or two or more gene subarrays, contiguously arranged where the individual genes, or subarrays, are either identical in sequence, or essentially so. http://purl.obolibrary.org/obo/SO_0005852 gene_subarray http://purl.obolibrary.org/obo/SO_0005855 gene_group A subarray is, by defintition, a member of a gene array (SO:0005851); the members of a subarray may differ substantially in sequence, but are closely related in function. http://purl.obolibrary.org/obo/SO_0005856 selenocysteine_tRNA_primary_transcript http://purl.obolibrary.org/obo/SO_0000210 tRNA_primary_transcript A primary transcript encoding seryl tRNA (SO:000269). http://purl.obolibrary.org/obo/SO_0005857 selenocysteinyl_tRNA http://purl.obolibrary.org/obo/SO_0000253 tRNA A tRNA sequence that has a selenocysteine anticodon, and a 3' selenocysteine binding region. http://purl.obolibrary.org/obo/SO_0005858 syntenic_region http://purl.obolibrary.org/obo/SO_0000330 conserved_region A region in which two or more pairs of homologous markers occur on the same chromosome in two or more species. http://purl.obolibrary.org/obo/SO_0100001 biochemical_region_of_peptide http://purl.obolibrary.org/obo/SO_0001067 polypeptide_motif A region of a peptide that is involved in a biochemical function. http://purl.obolibrary.org/obo/SO_0100002 molecular_contact_region http://purl.obolibrary.org/obo/SO_0100001 biochemical_region_of_peptide A region that is involved a contact with another molecule. http://purl.obolibrary.org/obo/SO_0100003 intrinsically_unstructured_polypeptide_region http://purl.obolibrary.org/obo/SO_0001070 polypeptide_structural_region A region of polypeptide chain with high conformational flexibility. http://purl.obolibrary.org/obo/SO_0100004 catmat_left_handed_three http://purl.obolibrary.org/obo/SO_0001078 polypeptide_secondary_structure A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1. http://purl.obolibrary.org/obo/SO_0100005 catmat_left_handed_four http://purl.obolibrary.org/obo/SO_0001078 polypeptide_secondary_structure A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170. The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2. http://purl.obolibrary.org/obo/SO_0100006 catmat_right_handed_three http://purl.obolibrary.org/obo/SO_0001078 polypeptide_secondary_structure A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1. http://purl.obolibrary.org/obo/SO_0100007 catmat_right_handed_four http://purl.obolibrary.org/obo/SO_0001078 polypeptide_secondary_structure A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170. The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2. http://purl.obolibrary.org/obo/SO_0100008 alpha_beta_motif http://purl.obolibrary.org/obo/SO_0001078 polypeptide_secondary_structure A motif of five consecutive residues and two H-bonds in which: H-bond between CO of residue(i) and NH of residue(i+4), H-bond between CO of residue(i) and NH of residue(i+3),Phi angles of residues(i+1), (i+2) and (i+3) are negative. http://purl.obolibrary.org/obo/SO_0100009 lipoprotein_signal_peptide http://purl.obolibrary.org/obo/SO_0100011 cleaved_peptide_region A peptide that acts as a signal for both membrane translocation and lipid attachment in prokaryotes. http://purl.obolibrary.org/obo/SO_0100010 no_output http://purl.obolibrary.org/obo/SO_0000703 experimental_result_region An experimental region wherean analysis has been run and not produced any annotation. http://purl.obolibrary.org/obo/SO_0100011 cleaved_peptide_region http://purl.obolibrary.org/obo/SO_0000839 polypeptide_region The cleaved_peptide_region is the region of a peptide sequence that is cleaved during maturation. http://purl.obolibrary.org/obo/SO_0100012 peptide_coil http://purl.obolibrary.org/obo/SO_0001078 polypeptide_secondary_structure Irregular, unstructured regions of a protein's backbone, as distinct from the regular region (namely alpha helix and beta strand - characterised by specific patterns of main-chain hydrogen bonds). http://purl.obolibrary.org/obo/SO_0100013 hydrophobic_region_of_peptide http://purl.obolibrary.org/obo/SO_0000839 polypeptide_region Hydrophobic regions are regions with a low affinity for water. http://purl.obolibrary.org/obo/SO_0100014 n_terminal_region http://purl.obolibrary.org/obo/SO_0100011 cleaved_peptide_region The amino-terminal positively-charged region of a signal peptide (approx 1-5 aa). http://purl.obolibrary.org/obo/SO_0100015 c_terminal_region http://purl.obolibrary.org/obo/SO_0100011 cleaved_peptide_region The more polar, carboxy-terminal region of the signal peptide (approx 3-7 aa). http://purl.obolibrary.org/obo/SO_0100016 central_hydrophobic_region_of_signal_peptide http://purl.obolibrary.org/obo/SO_0100011 cleaved_peptide_region The central, hydrophobic region of the signal peptide (approx 7-15 aa). http://purl.obolibrary.org/obo/SO_0100017 polypeptide_conserved_motif http://purl.obolibrary.org/obo/SO_0001067 polypeptide_motif A conserved motif is a short (up to 20 amino acids) region of biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found. http://purl.obolibrary.org/obo/SO_0100018 polypeptide_binding_motif http://purl.obolibrary.org/obo/SO_0100001 biochemical_region_of_peptide A polypeptide binding motif is a short (up to 20 amino acids) polypeptide region of biological interest that contains one or more amino acids experimentally shown to bind to a ligand. http://purl.obolibrary.org/obo/SO_0100019 polypeptide_catalytic_motif http://purl.obolibrary.org/obo/SO_0100001 biochemical_region_of_peptide A polypeptide catalytic motif is a short (up to 20 amino acids) polypeptide region that contains one or more active site residues. http://purl.obolibrary.org/obo/SO_0100020 polypeptide_DNA_contact http://purl.obolibrary.org/obo/SO_0100002 molecular_contact_region A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with DNA. http://purl.obolibrary.org/obo/SO_0100021 polypeptide_conserved_region http://purl.obolibrary.org/obo/SO_0000839 polypeptide_region A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found. http://purl.obolibrary.org/obo/SO_1000028 intrachromosomal_mutation http://purl.obolibrary.org/obo/SO_1000183 chromosome_structure_variation A chromosomal structure variation within a single chromosome. http://purl.obolibrary.org/obo/SO_1000029 chromosomal_deletion http://purl.obolibrary.org/obo/SO_1000028 intrachromosomal_mutation An incomplete chromosome. http://purl.obolibrary.org/obo/SO_1000030 chromosomal_inversion http://purl.obolibrary.org/obo/SO_1000028 intrachromosomal_mutation An interchromosomal mutation where a region of the chromosome is inverted with respect to wild type. http://purl.obolibrary.org/obo/SO_1000031 interchromosomal_mutation http://purl.obolibrary.org/obo/SO_1000183 chromosome_structure_variation A chromosomal structure variation whereby more than one chromosome is involved. http://purl.obolibrary.org/obo/SO_1000037 chromosomal_duplication http://purl.obolibrary.org/obo/SO_1000183 chromosome_structure_variation An extra chromosome. http://purl.obolibrary.org/obo/SO_1000038 intrachromosomal_duplication http://purl.obolibrary.org/obo/SO_1000037 chromosomal_duplication A duplication that occurred within a chromosome. http://purl.obolibrary.org/obo/SO_1000041 intrachromosomal_transposition http://purl.obolibrary.org/obo/SO_1000038 intrachromosomal_duplication A chromosome structure variation whereby a transposition occurred within a chromosome. http://purl.obolibrary.org/obo/SO_1000042 compound_chromosome http://purl.obolibrary.org/obo/SO_1000183 chromosome_structure_variation A chromosome structure variant where a monocentric element is caused by the fusion of two chromosome arms. http://purl.obolibrary.org/obo/SO_1000043 Robertsonian_fusion http://purl.obolibrary.org/obo/SO_1000044 chromosomal_translocation A non reciprocal translocation whereby the participating chromosomes break at their centromeres and the long arms fuse to form a single chromosome with a single centromere. http://purl.obolibrary.org/obo/SO_1000044 chromosomal_translocation http://purl.obolibrary.org/obo/SO_0000199 translocation A chromosomal mutation. Rearrangements that alter the pairing of telomeres are classified as translocations. http://purl.obolibrary.org/obo/SO_1000045 ring_chromosome http://purl.obolibrary.org/obo/SO_1000028 intrachromosomal_mutation A ring chromosome is a chromosome whose arms have fused together to form a ring, often with the loss of the ends of the chromosome. http://purl.obolibrary.org/obo/SO_1000046 pericentric_inversion http://purl.obolibrary.org/obo/SO_1000030 chromosomal_inversion A chromosomal inversion that includes the centromere. http://purl.obolibrary.org/obo/SO_1000047 paracentric_inversion http://purl.obolibrary.org/obo/SO_1000030 chromosomal_inversion A chromosomal inversion that does not include the centromere. http://purl.obolibrary.org/obo/SO_1000048 reciprocal_chromosomal_translocation http://purl.obolibrary.org/obo/SO_1000044 chromosomal_translocation A chromosomal translocation with two breaks; two chromosome segments have simply been exchanged. http://purl.obolibrary.org/obo/SO_1000136 autosynaptic_chromosome http://purl.obolibrary.org/obo/SO_1000183 chromosome_structure_variation An autosynaptic chromosome is the aneuploid product of recombination between a pericentric inversion and a cytologically wild-type chromosome. http://purl.obolibrary.org/obo/SO_1000138 homo_compound_chromosome http://purl.obolibrary.org/obo/SO_1000042 compound_chromosome A compound chromosome whereby two copies of the same chromosomal arm attached to a common centromere. The chromosome is diploid for the arm involved. http://purl.obolibrary.org/obo/SO_1000140 hetero_compound_chromosome http://purl.obolibrary.org/obo/SO_1000042 compound_chromosome A compound chromosome whereby two arms from different chromosomes are connected through the centromere of one of them. http://purl.obolibrary.org/obo/SO_1000141 chromosome_fission http://purl.obolibrary.org/obo/SO_1000028 intrachromosomal_mutation A chromosome that occurred by the division of a larger chromosome. http://purl.obolibrary.org/obo/SO_1000142 dextrosynaptic_chromosome http://purl.obolibrary.org/obo/SO_1000136 autosynaptic_chromosome An autosynaptic chromosome carrying the two right (D = dextro) telomeres. http://purl.obolibrary.org/obo/SO_1000143 laevosynaptic_chromosome http://purl.obolibrary.org/obo/SO_1000136 autosynaptic_chromosome LS is an autosynaptic chromosome carrying the two left (L = levo) telomeres. http://purl.obolibrary.org/obo/SO_1000144 free_duplication http://purl.obolibrary.org/obo/SO_1000037 chromosomal_duplication A chromosome structure variation whereby the duplicated sequences are carried as a free centric element. http://purl.obolibrary.org/obo/SO_1000145 free_ring_duplication http://purl.obolibrary.org/obo/SO_1000144 free_duplication A ring chromosome which is a copy of another chromosome. http://purl.obolibrary.org/obo/SO_1000147 deficient_translocation http://purl.obolibrary.org/obo/SO_1000044 chromosomal_translocation A chromosomal deletion whereby a translocation occurs in which one of the four broken ends loses a segment before re-joining. http://purl.obolibrary.org/obo/SO_1000148 inversion_cum_translocation http://purl.obolibrary.org/obo/SO_1000044 chromosomal_translocation A chromosomal translocation whereby the first two breaks are in the same chromosome, and the region between them is rejoined in inverted order to the other side of the first break, such that both sides of break one are present on the same chromosome. The remaining free ends are joined as a translocation with those resulting from the third break. http://purl.obolibrary.org/obo/SO_1000149 bipartite_duplication http://purl.obolibrary.org/obo/SO_1000038 intrachromosomal_duplication An interchromosomal mutation whereby the (large) region between the first two breaks listed is lost, and the two flanking segments (one of them centric) are joined as a translocation to the free ends resulting from the third break. http://purl.obolibrary.org/obo/SO_1000150 cyclic_translocation http://purl.obolibrary.org/obo/SO_0002060 interchromosomal_translocation A chromosomal translocation whereby three breaks occurred in three different chromosomes. The centric segment resulting from the first break listed is joined to the acentric segment resulting from the second, rather than the third. http://purl.obolibrary.org/obo/SO_1000151 bipartite_inversion http://purl.obolibrary.org/obo/SO_1000030 chromosomal_inversion A chromosomal inversion caused by three breaks in the same chromosome; both central segments are inverted in place (i.e., they are not transposed). http://purl.obolibrary.org/obo/SO_1000152 uninverted_insertional_duplication http://purl.obolibrary.org/obo/SO_1000154 insertional_duplication An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments. http://purl.obolibrary.org/obo/SO_1000153 inverted_insertional_duplication http://purl.obolibrary.org/obo/SO_1000154 insertional_duplication An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments. http://purl.obolibrary.org/obo/SO_1000154 insertional_duplication http://purl.obolibrary.org/obo/SO_1000037 chromosomal_duplication A chromosome duplication involving the insertion of a duplicated region (as opposed to a free duplication). http://purl.obolibrary.org/obo/SO_1000155 interchromosomal_transposition http://purl.obolibrary.org/obo/SO_1000031 interchromosomal_mutation A chromosome structure variation whereby a transposition occurred between chromosomes. http://purl.obolibrary.org/obo/SO_1000156 inverted_interchromosomal_transposition http://purl.obolibrary.org/obo/SO_1000155 interchromosomal_transposition An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segment. http://purl.obolibrary.org/obo/SO_1000157 uninverted_interchromosomal_transposition http://purl.obolibrary.org/obo/SO_1000155 interchromosomal_transposition An interchromosomal transition where the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments. http://purl.obolibrary.org/obo/SO_1000158 inverted_intrachromosomal_transposition http://purl.obolibrary.org/obo/SO_1000041 intrachromosomal_transposition An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically inverted orientation with respect to its flanking segments. http://purl.obolibrary.org/obo/SO_1000159 uninverted_intrachromosomal_transposition http://purl.obolibrary.org/obo/SO_1000041 intrachromosomal_transposition An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the insertion is in cytologically the same orientation as its flanking segments. http://purl.obolibrary.org/obo/SO_1000160 unoriented_insertional_duplication http://purl.obolibrary.org/obo/SO_1000154 insertional_duplication An insertional duplication where a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded. http://purl.obolibrary.org/obo/SO_1000161 unoriented_interchromosomal_transposition http://purl.obolibrary.org/obo/SO_1000155 interchromosomal_transposition An interchromosomal transposition whereby a copy of the segment between the first two breaks listed is inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded. http://purl.obolibrary.org/obo/SO_1000162 unoriented_intrachromosomal_transposition http://purl.obolibrary.org/obo/SO_1000041 intrachromosomal_transposition An intrachromosomal transposition whereby the segment between the first two breaks listed is removed and inserted at the third break; the orientation of the insertion with respect to its flanking segments is not recorded. http://purl.obolibrary.org/obo/SO_1000170 uncharacterized_chromosomal_mutation http://purl.obolibrary.org/obo/SO_1000183 chromosome_structure_variation A chromosome structure variant that has not been characterized. http://purl.obolibrary.org/obo/SO_1000171 deficient_inversion http://purl.obolibrary.org/obo/SO_1000030 chromosomal_inversion A chromosomal deletion whereby three breaks occur in the same chromosome; one central region is lost, and the other is inverted. http://purl.obolibrary.org/obo/SO_1000175 partially_characterized_chromosomal_mutation http://purl.obolibrary.org/obo/SO_1000170 uncharacterized_chromosomal_mutation A chromosome structure variant that has not been characterized fully. http://purl.obolibrary.org/obo/SO_1000182 chromosome_number_variation http://purl.obolibrary.org/obo/SO_0000240 chromosome_variation A kind of chromosome variation where the chromosome complement is not an exact multiple of the haploid number. http://purl.obolibrary.org/obo/SO_1000183 chromosome_structure_variation http://purl.obolibrary.org/obo/SO_0000240 chromosome_variation An alteration of the genome that leads to a change in the structure or number of one or more chromosomes. http://purl.obolibrary.org/obo/SO_1001187 alternatively_spliced_transcript http://purl.obolibrary.org/obo/SO_0000673 transcript A transcript that is alternatively spliced. http://purl.obolibrary.org/obo/SO_1001188 encodes_1_polypeptide http://purl.obolibrary.org/obo/SO_0000463 encodes_alternately_spliced_transcripts A gene that is alternately spliced, but encodes only one polypeptide. http://purl.obolibrary.org/obo/SO_1001189 encodes_greater_than_1_polypeptide http://purl.obolibrary.org/obo/SO_0000463 encodes_alternately_spliced_transcripts A gene that is alternately spliced, and encodes more than one polypeptide. http://purl.obolibrary.org/obo/SO_1001190 encodes_different_polypeptides_different_stop http://purl.obolibrary.org/obo/SO_1001195 encodes_overlapping_peptides A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different stop codons. http://purl.obolibrary.org/obo/SO_1001191 encodes_overlapping_peptides_different_start http://purl.obolibrary.org/obo/SO_1001195 encodes_overlapping_peptides A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different start codons. http://purl.obolibrary.org/obo/SO_1001192 encodes_disjoint_polypeptides http://purl.obolibrary.org/obo/SO_1001189 encodes_greater_than_1_polypeptide A gene that is alternately spliced, and encodes more than one polypeptide, that do not have overlapping peptide sequences. http://purl.obolibrary.org/obo/SO_1001193 encodes_overlapping_polypeptides_different_start_and_stop http://purl.obolibrary.org/obo/SO_1001195 encodes_overlapping_peptides A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences, but use different start and stop codons. http://purl.obolibrary.org/obo/SO_1001195 encodes_overlapping_peptides http://purl.obolibrary.org/obo/SO_1001189 encodes_greater_than_1_polypeptide A gene that is alternately spliced, and encodes more than one polypeptide, that have overlapping peptide sequences. http://purl.obolibrary.org/obo/SO_1001197 dicistronic_primary_transcript http://purl.obolibrary.org/obo/SO_0000631 polycistronic_primary_transcript A primary transcript that has the quality dicistronic. http://purl.obolibrary.org/obo/SO_1001217 member_of_regulon http://purl.obolibrary.org/obo/SO_0000081 gene_array_member A gene that is a member of a group of genes that are either regulated or transcribed together. http://purl.obolibrary.org/obo/SO_1001246 CDS_independently_known http://purl.obolibrary.org/obo/SO_0000316 CDS A CDS with the evidence status of being independently known. http://purl.obolibrary.org/obo/SO_1001247 orphan_CDS http://purl.obolibrary.org/obo/SO_1001254 CDS_predicted A CDS whose predicted amino acid sequence is unsupported by any experimental evidence or by any match with any other known sequence. http://purl.obolibrary.org/obo/SO_1001249 CDS_supported_by_domain_match_data http://purl.obolibrary.org/obo/SO_1001251 CDS_supported_by_sequence_similarity_data A CDS that is supported by domain similarity. http://purl.obolibrary.org/obo/SO_1001251 CDS_supported_by_sequence_similarity_data http://purl.obolibrary.org/obo/SO_1001254 CDS_predicted A CDS that is supported by sequence similarity data. http://purl.obolibrary.org/obo/SO_1001254 CDS_predicted http://purl.obolibrary.org/obo/SO_0000316 CDS A CDS that is predicted. http://purl.obolibrary.org/obo/SO_1001259 CDS_supported_by_EST_or_cDNA_data http://purl.obolibrary.org/obo/SO_1001251 CDS_supported_by_sequence_similarity_data A CDS that is supported by similarity to EST or cDNA data. http://purl.obolibrary.org/obo/SO_1001260 internal_Shine_Dalgarno_sequence http://purl.obolibrary.org/obo/SO_1001268 recoding_stimulatory_region A Shine-Dalgarno sequence that stimulates recoding through interactions with the anti-Shine-Dalgarno in the RNA of small ribosomal subunits of translating ribosomes. The signal is only operative in Bacteria. http://purl.obolibrary.org/obo/SO_1001262 minus_1_translationally_frameshifted http://purl.obolibrary.org/obo/SO_0000887 translationally_frameshifted An attribute describing a translational frameshift of -1. http://purl.obolibrary.org/obo/SO_1001263 plus_1_translationally_frameshifted http://purl.obolibrary.org/obo/SO_0000887 translationally_frameshifted An attribute describing a translational frameshift of +1. http://purl.obolibrary.org/obo/SO_1001268 recoding_stimulatory_region http://purl.obolibrary.org/obo/SO_0000836 mRNA_region A site in an mRNA sequence that stimulates the recoding of a region in the same mRNA. http://purl.obolibrary.org/obo/SO_1001269 four_bp_start_codon http://purl.obolibrary.org/obo/SO_0000680 non_canonical_start_codon A non-canonical start codon with 4 base pairs. http://purl.obolibrary.org/obo/SO_1001271 archaeal_intron http://purl.obolibrary.org/obo/SO_0001216 endonuclease_spliced_intron An intron characteristic of Archaeal tRNA and rRNA genes, where intron transcript generates a bulge-helix-bulge motif that is recognised by a splicing endoribonuclease. http://purl.obolibrary.org/obo/SO_1001272 tRNA_intron http://purl.obolibrary.org/obo/SO_0001216 endonuclease_spliced_intron An intron found in tRNA that is spliced via endonucleolytic cleavage and ligation rather than transesterification. http://purl.obolibrary.org/obo/SO_1001273 CTG_start_codon http://purl.obolibrary.org/obo/SO_0000680 non_canonical_start_codon A non-canonical start codon of sequence CTG. http://purl.obolibrary.org/obo/SO_1001274 SECIS_element http://purl.obolibrary.org/obo/SO_1001268 recoding_stimulatory_region The incorporation of selenocysteine into a protein sequence is directed by an in-frame UGA codon (usually a stop codon) within the coding region of the mRNA. Selenoprotein mRNAs contain a conserved secondary structure in the 3' UTR that is required for the distinction of UGA stop from UGA selenocysteine. The selenocysteine insertion sequence (SECIS) is around 60 nt in length and adopts a hairpin structure which is sufficiently well-defined and conserved to act as a computational screen for selenoprotein genes. http://purl.obolibrary.org/obo/SO_1001277 three_prime_recoding_site http://purl.obolibrary.org/obo/SO_1001268 recoding_stimulatory_region The recoding stimulatory signal located downstream of the recoding site. http://purl.obolibrary.org/obo/SO_1001279 three_prime_stem_loop_structure http://purl.obolibrary.org/obo/SO_1001277 three_prime_recoding_site A recoding stimulatory region, the stem-loop secondary structural element is downstream of the redefined region. http://purl.obolibrary.org/obo/SO_1001280 five_prime_recoding_site http://purl.obolibrary.org/obo/SO_1001268 recoding_stimulatory_region The recoding stimulatory signal located upstream of the recoding site. http://purl.obolibrary.org/obo/SO_1001281 flanking_three_prime_quadruplet_recoding_signal http://purl.obolibrary.org/obo/SO_1001277 three_prime_recoding_site Four base pair sequence immediately downstream of the redefined region. The redefined region is a frameshift site. The quadruplet is 2 overlapping codons. http://purl.obolibrary.org/obo/SO_1001282 UAG_stop_codon_signal http://purl.obolibrary.org/obo/SO_1001288 stop_codon_signal A stop codon signal for a UAG stop codon redefinition. http://purl.obolibrary.org/obo/SO_1001283 UAA_stop_codon_signal http://purl.obolibrary.org/obo/SO_1001288 stop_codon_signal A stop codon signal for a UAA stop codon redefinition. http://purl.obolibrary.org/obo/SO_1001284 regulon http://purl.obolibrary.org/obo/SO_0005855 gene_group A set of units of gene expression directly regulated by a common set of one or more common regulatory gene products. http://purl.obolibrary.org/obo/SO_1001285 UGA_stop_codon_signal http://purl.obolibrary.org/obo/SO_1001288 stop_codon_signal A stop codon signal for a UGA stop codon redefinition. http://purl.obolibrary.org/obo/SO_1001286 three_prime_repeat_recoding_signal http://purl.obolibrary.org/obo/SO_1001277 three_prime_recoding_site A recoding stimulatory signal, downstream sequence important for recoding that contains repetitive elements. http://purl.obolibrary.org/obo/SO_1001287 distant_three_prime_recoding_signal http://purl.obolibrary.org/obo/SO_1001277 three_prime_recoding_site A recoding signal that is found many hundreds of nucleotides 3' of a redefined stop codon. http://purl.obolibrary.org/obo/SO_1001288 stop_codon_signal http://purl.obolibrary.org/obo/SO_1001268 recoding_stimulatory_region A recoding stimulatory signal that is a stop codon and has effect on efficiency of recoding. http://purl.obolibrary.org/obo/SO_2000061 databank_entry http://purl.obolibrary.org/obo/SO_0000695 reagent The sequence referred to by an entry in a databank such as GenBank or SwissProt. http://purl.obolibrary.org/obo/SO_0002217 unspecified_indel http://purl.obolibrary.org/obo/SO_0001059 sequence_alteration A sequence alteration which includes an insertion or a deletion. This describes a sequence length change when the direction of the change is unspecified or when such changes are pooled into one category. http://purl.obolibrary.org/obo/SO_0002304 topologically_associated_domain http://purl.obolibrary.org/obo/SO_0001412 topologically_defined_region An instance of a self-interacting DNA region flanked by left and right TAD boundaries. http://purl.obolibrary.org/obo/SO_0002305 topologically_associated_domain_boundary http://purl.obolibrary.org/obo/SO_0000699 junction A DNA region enriched in DNA loop anchors and across which DNA loops occur less often than expected by chance. http://purl.obolibrary.org/obo/SO_0002306 chromatin_regulatory_region http://purl.obolibrary.org/obo/SO_0000830 chromosome_part A region of a chromosome where regulatory events occur, including epigenetic modifications. These epigenetic modifications can include nucleosome modifications and post-replicational DNA modifications. http://purl.obolibrary.org/obo/SO_0002307 DNA_loop http://purl.obolibrary.org/obo/SO_0000830 chromosome_part A region of DNA between two loop anchor positions that are held in close physical proximity. http://purl.obolibrary.org/obo/SO_0002308 DNA_loop_anchor http://purl.obolibrary.org/obo/SO_0000727 cis_regulatory_module The ends of a DNA loop where the two strands of DNA are held in close physical proximity. During interphase the anchors of DNA loops are convergently oriented CTCF binding sites. http://purl.obolibrary.org/obo/SO_0002309 core_promoter_element http://purl.obolibrary.org/obo/SO_0001659 promoter_element An element that always exists within the promoter region of a gene. When multiple transcripts exist for a gene, the separate transcripts may have separate core_promoter_elements. http://purl.obolibrary.org/obo/SO_0002310 cryptic_promoter http://purl.obolibrary.org/obo/SO_0000167 promoter The promoter of a cryptic gene. http://purl.obolibrary.org/obo/SO_0002311 viral_promoter http://purl.obolibrary.org/obo/SO_0000167 promoter A regulatory_region including the Transcription Start Site (TSS) of a gene found in genes of viruses. http://purl.obolibrary.org/obo/SO_0002312 core_prokaryotic_promoter_element http://purl.obolibrary.org/obo/SO_0002309 core_promoter_element An element that always exists within the promoter region of a prokaryotic gene. http://purl.obolibrary.org/obo/SO_0002313 core_viral_promoter_element http://purl.obolibrary.org/obo/SO_0002309 core_promoter_element An element that always exists within the promoter region of a viral gene. http://purl.obolibrary.org/obo/SO_0000002 sequence_secondary_structure http://purl.obolibrary.org/obo/SO_0001411 biological_region A folded sequence. http://purl.obolibrary.org/obo/SO_0000003 G_quartet http://purl.obolibrary.org/obo/SO_0000002 sequence_secondary_structure G-quartets are unusual nucleic acid structures consisting of a planar arrangement where each guanine is hydrogen bonded by hoogsteen pairing to another guanine in the quartet. http://purl.obolibrary.org/obo/SO_0000011 non_protein_coding http://purl.obolibrary.org/obo/SO_0000401 gene_attribute A gene which can be transcribed, but will not be translated into a protein. http://purl.obolibrary.org/obo/SO_0000101 transposable_element http://purl.obolibrary.org/obo/SO_0001039 integrated_mobile_genetic_element A transposon or insertion sequence. An element that can insert in a variety of DNA sequences. http://purl.obolibrary.org/obo/SO_0000162 splice_site http://purl.obolibrary.org/obo/SO_0000835 primary_transcript_region Consensus region of primary transcript bordering junction of splicing. A region that overlaps exactly 2 base and adjacent_to splice_junction. http://purl.obolibrary.org/obo/SO_0000167 promoter http://purl.obolibrary.org/obo/SO_0001055 transcriptional_cis_regulatory_region A regulatory_region composed of the TSS(s) and binding sites for TF_complexes of the core transcription machinery. A region (DNA) to which RNA polymerase binds, to begin transcription. http://purl.obolibrary.org/obo/SO_0000180 retrotransposon http://purl.obolibrary.org/obo/SO_0000101 transposable_element A transposable element that is incorporated into a chromosome by a mechanism that requires reverse transcriptase. http://purl.obolibrary.org/obo/SO_0000185 primary_transcript http://purl.obolibrary.org/obo/SO_0000673 transcript A transcript that in its initial state requires modification to be functional. http://purl.obolibrary.org/obo/SO_0000186 LTR_retrotransposon http://purl.obolibrary.org/obo/SO_0000180 retrotransposon A retrotransposon flanked by long terminal repeat sequences. http://purl.obolibrary.org/obo/SO_0000188 intron http://purl.obolibrary.org/obo/SO_0000835 primary_transcript_region A region of a primary transcript that is transcribed, but removed from within the transcript by splicing together the sequences (exons) on either side of it. http://purl.obolibrary.org/obo/SO_0000209 rRNA_primary_transcript http://purl.obolibrary.org/obo/SO_0000483 nc_primary_transcript A primary transcript encoding a ribosomal RNA. http://purl.obolibrary.org/obo/SO_0000210 tRNA_primary_transcript http://purl.obolibrary.org/obo/SO_0000483 nc_primary_transcript A primary transcript encoding a transfer RNA (SO:0000253). http://purl.obolibrary.org/obo/SO_0000233 mature_transcript http://purl.obolibrary.org/obo/SO_0000673 transcript A transcript which has undergone the necessary modifications, if any, for its function. In eukaryotes this includes, for example, processing of introns, cleavage, base modification, and modifications to the 5' and/or the 3' ends, other than addition of bases. In bacteria functional mRNAs are usually not modified. http://purl.obolibrary.org/obo/SO_0000235 TF_binding_site http://purl.obolibrary.org/obo/SO_0001654 nucleotide_to_protein_binding_site A DNA site where a transcription factor binds. http://purl.obolibrary.org/obo/SO_0000237 transcript_attribute http://purl.obolibrary.org/obo/SO_0000733 feature_attribute An attribute describing a transcript. http://purl.obolibrary.org/obo/SO_0000246 polyadenylated http://purl.obolibrary.org/obo/SO_0000863 mRNA_attribute A attribute describing the addition of a poly A tail to the 3' end of a mRNA molecule. http://purl.obolibrary.org/obo/SO_0000255 rRNA_small_subunit_primary_transcript http://purl.obolibrary.org/obo/SO_0000209 rRNA_primary_transcript A primary transcript encoding a small ribosomal subunit RNA. http://purl.obolibrary.org/obo/SO_0000298 recombination_feature http://purl.obolibrary.org/obo/SO_0001411 biological_region A feature where there has been exchange of genetic material in the event of mitosis or meiosis http://purl.obolibrary.org/obo/SO_0000330 conserved_region http://purl.obolibrary.org/obo/SO_0001410 experimental_feature Region of sequence similarity by descent from a common ancestor. http://purl.obolibrary.org/obo/SO_0000340 chromosome http://purl.obolibrary.org/obo/SO_0001235 replicon Structural unit composed of a nucleic acid molecule which controls its own replication through the interaction of specific proteins at one or more origins of replication. http://purl.obolibrary.org/obo/SO_0000401 gene_attribute http://purl.obolibrary.org/obo/SO_0000733 feature_attribute An attribute describing a gene. http://purl.obolibrary.org/obo/SO_0000409 binding_site http://purl.obolibrary.org/obo/SO_0001411 biological_region A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids. http://purl.obolibrary.org/obo/SO_0000410 protein_binding_site http://purl.obolibrary.org/obo/SO_0000409 binding_site A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules. http://purl.obolibrary.org/obo/SO_0000483 nc_primary_transcript http://purl.obolibrary.org/obo/SO_0000185 primary_transcript A primary transcript that is never translated into a protein. http://purl.obolibrary.org/obo/SO_0000577 centromere http://purl.obolibrary.org/obo/SO_0000628 chromosomal_structural_element A region of chromosome where the spindle fibers attach during mitosis and meiosis. http://purl.obolibrary.org/obo/SO_0000578 snoRNA_encoding http://purl.obolibrary.org/obo/SO_0000011 non_protein_coding A region that can be transcribed into a small nucleolar RNA (snoRNA). http://purl.obolibrary.org/obo/SO_0000628 chromosomal_structural_element http://purl.obolibrary.org/obo/SO_0000830 chromosome_part Regions of the chromosome that are important for structural elements. http://purl.obolibrary.org/obo/SO_0000650 cytosolic_SSU_rRNA http://purl.obolibrary.org/obo/SO_0002343 cytosolic_rRNA Cytosolic SSU rRNA is an RNA component of the small subunit of cytosolic ribosomes. http://purl.obolibrary.org/obo/SO_0000651 cytosolic_LSU_rRNA http://purl.obolibrary.org/obo/SO_0002343 cytosolic_rRNA Cytosolic LSU rRNA is an RNA component of the large subunit of cytosolic ribosomes. http://purl.obolibrary.org/obo/SO_0000657 repeat_region http://purl.obolibrary.org/obo/SO_0001411 biological_region A region of sequence containing one or more repeat units. http://purl.obolibrary.org/obo/SO_0000663 tRNA_encoding http://purl.obolibrary.org/obo/SO_0000011 non_protein_coding A region that can be transcribed into a transfer RNA (tRNA). http://purl.obolibrary.org/obo/SO_0000713 DNA_motif http://purl.obolibrary.org/obo/SO_0000714 nucleotide_motif A motif that is active in the DNA form of the sequence. http://purl.obolibrary.org/obo/SO_0000714 nucleotide_motif http://purl.obolibrary.org/obo/SO_0001683 sequence_motif A region of nucleotide sequence corresponding to a known motif. http://purl.obolibrary.org/obo/SO_0000726 repeat_unit http://purl.obolibrary.org/obo/SO_0001411 biological_region The simplest repeated component of a repeat region. A single repeat. http://purl.obolibrary.org/obo/SO_0000733 feature_attribute http://purl.obolibrary.org/obo/SO_0000400 sequence_attribute An attribute describing a located_sequence_feature. http://purl.obolibrary.org/obo/SO_0000830 chromosome_part http://purl.obolibrary.org/obo/SO_0001411 biological_region A region of a chromosome. http://purl.obolibrary.org/obo/SO_0000833 transcript_region http://purl.obolibrary.org/obo/SO_0001411 biological_region A region of a transcript. http://purl.obolibrary.org/obo/SO_0000835 primary_transcript_region http://purl.obolibrary.org/obo/SO_0000833 transcript_region A part of a primary transcript. http://purl.obolibrary.org/obo/SO_0000863 mRNA_attribute http://purl.obolibrary.org/obo/SO_0000237 transcript_attribute An attribute describing an mRNA feature. http://purl.obolibrary.org/obo/SO_0001037 mobile_genetic_element http://purl.obolibrary.org/obo/SO_0001411 biological_region A nucleotide region with either intra-genome or intracellular mobility, of varying length, which often carry the information necessary for transfer and recombination with the host genome. http://purl.obolibrary.org/obo/SO_0001039 integrated_mobile_genetic_element http://purl.obolibrary.org/obo/SO_0001037 mobile_genetic_element An MGE that is integrated into the host chromosome. http://purl.obolibrary.org/obo/SO_0001055 transcriptional_cis_regulatory_region http://purl.obolibrary.org/obo/SO_0005836 regulatory_region A regulatory_region that modulates the transcription of a gene or genes. http://purl.obolibrary.org/obo/SO_0001234 mobile http://purl.obolibrary.org/obo/SO_0000733 feature_attribute An attribute describing a feature that has either intra-genome or intracellular mobility. http://purl.obolibrary.org/obo/SO_0001235 replicon http://purl.obolibrary.org/obo/SO_0001411 biological_region A region containing at least one unique origin of replication and a unique termination site. http://purl.obolibrary.org/obo/SO_0001410 experimental_feature http://purl.obolibrary.org/obo/SO_0000001 region A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer. http://purl.obolibrary.org/obo/SO_0001654 nucleotide_to_protein_binding_site http://purl.obolibrary.org/obo/SO_0000410 protein_binding_site A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues. http://purl.obolibrary.org/obo/SO_0001659 promoter_element http://purl.obolibrary.org/obo/SO_0000713 DNA_motif An element that can exist within the promoter region of a gene. http://purl.obolibrary.org/obo/SO_0001683 sequence_motif http://purl.obolibrary.org/obo/SO_0001411 biological_region A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance. http://purl.obolibrary.org/obo/SO_0001797 centromeric_repeat http://purl.obolibrary.org/obo/SO_0000657 repeat_region A repeat region found within the modular centromere. http://purl.obolibrary.org/obo/SO_0001850 HSE http://purl.obolibrary.org/obo/SO_0001659 promoter_element A promoter element that consists of at least three copies of the pentanucleotide NGAAN, bound by the heat shock transcription factor HSF. http://purl.obolibrary.org/obo/SO_0001858 TR_box http://purl.obolibrary.org/obo/SO_0001659 promoter_element A promoter element with consensus sequence TTCTTTGTTY, bound an HMG-box transcription factor such as S. pombe Ste11, and found in promoters of genes up-regulated early in meiosis. http://purl.obolibrary.org/obo/SO_0002072 sequence_comparison http://purl.obolibrary.org/obo/SO_0000110 sequence_feature A position or feature where two sequences have been compared. http://purl.obolibrary.org/obo/SO_0002141 late_origin_of_replication http://purl.obolibrary.org/obo/SO_0000296 origin_of_replication An origin of replication that initiates late in S phase. http://purl.obolibrary.org/obo/SO_0005836 regulatory_region http://purl.obolibrary.org/obo/SO_0000831 gene_member_region A region of sequence that is involved in the control of a biological process. http://purl.obolibrary.org/obo/SO_0005853 gene_cassette http://purl.obolibrary.org/obo/SO_0000704 gene A gene that can be substituted for a related gene at a different site in the genome. http://purl.obolibrary.org/obo/SO_0005854 gene_cassette_array http://purl.obolibrary.org/obo/SO_0005855 gene_group An array of non-functional genes whose members, when captured by recombination form functional genes. http://purl.obolibrary.org/obo/SO_0005855 gene_group http://purl.obolibrary.org/obo/SO_0001411 biological_region A collection of related genes. http://purl.obolibrary.org/obo/SO_0000352 DNA http://purl.obolibrary.org/obo/SO_0000348 nucleic_acid An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a 2-deoxy-D-ribose ring connected to a phosphate backbone. http://purl.obolibrary.org/obo/SO_0000356 RNA http://purl.obolibrary.org/obo/SO_0000348 nucleic_acid An attribute describing a sequence consisting of nucleobases bound to a repeating unit made of a D-ribose ring connected to a phosphate backbone. http://purl.obolibrary.org/obo/SO_0002291 circular_ncRNA http://purl.obolibrary.org/obo/SO_0000655 ncRNA A non-coding RNA that is generated by backsplicing of exons or introns, resulting in a covalently closed loop without a 5’ cap or 3’ polyA tail. http://purl.obolibrary.org/obo/SO_0002292 circular_mRNA http://purl.obolibrary.org/obo/SO_0000234 mRNA An mRNA that is generated by backsplicing of exons or introns, resulting in a covalently closed loop without a 5’ cap or 3’ polyA tail. http://purl.obolibrary.org/obo/SO_0002319 NMD_triggering_variant http://purl.obolibrary.org/obo/SO_0002218 functionally_abnormal A sequence variant that leads to a change in the location of a termination codon in a transcript that leads to nonsense-mediated decay (NMD). The change in location of a termination codon can be caused by several different types of sequence variants, including stop_gained (SO:0001587), frameshift_variant (SO:0001589), splice_donor_variant (SO:0001575), and splice_acceptor_variant (SO:0001574) types of variants. http://purl.obolibrary.org/obo/SO_0002320 NMD_escaping_variant http://purl.obolibrary.org/obo/SO_0002218 functionally_abnormal A sequence variant that leads to a change in the location of a termination codon in a transcript but allows the transcript to escape nonsense-mediated decay (NMD). The change in location of a termination codon can be caused by several different types of sequence variants, including stop_gained (SO:0001587), frameshift_variant (SO:0001589), splice_donor_variant (SO:0001575), and splice_acceptor_variant (SO:0001574) types of variants. http://purl.obolibrary.org/obo/SO_0002321 stop_gained_NMD_triggering http://purl.obolibrary.org/obo/SO_0002319 NMD_triggering_variant A stop_gained (SO:0001587) variant that is degraded by nonsense-mediated decay (NMD). http://purl.obolibrary.org/obo/SO_0002322 stop_gained_NMD_escaping http://purl.obolibrary.org/obo/SO_0002320 NMD_escaping_variant A stop_gained (SO:0001587) variant that allows the transcript to escape nonsense-mediated decay (NMD). http://purl.obolibrary.org/obo/SO_0002323 frameshift_variant_NMD_triggering http://purl.obolibrary.org/obo/SO_0002319 NMD_triggering_variant A frameshift_variant (SO:0001589) that is degraded by nonsense-mediated decay (NMD). http://purl.obolibrary.org/obo/SO_0002324 frameshift_variant_NMD_escaping http://purl.obolibrary.org/obo/SO_0002320 NMD_escaping_variant A frameshift_variant (SO:0001589) that allows the transcript to escape nonsense-mediated decay (NMD). http://purl.obolibrary.org/obo/SO_0002325 splice_donor_variant_NMD_triggering http://purl.obolibrary.org/obo/SO_0002319 NMD_triggering_variant A splice_donor_variant (SO:0001575) that is degraded by nonsense-mediated decay (NMD). http://purl.obolibrary.org/obo/SO_0002326 splice_donor_variant_NMD_escaping http://purl.obolibrary.org/obo/SO_0002320 NMD_escaping_variant A splice_donor_variant (SO:0001575) that allows the transcript to escape nonsense-mediated decay (NMD). http://purl.obolibrary.org/obo/SO_0002327 splice_acceptor_variant_NMD_triggering http://purl.obolibrary.org/obo/SO_0002319 NMD_triggering_variant A splice_acceptor_variant (SO:0001574) that is degraded by nonsense-mediated decay (NMD). http://purl.obolibrary.org/obo/SO_0002328 splice_acceptor_variant_NMD_escaping http://purl.obolibrary.org/obo/SO_0002320 NMD_escaping_variant A splice_acceptor_variant (SO:0001574) that allows the transcript to escape nonsense-mediated decay (NMD). http://purl.obolibrary.org/obo/SO_0002394 decreased_enzyme_activity_variant http://purl.obolibrary.org/obo/SO_0001554 polypeptide_function_variant A decrease in the activity of an enzyme, as a result of a variant in the gene that encodes the enzyme or a regulatory region. http://purl.obolibrary.org/obo/SO_0002188 functional_gene_region http://purl.obolibrary.org/obo/SO_0000831 gene_member_region A gene_member_region that encodes sequence that directly contributes to the molecular function of its gene or gene product. http://purl.obolibrary.org/obo/SO_0001628 intergenic_variant http://purl.obolibrary.org/obo/SO_0001878 feature_variant A sequence variant located in the intergenic region, between genes. http://purl.obolibrary.org/obo/SO_0002349 fragile_site http://purl.obolibrary.org/obo/SO_0001021 chromosome_breakpoint A heritable locus on a chromosome that is prone to DNA breakage. http://purl.obolibrary.org/obo/SO_0002350 common_fragile_site http://purl.obolibrary.org/obo/SO_0002349 fragile_site A fragile site considered part of the normal chromosomal structure. http://purl.obolibrary.org/obo/SO_0002351 rare_fragile_site http://purl.obolibrary.org/obo/SO_0002349 fragile_site A fragile site found in the chromosomes of less than five percent of the human population. http://purl.obolibrary.org/obo/SO_0002352 sisRNA http://purl.obolibrary.org/obo/SO_0000655 ncRNA A non-coding RNA typically derived from intronic sequence of the sense strand of a cognate host gene, that is not rapidly degraded. It may contain exonic sequences, 5′ caps, and/or polyA tails. http://purl.obolibrary.org/obo/SO_0002353 sbRNA_gene http://purl.obolibrary.org/obo/SO_0001263 ncRNA_gene A gene encoding a stem-bulge RNA. http://purl.obolibrary.org/obo/SO_0002354 sbRNA http://purl.obolibrary.org/obo/SO_0000655 ncRNA A small non-coding stem-loop RNA present in nematodes and insects, functionally and structurally related to vertebrate Y RNA. http://purl.obolibrary.org/obo/SO_0002355 hpRNA_gene http://purl.obolibrary.org/obo/SO_0001263 ncRNA_gene A gene encoding a hpRNA. http://purl.obolibrary.org/obo/SO_0002356 hpRNA http://purl.obolibrary.org/obo/SO_0000655 ncRNA An RNA comprising an extended inverted repeat, the stem of which is typically much longer than that of miRNA precursors and can be up to 400 base pairs in length. hpRNAs are processed by Dicer-2 to generate endogenous short interfering RNAs (siRNAs). http://purl.obolibrary.org/obo/SO_0002357 biosynthetic_gene_cluster http://purl.obolibrary.org/obo/SO_0001411 biological_region A physically clustered group of two or more genes in a particular genome that together encode a biosynthetic pathway for the production of a specialized metabolite (including its chemical variants). http://purl.obolibrary.org/obo/SO_0002358 vault_RNA_gene http://purl.obolibrary.org/obo/SO_0001263 ncRNA_gene A gene that encodes a vault RNA. http://purl.obolibrary.org/obo/SO_0002359 Y_RNA_gene http://purl.obolibrary.org/obo/SO_0001263 ncRNA_gene A gene that encodes a Y RNA. http://purl.obolibrary.org/obo/SO_0002360 cytosolic_rRNA_gene http://purl.obolibrary.org/obo/SO_0001637 rRNA_gene A gene that codes for cytosolic rRNA. http://purl.obolibrary.org/obo/SO_0002361 cytosolic_LSU_rRNA_gene http://purl.obolibrary.org/obo/SO_0002360 cytosolic_rRNA_gene A gene that codes for cytosolic LSU rRNA. http://purl.obolibrary.org/obo/SO_0002362 cytosolic_SSU_rRNA_gene http://purl.obolibrary.org/obo/SO_0002360 cytosolic_rRNA_gene A gene that codes for cytosolic SSU rRNA. http://purl.obolibrary.org/obo/SO_0002363 mt_rRNA_gene http://purl.obolibrary.org/obo/SO_0001637 rRNA_gene A gene that codes for mitochondrial rRNA. http://purl.obolibrary.org/obo/SO_0002364 mt_LSU_rRNA_gene http://purl.obolibrary.org/obo/SO_0002363 mt_rRNA_gene A gene that codes for mitochondrial LSU rRNA. http://purl.obolibrary.org/obo/SO_0002365 mt_SSU_rRNA_gene http://purl.obolibrary.org/obo/SO_0002363 mt_rRNA_gene A gene that codes for mitochondrial SSU rRNA. http://purl.obolibrary.org/obo/SO_0002366 plastid_rRNA_gene http://purl.obolibrary.org/obo/SO_0001637 rRNA_gene A gene that codes for plastid rRNA. http://purl.obolibrary.org/obo/SO_0002367 plastid_LSU_rRNA_gene http://purl.obolibrary.org/obo/SO_0002366 plastid_rRNA_gene A gene that codes for plastid LSU rRNA. http://purl.obolibrary.org/obo/SO_0002368 plastid_SSU_rRNA_gene http://purl.obolibrary.org/obo/SO_0002366 plastid_rRNA_gene A gene that codes for plastid SSU rRNA. http://purl.obolibrary.org/obo/SO_0002369 C_D_box_scaRNA http://purl.obolibrary.org/obo/SO_0002095 scaRNA A scaRNA possessing a box C/D sequence motif, guiding the methylation of snRNAs. http://purl.obolibrary.org/obo/SO_0002370 H_ACA_box_scaRNA http://purl.obolibrary.org/obo/SO_0002095 scaRNA A scaRNA possessing a box H/ACA sequence motif, guiding the pseudouridylation of snRNAs. http://purl.obolibrary.org/obo/SO_0002371 C-D_H_ACA_box_scaRNA http://purl.obolibrary.org/obo/SO_0002095 scaRNA A scaRNA possessing both box C/D and box H/ACA sequence motifs, guiding both the methylation and pseudouridylation of snRNAs. http://purl.obolibrary.org/obo/SO_0002372 C_D_box_scaRNA_gene http://purl.obolibrary.org/obo/SO_0002339 scaRNA_gene A gene that codes for scaRNA possessing a box C/D sequence motif, guiding the methylation of snRNAs. http://purl.obolibrary.org/obo/SO_0002373 H_ACA_box_scaRNA_gene http://purl.obolibrary.org/obo/SO_0002339 scaRNA_gene A gene that codes for scaRNA possessing a box H/ACA sequence motif, guiding the pseudouridylation of snRNAs. http://purl.obolibrary.org/obo/SO_0002374 C-D_H_ACA_box_scaRNA_gene http://purl.obolibrary.org/obo/SO_0002339 scaRNA_gene A gene that codes for scaRNA possessing both box C/D and box H/ACA sequence motifs, guiding both the methylation and pseudouridylation of snRNAs. http://purl.obolibrary.org/obo/SO_0002375 C_D_box_snoRNA_gene http://purl.obolibrary.org/obo/SO_0001267 snoRNA_gene A gene that codes a C_D_box_snoRNA. Most box C/D snoRNAs also contain long (>10 nt) sequences complementary to rRNA. Boxes C and D, as well as boxes C' and D', are usually located in close proximity, and form a structure known as the box C/D motif. This motif is important for snoRNA stability, processing, nucleolar targeting and function. A small number of box C/D snoRNAs are involved in rRNA processing; most, however, are known or predicted to serve as guide RNAs in ribose methylation of rRNA. Targeting involves direct base pairing of the snoRNA at the rRNA site to be modified and selection of a rRNA nucleotide a fixed distance from box D or D'. http://purl.obolibrary.org/obo/SO_0002376 H_ACA_box_snoRNA_gene http://purl.obolibrary.org/obo/SO_0001267 snoRNA_gene A gene that codes for H_ACA_box_snoRNA. Members of the box H/ACA family contain an ACA triplet, exactly 3 nt upstream from the 3' end and an H-box in a hinge region that links two structurally similar functional domains of the molecule. Both boxes are important for snoRNA biosynthesis and function. A few box H/ACA snoRNAs are involved in rRNA processing; most others are known or predicted to participate in selection of uridine nucleosides in rRNA to be converted to pseudouridines. Site selection is mediated by direct base pairing of the snoRNA with rRNA through one or both targeting domains. http://purl.obolibrary.org/obo/SO_0002377 U14_snoRNA_gene http://purl.obolibrary.org/obo/SO_0002375 C_D_box_snoRNA_gene A gene that codes for U14_snoRNA. U14 small nucleolar RNA (U14 snoRNA) is required for early cleavages of eukaryotic precursor rRNAs. In yeasts, this molecule possess a stem-loop region (known as the Y-domain) which is essential for function. A similar structure, but with a different consensus sequence, is found in plants, but is absent in vertebrates. http://purl.obolibrary.org/obo/SO_0002378 U3_snoRNA_gene http://purl.obolibrary.org/obo/SO_0002375 C_D_box_snoRNA_gene A gene that codes for U3_snoRNA. U3 snoRNA is a member of the box C/D class of small nucleolar RNAs. The U3 snoRNA secondary structure is characterised by a small 5' domain (with boxes A and A'), and a larger 3' domain (with boxes B, C, C', and D), the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif, which appears to be exclusive to U3 snoRNAs, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localization, stability and hypermethylation of U3 snoRNA. Both box B/C and C'/D motifs are involved in specific protein interactions and are necessary for the rRNA processing functions of U3 snoRNA. http://purl.obolibrary.org/obo/SO_0002379 methylation_guide_snoRNA_gene http://purl.obolibrary.org/obo/SO_0002375 C_D_box_snoRNA_gene A gene that codes for methylation_guide_snoRNA. A snoRNA that specifies the site of 2'-O-ribose methylation in an RNA molecule by base pairing with a short sequence around the target residue. http://purl.obolibrary.org/obo/SO_0002380 pseudouridylation_guide_snoRNA_gene http://purl.obolibrary.org/obo/SO_0002376 H_ACA_box_snoRNA_gene A gene that codes for pseudouridylation_guide_snoRNA. A snoRNA that specifies the site of pseudouridylation in an RNA molecule by base pairing with a short sequence around the target residue. http://purl.obolibrary.org/obo/SO_0000418 signal_peptide http://purl.obolibrary.org/obo/SO_0001527 peptide_localization_signal The signal_peptide is a short region of the peptide located at the N-terminus that directs the protein to be secreted or part of membrane components. http://purl.obolibrary.org/obo/SO_0000725 transit_peptide http://purl.obolibrary.org/obo/SO_0001527 peptide_localization_signal The transit_peptide is a short region at the N-terminus of the peptide that directs the protein to an organelle (chloroplast, mitochondrion, microbody or cyanelle). http://purl.obolibrary.org/obo/SO_0001062 propeptide http://purl.obolibrary.org/obo/SO_0100011 cleaved_peptide_region Part of a peptide chain which is cleaved off during the formation of the mature protein. http://purl.obolibrary.org/obo/SO_0001217 protein_coding_gene http://purl.obolibrary.org/obo/SO_0000704 gene A gene that codes for an RNA that can be translated into a protein. http://purl.obolibrary.org/obo/SO_0000150 read http://purl.obolibrary.org/obo/SO_0000143 assembly_component A sequence obtained from a single sequencing experiment. Typically a read is produced when a base calling program interprets information from a chromatogram trace file produced from a sequencing machine. http://purl.obolibrary.org/obo/SO_0000165 enhancer http://purl.obolibrary.org/obo/SO_0000727 cis_regulatory_module A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter. http://purl.obolibrary.org/obo/SO_0000336 pseudogene http://purl.obolibrary.org/obo/SO_0001411 biological_region A sequence that closely resembles a known functional gene, at another locus within a genome, that is non-functional as a consequence of (usually several) mutations that prevent either its transcription or translation (or both). In general, pseudogenes result from either reverse transcription of a transcript of their "normal" paralog (SO:0000043) (in which case the pseudogene typically lacks introns and includes a poly(A) tail) or from recombination (SO:0000044) (in which case the pseudogene is typically a tandem duplication of its "normal" paralog). http://purl.obolibrary.org/obo/SO_0000443 polymer_attribute http://purl.obolibrary.org/obo/SO_0000400 sequence_attribute An attribute to describe the kind of biological sequence. http://purl.obolibrary.org/obo/SO_0000462 pseudogenic_region http://purl.obolibrary.org/obo/SO_0001411 biological_region A non-functional descendant of a functional entity. http://purl.obolibrary.org/obo/SO_0000590 SRP_RNA http://purl.obolibrary.org/obo/SO_0000655 ncRNA The signal recognition particle (SRP) is a universally conserved ribonucleoprotein. It is involved in the co-translational targeting of proteins to membranes. The eukaryotic SRP consists of a 300-nucleotide 7S RNA and six proteins: SRPs 72, 68, 54, 19, 14, and 9. Archaeal SRP consists of a 7S RNA and homologues of the eukaryotic SRP19 and SRP54 proteins. In most eubacteria, the SRP consists of a 4.5S RNA and the Ffh protein (a homologue of the eukaryotic SRP54 protein). Eukaryotic and archaeal 7S RNAs have very similar secondary structures, with eight helical elements. These fold into the Alu and S domains, separated by a long linker region. Eubacterial SRP is generally a simpler structure, with the M domain of Ffh bound to a region of the 4.5S RNA that corresponds to helix 8 of the eukaryotic and archaeal SRP S domain. Some Gram-positive bacteria (e.g. Bacillus subtilis), however, have a larger SRP RNA that also has an Alu domain. The Alu domain is thought to mediate the peptide chain elongation retardation function of the SRP. The universally conserved helix which interacts with the SRP54/Ffh M domain mediates signal sequence recognition. In eukaryotes and archaea, the SRP19-helix 6 complex is thought to be involved in SRP assembly and stabilizes helix 8 for SRP54 binding. http://purl.obolibrary.org/obo/SO_0000655 ncRNA http://purl.obolibrary.org/obo/SO_0000233 mature_transcript An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product. http://purl.obolibrary.org/obo/SO_0000673 transcript http://purl.obolibrary.org/obo/SO_0000831 gene_member_region An RNA synthesized on a DNA or RNA template by an RNA polymerase. http://purl.obolibrary.org/obo/SO_0000771 QTL http://purl.obolibrary.org/obo/SO_0001411 biological_region A quantitative trait locus (QTL) is a polymorphic locus which contains alleles that differentially affect the expression of a continuously distributed phenotypic trait. Usually it is a marker described by statistical association to quantitative variation in the particular phenotypic trait that is thought to be controlled by the cumulative action of alleles at multiple loci. http://purl.obolibrary.org/obo/SO_0000831 gene_member_region http://purl.obolibrary.org/obo/SO_0001411 biological_region A region of a gene. http://purl.obolibrary.org/obo/SO_0000902 transgene http://purl.obolibrary.org/obo/SO_0000704 gene A transgene is a gene that has been transferred naturally or by any of a number of genetic engineering techniques from one organism to another. http://purl.obolibrary.org/obo/SO_0000999 BAC_end http://purl.obolibrary.org/obo/SO_0000150 read A region of sequence from the end of a BAC clone that may provide a highly specific marker. http://purl.obolibrary.org/obo/SO_0001263 ncRNA_gene http://purl.obolibrary.org/obo/SO_0000704 gene A gene that encodes a non-coding RNA. http://purl.obolibrary.org/obo/SO_0001265 miRNA_gene http://purl.obolibrary.org/obo/SO_0002342 sncRNA_gene A small noncoding RNA of approximately 22 nucleotides in length which may be involved in regulation of gene expression. http://purl.obolibrary.org/obo/SO_0001266 scRNA_gene http://purl.obolibrary.org/obo/SO_0001263 ncRNA_gene A gene encoding a small noncoding RNA that is generally found only in the cytoplasm. http://purl.obolibrary.org/obo/SO_0001267 snoRNA_gene http://purl.obolibrary.org/obo/SO_0002342 sncRNA_gene A gene encoding a small noncoding RNA that participates in the processing or chemical modifications of many RNAs, including ribosomal RNAs and spliceosomal RNAs. http://purl.obolibrary.org/obo/SO_0001268 snRNA_gene http://purl.obolibrary.org/obo/SO_0002342 sncRNA_gene A gene that encodes a small nuclear RNA. http://purl.obolibrary.org/obo/SO_0001272 tRNA_gene http://purl.obolibrary.org/obo/SO_0002342 sncRNA_gene A noncoding RNA that binds to a specific amino acid to allow that amino acid to be used by the ribosome during translation of RNA. http://purl.obolibrary.org/obo/SO_0001411 biological_region http://purl.obolibrary.org/obo/SO_0000001 region A region defined by its disposition to be involved in a biological process. http://purl.obolibrary.org/obo/SO_0001498 YAC_end http://purl.obolibrary.org/obo/SO_0000150 read A region of sequence from the end of a YAC clone that may provide a highly specific marker. http://purl.obolibrary.org/obo/SO_0001500 heritable_phenotypic_marker http://purl.obolibrary.org/obo/SO_0001645 genetic_marker A biological_region characterized as a single heritable trait in a phenotype screen. The heritable phenotype may be mapped to a chromosome but generally has not been characterized to a specific gene locus. http://purl.obolibrary.org/obo/SO_0001637 rRNA_gene http://purl.obolibrary.org/obo/SO_0001263 ncRNA_gene A gene that encodes for ribosomal RNA. http://purl.obolibrary.org/obo/SO_0001639 RNase_P_RNA_gene http://purl.obolibrary.org/obo/SO_0002180 enzymatic_RNA_gene A gene that encodes an RNase P RNA. http://purl.obolibrary.org/obo/SO_0001640 RNase_MRP_RNA_gene http://purl.obolibrary.org/obo/SO_0002180 enzymatic_RNA_gene A gene that encodes a RNase_MRP_RNA. http://purl.obolibrary.org/obo/SO_0001641 lincRNA_gene http://purl.obolibrary.org/obo/SO_0002127 lncRNA_gene A gene that encodes a long, intervening non-coding RNA. http://purl.obolibrary.org/obo/SO_0001643 telomerase_RNA_gene http://purl.obolibrary.org/obo/SO_0001263 ncRNA_gene A telomerase RNA gene is a non coding RNA gene the RNA product of which is a component of telomerase. http://purl.obolibrary.org/obo/SO_0001741 pseudogenic_gene_segment http://purl.obolibrary.org/obo/SO_3000000 gene_segment A gene segment which when incorporated by somatic recombination in the final gene transcript results in a nonfunctional product. http://purl.obolibrary.org/obo/SO_3000000 gene_segment http://purl.obolibrary.org/obo/SO_0000842 gene_component_region A gene component region which acts as a recombinational unit of a gene whose functional form is generated through somatic recombination. http://purl.obolibrary.org/obo/SO_0002164 H2BK5_acetylation_site http://purl.obolibrary.org/obo/SO_0002143 histone_2B_acetylation_site A kind of histone modification site, whereby the 5th residue (a lysine), from the start of the H2B histone protein is acetylated. http://purl.obolibrary.org/obo/SO_0002209 genomic_DNA_contig http://purl.obolibrary.org/obo/SO_0000149 contig A contig composed of genomic DNA derived sequences. http://purl.obolibrary.org/obo/SO_0002210 presence_absence_variation http://purl.obolibrary.org/obo/SO_0001019 copy_number_variation A variation qualifying the presence of a sequence in a genome which is entirely missing in another genome. http://purl.obolibrary.org/obo/SO_0002213 transcription_termination_signal http://purl.obolibrary.org/obo/SO_0000951 eukaryotic_terminator Termination signal preferentially observed downstream of polyadenylation signal http://purl.obolibrary.org/obo/SO_0002264 Copia_LTR_retrotransposon http://purl.obolibrary.org/obo/SO_0000186 LTR_retrotransposon LTR retrotransposons in the Copia superfamily contain elements coding for specific proteins in this order: GAG, AP, INT, RT, RH. GAG is a structural protein for virus-like particles. AP is aspartic proteinase. INT is a DDE integrase. RT is a reverse transcriptase. RH is RNAse H. http://purl.obolibrary.org/obo/SO_0002265 Gypsy_LTR_retrotransposon http://purl.obolibrary.org/obo/SO_0000186 LTR_retrotransposon LTR retrotransposons in the Gypsy superfamily contain elements coding for specific proteins in this order: GAG, AP, RT, RH, INT. GAG is a structural protein for virus-like particles. AP is aspartic proteinase. INT is a DDE integrase. RT is a reverse transcriptase. RH is RNAse H. http://purl.obolibrary.org/obo/SO_0002266 Bel_Pao_LTR_retrotransposon http://purl.obolibrary.org/obo/SO_0000186 LTR_retrotransposon LTR retrotransposons in the Bel-Pao superfamily are similar to LTRs in the Gypsy and Retrovirus superfamilies. Mainly described in metazoan genomes, this superfamily contain elements coding for specific proteins in this order: GAG, AP, RT, RH and INT. GAG is a structural protein for virus-like particles. AP is aspartic proteinase. INT is a DDE integrase. RT is a reverse transcriptase. RH is RNAse H. http://purl.obolibrary.org/obo/SO_0002267 Retrovirus_LTR_retrotransposon http://purl.obolibrary.org/obo/SO_0000186 LTR_retrotransposon LTR retrotransposons in the retrovirus superfamily are similar to LTR retrotransposons in the Gypsy and Bel-Pao superfamilies. Mainly described in vertebrate animals, this superfamily contain elements coding for specific proteins in this order: GAG, AP, RT, RH, INT, and ENV. GAG is a structural protein for virus-like particles. AP is aspartic proteinase. INT is a DDE integrase. RT is a reverse transcriptase. RH is RNAse H. ENV is envelop protein. http://purl.obolibrary.org/obo/SO_0002268 Endogenous_Retrovirus_LTR_retrotransposon http://purl.obolibrary.org/obo/SO_0000186 LTR_retrotransposon Endogenous retrovirus (ERV) retrotransposons are abundant in the genomes of jawed vertebrates. Human ERVs (HERVs) are classified based on their homologies to animal retroviruses. Class I families are similar in sequence to mammalian Gammaretroviruses (type C) and Epsilonretroviruses (Type E). Class II families show homology to mammalian Betaretroviruses (Type B) and Deltaretroviruses (Type D). F-Class III families are similar to foamy viruses. http://purl.obolibrary.org/obo/SO_0002269 R2_LINE_retrotransposon http://purl.obolibrary.org/obo/SO_0000194 LINE_element R2 retrotransposons are LINE elements (SO:0000194) that insert site-specifically into the host organism's 28S ribosomal RNA (rRNA) genes. http://purl.obolibrary.org/obo/SO_0002270 RTE_LINE_retrotransposon http://purl.obolibrary.org/obo/SO_0000194 LINE_element RTE retrotransposons are LINE elements (SO:0000194) that contain a domain with homology to the apurinic-apyrimidic (AP) endonucleases in addition to the previously identified reverse transcriptase domain. http://purl.obolibrary.org/obo/SO_0002271 Jockey_LINE_retrotransposon http://purl.obolibrary.org/obo/SO_0000194 LINE_element Jockey retrotransposons are LINE elements (SO:0000194) found only in arthropods. The full-length element is ~ 5 kb and contains two open reading frames (SO:0000236), ORF1 (568 aa) and ORF2 (916 aa), the second of which encodes an apurinic endonuclease (APE) and a reverse transcriptase (RT). http://purl.obolibrary.org/obo/SO_0002272 L1_LINE_retrotransposon http://purl.obolibrary.org/obo/SO_0000194 LINE_element Long interspersed element-1 (LINE-1) elements are found in the human genome, which contains ORF1 (open reading frame1, including CC, coiled coil; RRM, RNA recognition motif; CTD, carboxyl-terminal domain) and ORF2 (including EN, endonuclease; RT, reverse transcriptase; C, cysteine-rich domain). The L1-encoded proteins (ORF1p and ORF2p) can mobilize nonautonomous retrotransposons, other noncoding RNAs, and messenger RNAs. http://purl.obolibrary.org/obo/SO_0002273 I_LINE_retrotransposon http://purl.obolibrary.org/obo/SO_0000194 LINE_element Elements of the LINE I superfamily are similar to the Jockey and L1 superfamily. They contains two ORFs, the.second of which includes  Apurinic endonuclease (APE) and  reverse transcriptase (RT). The I superfamily encodes an RH (RNase H) domain downstream of the RT domain. http://purl.obolibrary.org/obo/SO_0002274 tRNA_SINE_retrotransposon http://purl.obolibrary.org/obo/SO_0000206 SINE_element Short interspersed elements that originated from tRNAs. http://purl.obolibrary.org/obo/SO_0002275 7SL_SINE_retrotransposon http://purl.obolibrary.org/obo/SO_0000206 SINE_element Short interspersed elements that originated from 7SL RNAs. http://purl.obolibrary.org/obo/SO_0002276 5S_SINE_retrotransposon http://purl.obolibrary.org/obo/SO_0000206 SINE_element Short interspersed elements that originated from 5S rRNAs. http://purl.obolibrary.org/obo/SO_0002277 Crypton_YR_transposon http://purl.obolibrary.org/obo/SO_0000182 DNA_transposon Crypton is a superfamily of DNA transposons that use tyrosine recombinase (YR) to cut and rejoin the recombining DNA molecules. http://purl.obolibrary.org/obo/SO_0002278 Tc1_Mariner_TIR_transposon http://purl.obolibrary.org/obo/SO_0000208 terminal_inverted_repeat_element Elements of the Tc1-Mariner terminal inverted repeat transposon superfamily (also called mariner transposons) are named after the Transponon of C. elegans number 1 transposasse. Their activity creates a 2-bp (TA) target-site duplication (TSD). Stowaway is the non-autonomous element in this superfamily usually shorter than 600 bp. http://purl.obolibrary.org/obo/SO_0002279 hAT_TIR_transposon http://purl.obolibrary.org/obo/SO_0000208 terminal_inverted_repeat_element The hAT terminal inverted repeat transposon superfamily elements were first found in maize (the Ac/Ds elements). Members of the hAT superfamily have TSDs of 8 bp, relatively short TIRs of 5–27 bp and overall lengths of less than 4 kb. http://purl.obolibrary.org/obo/SO_0002280 Mutator_TIR_transposon http://purl.obolibrary.org/obo/SO_0000208 terminal_inverted_repeat_element Members of the Mutator family of terminal inverted repeat (TIR) transposon are usually long but are also highly divergent, either sharing only terminal G…C nucleotides, or with the G…C nucleotides absent. The length of the TSD (7-11 bp, usually 9 bp) remains probably the most useful criterion for identification. http://purl.obolibrary.org/obo/SO_0002281 Merlin_TIR_transposon http://purl.obolibrary.org/obo/SO_0000208 terminal_inverted_repeat_element Terminal inverted repeat transposon superfamily Merlin elements create 8-9 bp target-site duplications (TSD). http://purl.obolibrary.org/obo/SO_0002282 Transib_TIR_transposon http://purl.obolibrary.org/obo/SO_0000208 terminal_inverted_repeat_element Terminal inverted repeat (TIR) transposons of the superfamily Transib contain the DDE motif, which is related to the RAG1 protein involved in V(D)J recombination. http://purl.obolibrary.org/obo/SO_0002283 piggyBac_TIR_transposon http://purl.obolibrary.org/obo/SO_0000208 terminal_inverted_repeat_element Primarily found in animals, the terminal inverted repeat (TIR) transposon superfamily piggyBac elements favour insertion adjacent to TTAA. http://purl.obolibrary.org/obo/SO_0002284 PIF_Harbinger_TIR_transposon http://purl.obolibrary.org/obo/SO_0000208 terminal_inverted_repeat_element Terminal inverted repeat transposons in the PIF/Harbinger/tourist superfamily create 3-bp target site duplication that are mainly 'TAA' or 'TTA'. The autonomous PIF-Harbinger elements are relatively small in size, usually a few kb in length. Non-autonomous elements in this superfamily usually shorter than 600 bp are referrred to as Tourist elements. The terminal sequences for PIF/Harbinger/Tourist elements are 'GGG/CCC…GGC/GCC' or 'GA/GGCA…TGCC/TC'. http://purl.obolibrary.org/obo/SO_0002285 CACTA_TIR_transposon http://purl.obolibrary.org/obo/SO_0000208 terminal_inverted_repeat_element This terminal inverted repeat of the CACTA family generate 3-bp target site duplication (TSD) upon insertion. CACTA elements do not have a significant preference for genic region insertions. This terminal inverted repeat (TIR) transposon superfamily is named CACTA because their terminal sequences are 'CACTA/G…C/TAGTG'. http://purl.obolibrary.org/obo/SO_0002286 YR_retrotransposon http://purl.obolibrary.org/obo/SO_0000189 non_LTR_retrotransposon Tyrosine Kinase (YR) retrotransposons are a subclass of non-LTR retrotransposons. These YR-encoding elements consist of central gag, pol and tyrosine recombinase (YR) open reading frames (ORFs) flanked with terminal repeat. The pol ORF includes a reverse transcriptase (RT), a RNase H (RH) and, in case of DIRS, a domain similar to bacterial and phage DNA N-6-adenine-methyltransferase (MT). Compared to the retroviral pol (LTR retrotransposons, non-LTR retrotransposons and Penelope elements), both aspartic protease and DDE integrase are absent from YR retrotransposons. YR retrotransposons have inverted terminal repeats (ITRs). http://purl.obolibrary.org/obo/SO_0002287 DIRS_YR_retrotransposon http://purl.obolibrary.org/obo/SO_0002286 YR_retrotransposon Dictyostelium intermediate repeat sequence (DIRS) retrotransposons are members of the YR_retrotransposon (SO:0002286) superfamily with the following protein domains: RT, RH, YR, and MT. RT is a reverse transcriptase. RH is RNAse H. YR is tyrosine recombinase. MT is DNA N-6-adenine-methyltransferase. http://purl.obolibrary.org/obo/SO_0002288 Ngaro_YR_retrotransposon http://purl.obolibrary.org/obo/SO_0002286 YR_retrotransposon Ngaro retrotransposons are members of the YR_retrotransposon (SO:0002286) superfamily with the following protein domains: RT, RH, YR. RT is a reverse transcriptase. RH is RNAse H. YR is Tyrosine recombinase. Inverted terminal repeats (ITRs) in Ngaro are arranged in A-pol-B-A-B order where A and B represent ITRs. http://purl.obolibrary.org/obo/SO_0002289 Viper_YR_retrotransposon http://purl.obolibrary.org/obo/SO_0002286 YR_retrotransposon VIPER retrotransposons are members of the YR_retrotransposon (SO:0002286 superfamily with protein domains: RT, RH, YR. RT is a reverse transcriptase. RH is RNAse H. YR is Tyrosine recombinase. Inverted terminal repeats (ITRs) in VIPER are arranged in A-pol-B-A-B order where A and B represent ITRs. VIPER is only found in kinetoplastida genomes. http://purl.obolibrary.org/obo/SO_0002290 Penelope_retrotransposon http://purl.obolibrary.org/obo/SO_0000189 non_LTR_retrotransposon Penelope is a subclass of non_LTR_retrotransposons (SO:0000189). Penelope retrotransposons contains structural features of TR, RT, EN, TR, terminal repeats which can be in tandem or inverse orientation in different Penelope copies. RT is reverse transcriptase. EN is endonuclease. http://purl.obolibrary.org/obo/SO_0002398 selenocysteine_gain http://purl.obolibrary.org/obo/SO_0002008 rare_amino_acid_variant A sequence variant whereby at least one base of a codon is changed, resulting in a selenocysteine. http://purl.obolibrary.org/obo/SO_0000010 protein_coding http://purl.obolibrary.org/obo/SO_0000401 gene_attribute A gene which, when transcribed, can be translated into a protein. http://purl.obolibrary.org/obo/SO_0000704 gene http://purl.obolibrary.org/obo/SO_0001411 biological_region A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions. http://purl.obolibrary.org/obo/SO_0002169 splice_polypyrimidine_tract_variant http://purl.obolibrary.org/obo/SO_0001568 splicing_variant A sequence variant that falls in the polypyrimidine tract at 3' end of intron between 17 and 3 bases from the end (acceptor -3 to acceptor -17). http://purl.obolibrary.org/obo/SO_0002170 splice_donor_region_variant http://purl.obolibrary.org/obo/SO_0001630 splice_region_variant A sequence variant that falls in the region between the 3rd and 6th base after splice junction (5' end of intron). http://purl.obolibrary.org/obo/SO_0002171 telomeric_D_loop http://purl.obolibrary.org/obo/SO_0000296 origin_of_replication A telomeric D-loop is a three-stranded DNA displacement loop that forms at the site where the telomeric 3' single-stranded DNA overhang (formed of the repeat sequence TTAGGG in mammals) is tucked back inside the double-stranded component of telomeric DNA molecule, thus forming a t-loop or telomeric-loop and protecting the chromosome terminus. http://purl.obolibrary.org/obo/SO_0002232 selection_marker http://purl.obolibrary.org/obo/SO_0001645 genetic_marker A genetic feature that encodes a trait used for artificial selection of a subpopulation. http://purl.obolibrary.org/obo/SO_0002244 partially_duplicated_transcript http://purl.obolibrary.org/obo/SO_0001576 transcript_variant A transcript which is partially duplicated due to duplication of DNA, leading to a new transcript that is only partial and likely nonfunctional. http://purl.obolibrary.org/obo/SO_0002245 five_prime_duplicated_transcript http://purl.obolibrary.org/obo/SO_0002244 partially_duplicated_transcript A partially_duplicated_transcript where the 5' end of the transcript is duplicated. http://purl.obolibrary.org/obo/SO_0002246 three_prime_duplicated_transcript http://purl.obolibrary.org/obo/SO_0002244 partially_duplicated_transcript A partially_duplicated_transcript where the 3' end of the transcript is duplicated. http://purl.obolibrary.org/obo/SO_0002247 sncRNA http://purl.obolibrary.org/obo/SO_0000655 ncRNA A non-coding RNA less than 200 nucleotides in length. http://purl.obolibrary.org/obo/SO_0002248 spurious_protein http://purl.obolibrary.org/obo/SO_0001410 experimental_feature A region of DNA that is predicted to be translated and transcribed into a protein by a protein detection algorithm that does not get transcribed in nature. http://purl.obolibrary.org/obo/SO_0002249 mature_protein_region_of_CDS http://purl.obolibrary.org/obo/SO_0000851 CDS_region A CDS region corresponding to a mature protein region of a polypeptide. http://purl.obolibrary.org/obo/SO_0002250 propeptide_region_of_CDS http://purl.obolibrary.org/obo/SO_0000851 CDS_region A CDS region corresponding to a propeptide of a polypeptide. http://purl.obolibrary.org/obo/SO_0002251 signal_peptide_region_of_CDS http://purl.obolibrary.org/obo/SO_0000851 CDS_region A CDS region corresponding to a signal peptide of a polypeptide. http://purl.obolibrary.org/obo/SO_0002252 transit_peptide_region_of_CDS http://purl.obolibrary.org/obo/SO_0000851 CDS_region CDS region corresponding to a transit peptide region of a polypeptide. http://purl.obolibrary.org/obo/SO_0002253 stem_loop_region http://purl.obolibrary.org/obo/SO_0000122 RNA_sequence_secondary_structure A portion of a stem loop secondary structure in RNA. http://purl.obolibrary.org/obo/SO_0002254 loop http://purl.obolibrary.org/obo/SO_0002253 stem_loop_region The loop portion of a stem loop, which is not folded back upon itself. http://purl.obolibrary.org/obo/SO_0002255 stem http://purl.obolibrary.org/obo/SO_0002253 stem_loop_region The portion of a stem loop where the RNA is folded back upon itself. http://purl.obolibrary.org/obo/SO_0002256 non_complimentary_stem http://purl.obolibrary.org/obo/SO_0002255 stem A region of a stem in a stem loop structure where the sequences are non-complimentary. http://purl.obolibrary.org/obo/SO_0002333 amber_stop_codon http://purl.obolibrary.org/obo/SO_0000319 stop_codon A stop codon with the DNA sequence TAG. http://purl.obolibrary.org/obo/SO_0002334 ochre_stop_codon http://purl.obolibrary.org/obo/SO_0000319 stop_codon A stop codon with the DNA sequence TAA. http://purl.obolibrary.org/obo/SO_0002335 opal_stop_codon http://purl.obolibrary.org/obo/SO_0000319 stop_codon A stop codon with the DNA sequence TGA. http://purl.obolibrary.org/obo/SO_0002336 cytosolic_rRNA_2S_gene http://purl.obolibrary.org/obo/SO_0002361 cytosolic_LSU_rRNA_gene A gene that encodes for 2S ribosomal RNA, which functions as a component of the large subunit of the ribosome in Drosophila and at least some other Diptera. http://purl.obolibrary.org/obo/SO_0002337 cytosolic_2S_rRNA http://purl.obolibrary.org/obo/SO_0000651 cytosolic_LSU_rRNA Cytosolic 2S rRNA is a 30 nucleotide RNA component of the large subunit of cytosolic ribosomes in Drosophila and at least some other Diptera. It is homologous to the 3' part of other 5.8S rRNA molecules. The 3' end of the 5.8S molecule is able to base-pair with the 5' end of the 2S rRNA to generate a helical region equivalent in position to the 'GC-rich hairpin' found in all previously sequenced 5.8S molecules. http://purl.obolibrary.org/obo/SO_0002338 U7_snRNA http://purl.obolibrary.org/obo/SO_0000274 snRNA A 57 to 71 nucleotide RNA that is a component of the U7 small nuclear ribonucleoprotein complex (U7 snRNP). The U7 snRNP is required for histone pre-mRNA processing. http://purl.obolibrary.org/obo/SO_0002339 scaRNA_gene http://purl.obolibrary.org/obo/SO_0001267 snoRNA_gene A gene that encodes for a scaRNA (small Cajal body-specific RNA). http://purl.obolibrary.org/obo/SO_0002340 RNA_7SK http://purl.obolibrary.org/obo/SO_0000655 ncRNA An abundant small nuclear RNA that, together with associated cellular proteins, regulates the activity of the positive transcription elongation factor b (P-TEFb). It is often described in literature as similar to a snRNA, except of longer length. http://purl.obolibrary.org/obo/SO_0002341 RNA_7SK_gene http://purl.obolibrary.org/obo/SO_0001263 ncRNA_gene A gene encoding a 7SK RNA (SO:0002340). http://purl.obolibrary.org/obo/SO_0002344 mt_SSU_rRNA http://purl.obolibrary.org/obo/SO_0002128 mt_rRNA Mitochondrial SSU rRNA is an RNA component of the small subunit of mitochondrial ribosomes. http://purl.obolibrary.org/obo/SO_0002345 mt_LSU_rRNA http://purl.obolibrary.org/obo/SO_0002128 mt_rRNA Mitochondrial LSU rRNA is an RNA component of the large subunit of mitochondrial ribosomes. http://purl.obolibrary.org/obo/SO_0002346 plastid_rRNA http://purl.obolibrary.org/obo/SO_0000252 rRNA Plastid rRNA is an RNA component of the small or large subunits of plastid (such as chloroplast) ribosomes. http://purl.obolibrary.org/obo/SO_0002347 plastid_SSU_rRNA http://purl.obolibrary.org/obo/SO_0002346 plastid_rRNA Plastid SSU rRNA is an RNA component of the small subunit of plastid (such as chloroplast) ribosomes. http://purl.obolibrary.org/obo/SO_0002348 plastid_LSU_rRNA http://purl.obolibrary.org/obo/SO_0002346 plastid_rRNA Plastid LSU rRNA is an RNA component of the large subunit of plastid (such as chloroplast) ribosomes. http://purl.obolibrary.org/obo/SO_0002381 bidirectional_promoter_lncRNA http://purl.obolibrary.org/obo/SO_0001877 lncRNA A long non-coding RNA which is produced using the promoter of a protein-coding gene but with transcription occurring in the opposite direction. http://purl.obolibrary.org/obo/SO_0000355 haplotype_block http://purl.obolibrary.org/obo/SO_0000298 recombination_feature A region of the genome which is co-inherited as the result of the lack of historic recombination within it. http://purl.obolibrary.org/obo/SO_0001024 haplotype http://purl.obolibrary.org/obo/SO_0001507 variant_collection A haplotype is one of a set of coexisting sequence variants of a haplotype block. http://purl.obolibrary.org/obo/SO_0000159 deletion http://purl.obolibrary.org/obo/SO_0001059 sequence_alteration The point at which one or more contiguous nucleotides were excised. http://purl.obolibrary.org/obo/SO_0000199 translocation http://purl.obolibrary.org/obo/SO_0001785 structural_alteration A region of nucleotide sequence that has translocated to a new position. The observed adjacency of two previously separated regions. http://purl.obolibrary.org/obo/SO_0000207 simple_sequence_length_variation http://purl.obolibrary.org/obo/SO_0000248 sequence_length_alteration SSLP are a kind of sequence alteration where the number of repeated sequences in intergenic regions may differ. http://purl.obolibrary.org/obo/SO_0000248 sequence_length_alteration http://purl.obolibrary.org/obo/SO_0001059 sequence_alteration A kind of kind of sequence alteration where the copies of a region present varies across a population. http://purl.obolibrary.org/obo/SO_0000667 insertion http://purl.obolibrary.org/obo/SO_0001059 sequence_alteration The sequence of one or more nucleotides added between two adjacent nucleotides in the sequence. http://purl.obolibrary.org/obo/SO_0000694 SNP http://purl.obolibrary.org/obo/SO_0001483 SNV SNPs are single base pair positions in genomic DNA at which different sequence alternatives exist in normal individuals in some population(s), wherein the least frequent variant has an abundance of 1% or greater. http://purl.obolibrary.org/obo/SO_0001013 MNP http://purl.obolibrary.org/obo/SO_0002007 MNV A multiple nucleotide polymorphism with alleles of common length > 1, for example AAA/TTT. http://purl.obolibrary.org/obo/SO_0001019 copy_number_variation http://purl.obolibrary.org/obo/SO_0000248 sequence_length_alteration A variation that increases or decreases the copy number of a given region. http://purl.obolibrary.org/obo/SO_0001059 sequence_alteration http://purl.obolibrary.org/obo/SO_0002072 sequence_comparison A sequence_alteration is a sequence_feature whose extent is the deviation from another sequence. http://purl.obolibrary.org/obo/SO_0001218 transgenic_insertion http://purl.obolibrary.org/obo/SO_0000667 insertion An insertion that derives from another organism, via the use of recombinant DNA technology. http://purl.obolibrary.org/obo/SO_0001483 SNV http://purl.obolibrary.org/obo/SO_1000002 substitution SNVs are single nucleotide positions in genomic DNA at which different sequence alternatives exist. http://purl.obolibrary.org/obo/SO_1000002 substitution http://purl.obolibrary.org/obo/SO_0001059 sequence_alteration A sequence alteration where the length of the change in the variant is the same as that of the reference. http://purl.obolibrary.org/obo/SO_1000005 complex_substitution http://purl.obolibrary.org/obo/SO_1000002 substitution When no simple or well defined DNA mutation event describes the observed DNA change, the keyword "complex" should be used. Usually there are multiple equally plausible explanations for the change. http://purl.obolibrary.org/obo/SO_1000008 point_mutation http://purl.obolibrary.org/obo/SO_0001483 SNV A single nucleotide change which has occurred at the same position of a corresponding nucleotide in a reference sequence. http://purl.obolibrary.org/obo/SO_1000009 transition http://purl.obolibrary.org/obo/SO_0001483 SNV Change of a pyrimidine nucleotide, C or T, into an other pyrimidine nucleotide, or change of a purine nucleotide, A or G, into an other purine nucleotide. http://purl.obolibrary.org/obo/SO_1000010 pyrimidine_transition http://purl.obolibrary.org/obo/SO_1000009 transition A substitution of a pyrimidine, C or T, for another pyrimidine. http://purl.obolibrary.org/obo/SO_1000011 C_to_T_transition http://purl.obolibrary.org/obo/SO_1000010 pyrimidine_transition A transition of a cytidine to a thymine. http://purl.obolibrary.org/obo/SO_1000012 C_to_T_transition_at_pCpG_site http://purl.obolibrary.org/obo/SO_1000011 C_to_T_transition The transition of cytidine to thymine occurring at a pCpG site as a consequence of the spontaneous deamination of 5'-methylcytidine. http://purl.obolibrary.org/obo/SO_1000013 T_to_C_transition http://purl.obolibrary.org/obo/SO_1000010 pyrimidine_transition A transition of a thymine to a cytidine. http://purl.obolibrary.org/obo/SO_1000014 purine_transition http://purl.obolibrary.org/obo/SO_1000009 transition A substitution of a purine, A or G, for another purine. http://purl.obolibrary.org/obo/SO_1000015 A_to_G_transition http://purl.obolibrary.org/obo/SO_1000014 purine_transition A transition of an adenine to a guanine. http://purl.obolibrary.org/obo/SO_1000016 G_to_A_transition http://purl.obolibrary.org/obo/SO_1000014 purine_transition A transition of a guanine to an adenine. http://purl.obolibrary.org/obo/SO_1000017 transversion http://purl.obolibrary.org/obo/SO_0001483 SNV Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G, or vice versa. http://purl.obolibrary.org/obo/SO_1000018 pyrimidine_to_purine_transversion http://purl.obolibrary.org/obo/SO_1000017 transversion Change of a pyrimidine nucleotide, C or T, into a purine nucleotide, A or G. http://purl.obolibrary.org/obo/SO_1000019 C_to_A_transversion http://purl.obolibrary.org/obo/SO_1000018 pyrimidine_to_purine_transversion A transversion from cytidine to adenine. http://purl.obolibrary.org/obo/SO_1000020 C_to_G_transversion http://purl.obolibrary.org/obo/SO_1000018 pyrimidine_to_purine_transversion A transversion of a cytidine to a guanine. http://purl.obolibrary.org/obo/SO_1000021 T_to_A_transversion http://purl.obolibrary.org/obo/SO_1000018 pyrimidine_to_purine_transversion A transversion from T to A. http://purl.obolibrary.org/obo/SO_1000022 T_to_G_transversion http://purl.obolibrary.org/obo/SO_1000018 pyrimidine_to_purine_transversion A transversion from T to G. http://purl.obolibrary.org/obo/SO_1000023 purine_to_pyrimidine_transversion http://purl.obolibrary.org/obo/SO_1000017 transversion Change of a purine nucleotide, A or G , into a pyrimidine nucleotide C or T. http://purl.obolibrary.org/obo/SO_1000024 A_to_C_transversion http://purl.obolibrary.org/obo/SO_1000023 purine_to_pyrimidine_transversion A transversion from adenine to cytidine. http://purl.obolibrary.org/obo/SO_1000025 A_to_T_transversion http://purl.obolibrary.org/obo/SO_1000023 purine_to_pyrimidine_transversion A transversion from adenine to thymine. http://purl.obolibrary.org/obo/SO_1000026 G_to_C_transversion http://purl.obolibrary.org/obo/SO_1000023 purine_to_pyrimidine_transversion A transversion from guanine to cytidine. http://purl.obolibrary.org/obo/SO_1000027 G_to_T_transversion http://purl.obolibrary.org/obo/SO_1000023 purine_to_pyrimidine_transversion A transversion from guanine to thymine. http://purl.obolibrary.org/obo/SO_1000032 delins http://purl.obolibrary.org/obo/SO_0001059 sequence_alteration A sequence alteration which included an insertion and a deletion, affecting 2 or more bases. http://purl.obolibrary.org/obo/SO_1000035 duplication http://purl.obolibrary.org/obo/SO_0000667 insertion An insertion which derives from, or is identical in sequence to, nucleotides present at a known location in the genome. http://purl.obolibrary.org/obo/SO_1000036 inversion http://purl.obolibrary.org/obo/SO_0001059 sequence_alteration A continuous nucleotide sequence is inverted in the same position. http://purl.obolibrary.org/obo/SO_1000039 direct_tandem_duplication http://purl.obolibrary.org/obo/SO_1000173 tandem_duplication A tandem duplication where the individual regions are in the same orientation. http://purl.obolibrary.org/obo/SO_1000040 inverted_tandem_duplication http://purl.obolibrary.org/obo/SO_1000173 tandem_duplication A tandem duplication where the individual regions are not in the same orientation. http://purl.obolibrary.org/obo/SO_1000173 tandem_duplication http://purl.obolibrary.org/obo/SO_1000035 duplication A duplication consisting of 2 identical adjacent regions. http://purl.obolibrary.org/obo/SO_0002160 sequence_length_variant http://purl.obolibrary.org/obo/SO_0001537 structural_variant A sequence variant that changes the length of one or more sequence features. http://purl.obolibrary.org/obo/SO_0002161 short_tandem_repeat_change http://purl.obolibrary.org/obo/SO_0002160 sequence_length_variant A sequence variant where the copies of a short tandem repeat (STR) feature are either contracted or expanded. http://purl.obolibrary.org/obo/SO_0002162 short_tandem_repeat_expansion http://purl.obolibrary.org/obo/SO_0002161 short_tandem_repeat_change A short tandem repeat variant containing more repeat units than the reference sequence. http://purl.obolibrary.org/obo/SO_0002163 short_tandem_repeat_contraction http://purl.obolibrary.org/obo/SO_0002161 short_tandem_repeat_change A short tandem repeat variant containing fewer repeat units than the reference sequence. http://purl.obolibrary.org/obo/SO_0002168 RNA_thermometer http://purl.obolibrary.org/obo/SO_0000836 mRNA_region An RNA_thermometer is a cis element in the 5' end of an mRNA that can change its secondary structure in response to temperature and coordinate temperature-dependent gene expression. http://purl.obolibrary.org/obo/SO_0002293 mitochondrial_control_region http://purl.obolibrary.org/obo/SO_0000296 origin_of_replication The non-coding region of the mitochondrial genome that controls RNA and DNA synthesis. http://purl.obolibrary.org/obo/SO_0002218 functionally_abnormal http://purl.obolibrary.org/obo/SO_0001536 functional_effect_variant A sequence variant in which the function of a gene product is altered with respect to a reference. http://purl.obolibrary.org/obo/SO_0002219 functionally_normal http://purl.obolibrary.org/obo/SO_0001536 functional_effect_variant A sequence variant in which the function of a gene product is retained with respect to a reference. http://purl.obolibrary.org/obo/SO_0002220 function_uncertain_variant http://purl.obolibrary.org/obo/SO_0001536 functional_effect_variant A sequence variant in which the function of a gene product is unknown with respect to a reference. http://purl.obolibrary.org/obo/SO_0002225 LOZ1_response_element http://purl.obolibrary.org/obo/SO_0002006 zinc_repressed_element A conserved sequence (5'-CGNMGATCNTY-3') transcription repressor binding site required for gene repression in the presence of high zinc. http://purl.obolibrary.org/obo/SO_0002233 homologous_chromosome_recognition_and_pairing_locus http://purl.obolibrary.org/obo/SO_0000409 binding_site A chromosomal locus where complementary lncRNA and associated proteins accumulate at the corresponding lncRNA gene loci to tether homologous chromosome during chromosome pairing at meiosis I. http://purl.obolibrary.org/obo/SO_0002234 pumilio_response_element http://purl.obolibrary.org/obo/SO_0000837 UTR_region A cis-acting element involved in RNA stability found in the 3' UTR of some RNA (consensus UGUAAAUA). http://purl.obolibrary.org/obo/SO_0002262 Watson_strand http://purl.obolibrary.org/obo/SO_0000830 chromosome_part An absolute reference to the strand. When a chromosome has p and q arms, the Watson strand is the strand whose 5'-end is on the short arm of the chromosome. Of note, the term 'plus strand' is typically based on a reference sequence where it's preferred for the plus strand to be the Watson strand, but might not be and 'plus strand' is therefore not an exact synonym. http://purl.obolibrary.org/obo/SO_0002263 Crick_strand http://purl.obolibrary.org/obo/SO_0000830 chromosome_part An absolute reference to the strand. When a chromosome has p and q arms, the Crick strand is the strand whose 5'-end is on the long arm of the chromosome. Of note, the term 'minus strand' is typically based on a reference sequence where it's preferred for the minus strand to be the Crick strand, but might not be and 'minus strand' is therefore not an exact synonym. http://purl.obolibrary.org/obo/SO_0002342 sncRNA_gene http://purl.obolibrary.org/obo/SO_0001263 ncRNA_gene A ncRNA_gene that encodes an ncRNA less than 200 nucleotides in length. http://purl.obolibrary.org/obo/SO_0002235 SUMO_interaction_motif http://purl.obolibrary.org/obo/SO_0001093 protein_protein_contact A polypeptide region that mediates binding to SUMO. The motif contains a hydrophobic core sequence consisting of three or four Ile, Leu, or Val residues plus one acidic or polar residue at position 2 or 3. http://purl.obolibrary.org/obo/SO_0002382 range_extender_element http://purl.obolibrary.org/obo/SO_0001055 transcriptional_cis_regulatory_region A conserved cis-acting element that confers extreme-distance regulatory activity to an enhancer. http://purl.obolibrary.org/obo/SO_0002383 oncogenic_variant http://purl.obolibrary.org/obo/SO_0001771 disease_associated_variant A variant that has been found to be pathogenic in the context of a neoplastic disease. http://purl.obolibrary.org/obo/SO_0002390 pseudoexon_variant http://purl.obolibrary.org/obo/SO_0001568 splicing_variant Inclusion of a non-conserved, unannotated exon in the spliced transcript, as a consequence of a variant in the gene. http://purl.obolibrary.org/obo/SO_0002391 abolished_transcription_level_variant http://purl.obolibrary.org/obo/SO_0001541 decreased_transcript_level_variant Complete lack of transcription of a gene, as a consequence of a variant in the gene or a regulatory region. http://purl.obolibrary.org/obo/SO_0002400 frameshift_unidirectional_gene_fusion http://purl.obolibrary.org/obo/SO_0002085 unidirectional_gene_fusion A sequence variant whereby two genes, on the same strand have become joined with a disruption of the translational reading frame, because the number of nucleotides between the reading frames of the joined genes is not a multiple of three. http://purl.obolibrary.org/obo/SO_0000139 ribosome_entry_site http://purl.obolibrary.org/obo/SO_0000836 mRNA_region Region in mRNA where ribosome assembles. http://purl.obolibrary.org/obo/SO_0002180 enzymatic_RNA_gene http://purl.obolibrary.org/obo/SO_0001263 ncRNA_gene A gene that encodes an enzymatic RNA. http://purl.obolibrary.org/obo/SO_0002181 ribozyme_gene http://purl.obolibrary.org/obo/SO_0002180 enzymatic_RNA_gene A gene that encodes a ribozyme. http://purl.obolibrary.org/obo/SO_0002182 antisense_lncRNA_gene http://purl.obolibrary.org/obo/SO_0002127 lncRNA_gene A gene that encodes an antisense long, non-coding RNA. http://purl.obolibrary.org/obo/SO_0002183 sense_overlap_lncRNA_gene http://purl.obolibrary.org/obo/SO_0002127 lncRNA_gene A gene that encodes a sense overlap long non-coding RNA. http://purl.obolibrary.org/obo/SO_0002184 sense_intronic_lncRNA_gene http://purl.obolibrary.org/obo/SO_0002127 lncRNA_gene A gene that encodes a sense intronic long non-coding RNA. http://purl.obolibrary.org/obo/SO_0002185 bidirectional_promoter_lncRNA_gene http://purl.obolibrary.org/obo/SO_0002127 lncRNA_gene A non-coding locus that originates from within the promoter region of a protein-coding gene, with transcription proceeding in the opposite direction on the other strand. http://purl.obolibrary.org/obo/SO_0002224 2A_self_cleaving_peptide_region http://purl.obolibrary.org/obo/SO_0000839 polypeptide_region A region that codes for a 2A self-cleaving polypeptide region, which is a region that can result in a break in the peptide sequence at its terminal G-P junction. http://purl.obolibrary.org/obo/SO_0002294 mitochondrial_D_loop http://purl.obolibrary.org/obo/SO_0002293 mitochondrial_control_region Mitochondrial displacement loop; a region within mitochondrial DNA in which a short stretch of RNA is paired with one strand of DNA, displacing the original partner DNA strand in this region. http://purl.obolibrary.org/obo/SO_0002329 minus_1_translational_frameshift http://purl.obolibrary.org/obo/SO_0001210 translational_frameshift The region of mRNA 1 base long that is included as part of two separate codons during the process of translational frameshifting (GO:0006452), causing the reading frame to be different. http://purl.obolibrary.org/obo/SO_0002330 minus_2_translational_frameshift http://purl.obolibrary.org/obo/SO_0001210 translational_frameshift The region of mRNA 2 bases long that is included as part of two separate codons during the process of translational frameshifting (GO:0006452), causing the reading frame to be different. http://purl.obolibrary.org/obo/SO_0002395 lost_polypeptide http://purl.obolibrary.org/obo/SO_0002317 absent_gene_product A complete loss of polypeptide (i.e. protein) expression, as a consequence of a variant in the gene. http://purl.obolibrary.org/obo/SO_0002396 decreased_polypeptide_level http://purl.obolibrary.org/obo/SO_0001555 decreased_translational_product_level A decrease in polypeptide (i.e. protein) expression, as a consequence of a variant in the gene. http://purl.obolibrary.org/obo/SO_0002397 cellular_mislocalization_variant http://purl.obolibrary.org/obo/SO_0001536 functional_effect_variant Trafficking of a polypeptide (i.e. protein) sequence to the wrong cellular location, as a consequence of a variant in the gene. http://purl.obolibrary.org/obo/SO_0002165 trinucleotide_repeat_expansion http://purl.obolibrary.org/obo/SO_0002162 short_tandem_repeat_expansion A short tandem repeat expansion with an increase in a sequence of three nucleotide units repeated in tandem compared to a reference sequence. http://purl.obolibrary.org/obo/SO_0002215 Zas1_recognition_motif http://purl.obolibrary.org/obo/SO_0000713 DNA_motif A DNA motif to which the S. pombe Zas1 protein binds. The consensus sequence is 5'-(Y)CCCCAY-3'. http://purl.obolibrary.org/obo/SO_0002223 inert_DNA_spacer http://purl.obolibrary.org/obo/SO_0005836 regulatory_region Sequences that decrease interactions between biological regions, such as between a promoter, its 5' context and/or the translational unit(s) it regulates. Spacers can affect regulation of translation, transcription, and other biological processes. http://purl.obolibrary.org/obo/SO_0002226 group_IIC_intron http://purl.obolibrary.org/obo/SO_0000603 group_II_intron A group II intron that recognizes IBS1/EBS1 for the 5-prime exon and IBS3/EBS3 for the 3-prime exon and may also recognize a stem-loop in the RNA. http://purl.obolibrary.org/obo/SO_0002227 CDS_extension http://purl.obolibrary.org/obo/SO_0000316 CDS A sequence variant extending the CDS, that causes elongation of the resulting polypeptide sequence. http://purl.obolibrary.org/obo/SO_0002228 CDS_five_prime_extension http://purl.obolibrary.org/obo/SO_0002227 CDS_extension A sequence variant extending the CDS at the 5' end, that causes elongation of the resulting polypeptide sequence at the N terminus. http://purl.obolibrary.org/obo/SO_0002229 CDS_three_prime_extension http://purl.obolibrary.org/obo/SO_0002227 CDS_extension A sequence variant extending the CDS at the 3' end, that causes elongation of the resulting polypeptide sequence at the C terminus. http://purl.obolibrary.org/obo/SO_0002230 CAAX_box http://purl.obolibrary.org/obo/SO_0100017 polypeptide_conserved_motif A C-terminus protein motif (CAAX) serving as a post-translational prenylation site modified by the attachment of either a farnesyl or a geranyl-geranyl group to a cysteine residue. Farnesyltransferase recognizes CaaX boxes where X = M, S, Q, A, or C, whereas Geranylgeranyltransferase I recognizes CaaX boxes with X = L or E. http://purl.obolibrary.org/obo/SO_0002314 altered_gene_product_level http://purl.obolibrary.org/obo/SO_0001536 functional_effect_variant A sequence variant that alters the level or amount of gene product produced. This high level term can be applied where the direction of level change (increased vs decreased gene product level) is unknown or not confirmed. http://purl.obolibrary.org/obo/SO_0002315 increased_gene_product_level http://purl.obolibrary.org/obo/SO_0002314 altered_gene_product_level A variant that increases the level or amount of gene product produced. http://purl.obolibrary.org/obo/SO_0002316 decreased_gene_product_level http://purl.obolibrary.org/obo/SO_0002314 altered_gene_product_level A sequence variant that decreases the level or amount of gene product produced. http://purl.obolibrary.org/obo/SO_0002317 absent_gene_product http://purl.obolibrary.org/obo/SO_0002316 decreased_gene_product_level A sequence variant that results in no gene product. http://purl.obolibrary.org/obo/SO_0002318 altered_gene_product_sequence http://purl.obolibrary.org/obo/SO_0001536 functional_effect_variant A sequence variant that alters the sequence of a gene product. http://purl.obolibrary.org/obo/SO_0002331 accessible_DNA_region http://purl.obolibrary.org/obo/SO_0001411 biological_region A region of DNA that is depleted of nucleosomes and accessible to DNA-binding proteins including transcription factors and nucleases. http://purl.obolibrary.org/obo/SO_0002332 epigenomically_modified_region http://purl.obolibrary.org/obo/SO_0001720 epigenetically_modified_region A biological region implicated in inherited changes caused by mechanisms other than changes in the underlying DNA sequence. http://purl.obolibrary.org/obo/SO_0002186 mutational_hotspot http://purl.obolibrary.org/obo/SO_0001411 biological_region A region of genomic sequence known to undergo mutational events with greater frequency than expected by chance. http://purl.obolibrary.org/obo/SO_0002385 5_prime_UTR_uORF_variant http://purl.obolibrary.org/obo/SO_0001623 5_prime_UTR_variant A 5' UTR variant within an upstream open reading frame. http://purl.obolibrary.org/obo/SO_0002386 5_prime_UTR_uORF_stop_codon_variant http://purl.obolibrary.org/obo/SO_0002385 5_prime_UTR_uORF_variant A 5' UTR variant where a stop codon in an upstream open reading frame is introduced, moved or lost. http://purl.obolibrary.org/obo/SO_0002387 5_prime_UTR_uORF_frameshift_variant http://purl.obolibrary.org/obo/SO_0002385 5_prime_UTR_uORF_variant A 5' UTR variant which disrupts the translation of an upstream open reading frame because the number of nucleotides inserted or deleted is not a multiple of three. http://purl.obolibrary.org/obo/SO_0002388 5_prime_UTR_uORF_stop_codon_gain_variant http://purl.obolibrary.org/obo/SO_0002386 5_prime_UTR_uORF_stop_codon_variant A 5' UTR variant where a premature stop codon is gained in an upstream open reading frame. http://purl.obolibrary.org/obo/SO_0002389 5_prime_UTR_uORF_stop_codon_loss_variant http://purl.obolibrary.org/obo/SO_0002386 5_prime_UTR_uORF_stop_codon_variant A 5' UTR variant where the stop codon of an upstream open reading frame is lost. http://purl.obolibrary.org/obo/SO_0000027 RNA_hook_turn http://purl.obolibrary.org/obo/SO_0000026 RNA_junction_loop http://purl.obolibrary.org/obo/SO_0000026 RNA_junction_loop http://purl.obolibrary.org/obo/SO_0000715 RNA_motif http://purl.obolibrary.org/obo/SO_0000067 gene_to_gene_feature http://purl.obolibrary.org/obo/SO_0000401 gene_attribute http://purl.obolibrary.org/obo/SO_0000081 gene_array_member http://purl.obolibrary.org/obo/SO_0000401 gene_attribute http://purl.obolibrary.org/obo/SO_0000977 anchor_binding_site http://purl.obolibrary.org/obo/SO_0000833 transcript_region http://purl.obolibrary.org/obo/SO_0002241 rRNA_21S_gene A gene which codes for 21S_rRNA, which functions as a component of the large subunit of the ribosome in mitochondria. http://purl.obolibrary.org/obo/SO_0001260 sequence_collection A collection of discontinuous sequences. http://purl.obolibrary.org/obo/SO_0000038 match_set A collection of match parts. http://purl.obolibrary.org/obo/SO_0000041 sequence_operation An operation that can be applied to a sequence, that results in a change. http://purl.obolibrary.org/obo/SO_0000042 pseudogene_attribute An attribute of a pseudogene (SO:0000336). http://purl.obolibrary.org/obo/SO_0000045 delete To remove a subsection of sequence. http://purl.obolibrary.org/obo/SO_0000046 insert To insert a subsection of sequence. http://purl.obolibrary.org/obo/SO_0000047 invert To invert a subsection of sequence. http://purl.obolibrary.org/obo/SO_0000048 substitute To substitute a subsection of sequence for another. http://purl.obolibrary.org/obo/SO_0000049 translocate To translocate a subsection of sequence. http://purl.obolibrary.org/obo/SO_0000050 gene_part A part of a gene, that has no other route in the ontology back to region. This concept is necessary for logical inference as these parts must have the properties of region. It also allows us to associate all the parts of genes with a gene. http://purl.obolibrary.org/obo/SO_0000053 sequence_variant_affecting_regulatory_region A sequence_variant_effect which changes the regulatory region of a gene. http://purl.obolibrary.org/obo/SO_0000109 sequence_variant_obs A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration. http://purl.obolibrary.org/obo/SO_0000160 lambda_clone A linear clone derived from lambda bacteriophage. The genes involved in the lysogenic pathway are removed from the from the viral DNA. Up to 25 kb of foreign DNA can then be inserted into the lambda genome. http://purl.obolibrary.org/obo/SO_0000168 restriction_enzyme_cut_site A specific nucleotide sequence of DNA at or near which a particular restriction enzyme cuts the DNA. http://purl.obolibrary.org/obo/SO_0000187 repeat_family A group of characterized repeat sequences. http://purl.obolibrary.org/obo/SO_0000284 type_I_enzyme_restriction_site The recognition site is bipartite and interrupted. http://purl.obolibrary.org/obo/SO_0000304 type_II_enzyme_restriction_site The recognition site is either palindromic, partially palindromic or an interrupted palindrome. Cleavage occurs within the recognition site. http://purl.obolibrary.org/obo/SO_0000311 computed_feature_by_similarity . http://purl.obolibrary.org/obo/SO_0000408 site The interbase position where something (eg an aberration) occurred. http://purl.obolibrary.org/obo/SO_0000477 polycistronic_gene A gene that is polycistronic. http://purl.obolibrary.org/obo/SO_0000502 transcribed_region A region of sequence that is transcribed. This region may cover the transcript of a gene, it may emcompas the sequence covered by all of the transcripts of a alternately spliced gene, or it may cover the region transcribed by a polycistronic transcript. A gene may have 1 or more transcribed regions and a transcribed_region may belong to one or more genes. http://purl.obolibrary.org/obo/SO_0000597 transcript_edited_by_U_insertion/deletion The insertion and deletion of uridine (U) residues, usually within coding regions of mRNA transcripts of cryptogenes in the mitochondrial genome of kinetoplastid protozoa. http://purl.obolibrary.org/obo/SO_0000674 non_canonical_splice_site A splice site where the donor and acceptor sites differ from the canonical form. http://purl.obolibrary.org/obo/SO_0000675 canonical_splice_site The major class of splice site with dinucleotides GT and AG for donor and acceptor sites, respectively. http://purl.obolibrary.org/obo/SO_0000752 gene_group_regulatory_region A region that is involved in the regulation of transcription of a group of regulated genes. http://purl.obolibrary.org/obo/SO_0000832 promoter_region A region of sequence which is part of a promoter. http://purl.obolibrary.org/obo/SO_0000843 bacterial_RNApol_promoter_region A region which is part of a bacterial RNA polymerase promoter. http://purl.obolibrary.org/obo/SO_0000844 RNApol_II_promoter_region A region of sequence which is a promoter for RNA polymerase II. http://purl.obolibrary.org/obo/SO_0000845 RNApol_III_promoter_type_1_region A region of sequence which is a promoter for RNA polymerase III type 1. http://purl.obolibrary.org/obo/SO_0000846 RNApol_III_promoter_type_2_region A region of sequence which is a promoter for RNA polymerase III type 2. http://purl.obolibrary.org/obo/SO_0000899 nuclear_mitochondrial An attribute describing a nuclear pseudogene of a mitochndrial gene. http://purl.obolibrary.org/obo/SO_0000900 processed An attribute describing a pseudogene where by an mRNA was retrotransposed. The mRNA sequence is transcribed back into the genome, lacking introns and promotors, but often including a polyA tail. http://purl.obolibrary.org/obo/SO_0000901 unequally_crossed_over An attribute describing a pseudogene that was created by tandem duplication and unequal crossing over during recombination. http://purl.obolibrary.org/obo/SO_0000917 insert_U An edit to insert a U. http://purl.obolibrary.org/obo/SO_0000918 delete_U An edit to delete a uridine. http://purl.obolibrary.org/obo/SO_0000919 substitute_A_to_I An edit to substitute an I for an A. http://purl.obolibrary.org/obo/SO_0000920 insert_C An edit to insert a cytidine. http://purl.obolibrary.org/obo/SO_0000921 insert_dinucleotide An edit to insert a dinucleotide. http://purl.obolibrary.org/obo/SO_0000922 substitute_C_to_U An edit to substitute an U for a C. http://purl.obolibrary.org/obo/SO_0000923 insert_G An edit to insert a G. http://purl.obolibrary.org/obo/SO_0000924 insert_GC An edit to insert a GC dinucleotide. http://purl.obolibrary.org/obo/SO_0000925 insert_GU An edit to insert a GU dinucleotide. http://purl.obolibrary.org/obo/SO_0000926 insert_CU An edit to insert a CU dinucleotide. http://purl.obolibrary.org/obo/SO_0000927 insert_AU An edit to insert a AU dinucleotide. http://purl.obolibrary.org/obo/SO_0000928 insert_AA An edit to insert a AA dinucleotide. http://purl.obolibrary.org/obo/SO_0001060 sequence_variant A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration. http://purl.obolibrary.org/obo/SO_0001087 cross_link Posttranslationally formed amino acid bonds. http://purl.obolibrary.org/obo/SO_0001088 disulfide_bond The covalent bond between sulfur atoms that binds two peptide chains or different parts of one peptide chain and is a structural determinant in many protein molecules. http://purl.obolibrary.org/obo/SO_0001090 covalent_binding_site Binding involving a covalent bond. http://purl.obolibrary.org/obo/SO_0001091 non_covalent_binding_site Binding site for any chemical group (co-enzyme, prosthetic group, etc.). http://purl.obolibrary.org/obo/SO_0001171 rRNA_21S A component of the large ribosomal subunit in mitochondrial rRNA. http://purl.obolibrary.org/obo/SO_0001240 TSS_region The region of a gene from the 5' most TSS to the 3' TSS. http://purl.obolibrary.org/obo/SO_0001721 H3K27_acylation_site A kind of histone modification site, whereby the 27th residue (a lysine), from the start of the H3 histone protein is acylated. http://purl.obolibrary.org/obo/SO_0001957 RNA_stability_element RNA secondary structure that affects the stability of an RNA molecule. http://purl.obolibrary.org/obo/SO_1000049 sequence_variation_affecting_transcript Any change in mature, spliced and processed, RNA that results from a change in the corresponding DNA sequence. http://purl.obolibrary.org/obo/SO_1000050 sequence_variant_causing_no_change_in_transcript No effect on the state of the RNA. http://purl.obolibrary.org/obo/SO_1000054 sequence_variation_affecting_coding_sequence Any of the amino acid coding triplets of a gene are affected by the DNA mutation. http://purl.obolibrary.org/obo/SO_1000055 sequence_variant_causing_initiator_codon_change_in_transcript The DNA mutation changes, usually destroys, the first coding triplet of a gene. Usually prevents translation although another initiator codon may be used. http://purl.obolibrary.org/obo/SO_1000056 sequence_variant_causing_amino_acid_coding_codon_change_in_transcript The DNA mutation affects the amino acid coding sequence of a gene; this region includes both the initiator and terminator codons. http://purl.obolibrary.org/obo/SO_1000057 sequence_variant_causing_synonymous_codon_change_in_transcript The changed codon has the same translation product as the original codon. http://purl.obolibrary.org/obo/SO_1000058 sequence_variant_causing_non_synonymous_codon_change_in_transcript A DNA point mutation that causes a substitution of an amino acid by an other. http://purl.obolibrary.org/obo/SO_1000059 sequence_variant_causing_missense_codon_change_in_transcript The nucleotide change in the codon leads to a new codon coding for a new amino acid. http://purl.obolibrary.org/obo/SO_1000060 sequence_variant_causing_conservative_missense_codon_change_in_transcript The amino acid change following from the codon change does not change the gross properties (size, charge, hydrophobicity) of the amino acid at that position. http://purl.obolibrary.org/obo/SO_1000061 sequence_variant_causing_nonconservative_missense_codon_change_in_transcript The amino acid change following from the codon change changes the gross properties (size, charge, hydrophobicity) of the amino acid in that position. http://purl.obolibrary.org/obo/SO_1000062 sequence_variant_causing_nonsense_codon_change_in_transcript The nucleotide change in the codon triplet creates a terminator codon. http://purl.obolibrary.org/obo/SO_1000063 sequence_variant_causing_terminator_codon_change_in_transcript The nucleotide change in the codon triplet changes the stop codon, causing an elongated transcript sequence. http://purl.obolibrary.org/obo/SO_1000064 sequence_variation_affecting_reading_frame An umbrella term for terms describing an effect of a sequence variation on the frame of translation. http://purl.obolibrary.org/obo/SO_1000065 frameshift_sequence_variation A mutation causing a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three. http://purl.obolibrary.org/obo/SO_1000066 sequence_variant_causing_plus_1_frameshift_mutation A mutation causing a disruption of the translational reading frame, due to the insertion of a nucleotide. http://purl.obolibrary.org/obo/SO_1000067 sequence_variant_causing_minus_1_frameshift A mutation causing a disruption of the translational reading frame, due to the deletion of a nucleotide. http://purl.obolibrary.org/obo/SO_1000068 sequence_variant_causing_plus_2_frameshift A mutation causing a disruption of the translational reading frame, due to the insertion of two nucleotides. http://purl.obolibrary.org/obo/SO_1000069 sequence_variant_causing_minus_2_frameshift A mutation causing a disruption of the translational reading frame, due to the deletion of two nucleotides. http://purl.obolibrary.org/obo/SO_1000070 sequence_variant_affecting_transcript_processing Sequence variant affects the way in which the primary transcriptional product is processed to form the mature transcript. http://purl.obolibrary.org/obo/SO_1000071 sequence_variant_affecting_splicing A sequence_variant_effect where the way in which the primary transcriptional product is processed to form the mature transcript, specifically by the removal (splicing) of intron sequences is changed. http://purl.obolibrary.org/obo/SO_1000072 sequence_variant_affecting_splice_donor A sequence_variant_effect that changes the splice donor sequence. http://purl.obolibrary.org/obo/SO_1000073 sequence_variant_affecting_splice_acceptor A sequence_variant_effect that changes the splice acceptor sequence. http://purl.obolibrary.org/obo/SO_1000074 sequence_variant_causing_cryptic_splice_activation A sequence variant causing a new (functional) splice site. http://purl.obolibrary.org/obo/SO_1000075 sequence_variant_affecting_editing Sequence variant affects the editing of the transcript. http://purl.obolibrary.org/obo/SO_1000076 sequence_variant_affecting_transcription Mutation affects the process of transcription, its initiation, progression or termination. http://purl.obolibrary.org/obo/SO_1000078 sequence_variant_decreasing_rate_of_transcription A sequence variation that decreases the rate a which transcription of the sequence occurs. http://purl.obolibrary.org/obo/SO_1000081 sequence_variant_affecting_rate_of_transcription A mutation that alters the rate a which transcription of the sequence occurs. http://purl.obolibrary.org/obo/SO_1000082 sequence variant_affecting_transcript_stability Sequence variant affects the stability of the transcript. http://purl.obolibrary.org/obo/SO_1000083 sequence_variant_increasing_transcript_stability Sequence variant increases the stability (half-life) of the transcript. http://purl.obolibrary.org/obo/SO_1000084 sequence_variant_decreasing_transcript_stability Sequence variant decreases the stability (half-life) of the transcript. http://purl.obolibrary.org/obo/SO_1000085 sequence_variation_affecting_level_of_transcript A sequence variation that causes a change in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence. http://purl.obolibrary.org/obo/SO_1000086 sequence_variation_decreasing_level_of_transcript A sequence variation that causes a decrease in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence. http://purl.obolibrary.org/obo/SO_1000087 sequence_variation_increasing_level_of_transcript A sequence_variation that causes an increase in the level of mature, spliced and processed RNA, resulting from a change in the corresponding DNA sequence. http://purl.obolibrary.org/obo/SO_1000088 sequence_variant_affecting_translational_product A sequence variant causing a change in primary translation product of a transcript. http://purl.obolibrary.org/obo/SO_1000089 sequence_variant_causing_no_change_of_translational_product The sequence variant at RNA level does not lead to any change in polypeptide. http://purl.obolibrary.org/obo/SO_1000092 sequence_variant_causing_complex_change_of_translational_product Any sequence variant effect that is known at nucleotide level but cannot be explained by using other key terms. http://purl.obolibrary.org/obo/SO_1000093 sequence_variant_causing_amino_acid_substitution The replacement of a single amino acid by another. http://purl.obolibrary.org/obo/SO_1000096 sequence_variant_causing_amino_acid_insertion The insertion of one or more amino acids from the polypeptide, without affecting the surrounding sequence. http://purl.obolibrary.org/obo/SO_1000097 sequence_variant_causing_amino_acid_deletion The deletion of one or more amino acids from the polypeptide, without affecting the surrounding sequence. http://purl.obolibrary.org/obo/SO_1000098 sequence_variant_causing_polypeptide_truncation The translational product is truncated at its C-terminus, usually a result of a nonsense codon change in transcript (SO:1000062). http://purl.obolibrary.org/obo/SO_1000099 sequence_variant_causing_polypeptide_elongation The extension of the translational product at either (or both) the N-terminus and/or the C-terminus. http://purl.obolibrary.org/obo/SO_1000100 mutation_causing_polypeptide_N_terminal_elongation . http://purl.obolibrary.org/obo/SO_1000101 mutation_causing_polypeptide_C_terminal_elongation . http://purl.obolibrary.org/obo/SO_1000110 frame_restoring_sequence_variant A mutation that reverts the sequence of a previous frameshift mutation back to the initial frame. http://purl.obolibrary.org/obo/SO_1000111 sequence_variant_affecting_3D_structure_of_polypeptide A mutation that changes the amino acid sequence of the peptide in such a way that it changes the 3D structure of the molecule. http://purl.obolibrary.org/obo/SO_1000126 sequence_variant_affecting_transcript_secondary_structure A sequence variant that affects the secondary structure (folding) of the RNA transcript molecule. http://purl.obolibrary.org/obo/SO_1000132 sequence_variant_effect The effect of a change in nucleotide sequence. http://purl.obolibrary.org/obo/SO_1000180 sequence_variant_affecting_gene_structure A sequence_variant_effect that changes the gene structure. http://purl.obolibrary.org/obo/SO_1000181 sequence_variant_causing_gene_fusion A sequence_variant_effect that changes the gene structure by causing a fusion to another gene. http://purl.obolibrary.org/obo/SO_1000184 sequence_variant_causes_exon_loss A sequence variant affecting splicing and causes an exon loss. http://purl.obolibrary.org/obo/SO_1000185 sequence_variant_causes_intron_gain A sequence variant effect, causing an intron to be gained by the processed transcript; usually a result of a donor acceptor mutation (SO:1000072). http://purl.obolibrary.org/obo/SO_0000400 sequence_attribute An attribute describes a quality of sequence. http://purl.obolibrary.org/obo/SO_0001203 RNA_polymerase_promoter A region (DNA) to which RNA polymerase binds, to begin transcription. http://purl.obolibrary.org/obo/SO_0001679 transcription_regulatory_region A regulatory region that is involved in the control of the process of transcription. http://purl.obolibrary.org/obo/SO_0000110 sequence_feature Any extent of continuous biological sequence. http://purl.obolibrary.org/obo/SO_0000000 Sequence_Ontology http://purl.obolibrary.org/obo/SO_0000008 gene_sensu_your_favorite_organism http://purl.obolibrary.org/obo/SO_0000009 gene_class http://purl.obolibrary.org/obo/SO_0000052 assortment_derived_deficiency http://purl.obolibrary.org/obo/SO_0000058 assortment_derived_aneuploid http://purl.obolibrary.org/obo/SO_0000064 gene_by_transcript_attribute http://purl.obolibrary.org/obo/SO_0000066 gene_by_polyadenylation_attribute http://purl.obolibrary.org/obo/SO_0000072 end_overlapping_gene http://purl.obolibrary.org/obo/SO_0000082 processed_transcript_attribute http://purl.obolibrary.org/obo/SO_0000085 gene_by_genome_location http://purl.obolibrary.org/obo/SO_0000086 gene_by_organelle_of_genome http://purl.obolibrary.org/obo/SO_0000106 non_capped_primary_transcript http://purl.obolibrary.org/obo/SO_0000115 transcript_feature http://purl.obolibrary.org/obo/SO_0000117 transcript_with_readthrough_stop_codon http://purl.obolibrary.org/obo/SO_0000144 primary_transcript_attribute http://purl.obolibrary.org/obo/SO_0000244 four_cutter_restriction_site http://purl.obolibrary.org/obo/SO_0000245 mRNA_by_polyadenylation_status http://purl.obolibrary.org/obo/SO_0000247 mRNA_not_polyadenylated http://purl.obolibrary.org/obo/SO_0000249 six_cutter_restriction_site http://purl.obolibrary.org/obo/SO_0000251 eight_cutter_restriction_site http://purl.obolibrary.org/obo/SO_0000292 repetitive_element http://purl.obolibrary.org/obo/SO_0000308 sequence_feature_locating_method http://purl.obolibrary.org/obo/SO_0000309 computed_feature http://purl.obolibrary.org/obo/SO_0000310 predicted_ab_initio_computation http://purl.obolibrary.org/obo/SO_0000369 integrase_coding_region http://purl.obolibrary.org/obo/SO_0000402 enhancer_attribute http://purl.obolibrary.org/obo/SO_0000437 assortment_derived_duplication http://purl.obolibrary.org/obo/SO_0000438 gene_not_polyadenylated http://purl.obolibrary.org/obo/SO_0000452 transgene_attribute http://purl.obolibrary.org/obo/SO_0000503 alternately_spliced_gene_encodeing_one_transcript http://purl.obolibrary.org/obo/SO_0000543 alternately_spliced_gene_encoding_greater_than_one_transcript http://purl.obolibrary.org/obo/SO_0000554 assortment_derived_deficiency_plus_duplication http://purl.obolibrary.org/obo/SO_0000598 edited_by_C_insertion_and_dinucleotide_insertion http://purl.obolibrary.org/obo/SO_0000599 edited_by_C_to_U_substitution http://purl.obolibrary.org/obo/SO_0000600 edited_by_A_to_I_substitution http://purl.obolibrary.org/obo/SO_0000601 edited_by_G_addition http://purl.obolibrary.org/obo/SO_0000660 DNA_invertase_target_sequence http://purl.obolibrary.org/obo/SO_0000661 intron_attribute http://purl.obolibrary.org/obo/SO_0000682 splicing_feature http://purl.obolibrary.org/obo/SO_0000759 plasmid_clone http://purl.obolibrary.org/obo/SO_0000760 YAC_clone http://purl.obolibrary.org/obo/SO_0000761 phagemid_clone http://purl.obolibrary.org/obo/SO_0000762 PAC_clone http://purl.obolibrary.org/obo/SO_0000763 fosmid_clone http://purl.obolibrary.org/obo/SO_0000764 BAC_clone http://purl.obolibrary.org/obo/SO_0000765 cosmid_clone http://purl.obolibrary.org/obo/SO_0000767 clone_insert_start http://purl.obolibrary.org/obo/SO_0000780 transposable_element_attribute http://purl.obolibrary.org/obo/SO_0000786 reagent_attribute http://purl.obolibrary.org/obo/SO_0000787 clone_attribute http://purl.obolibrary.org/obo/SO_0000788 cloned http://purl.obolibrary.org/obo/SO_0000791 cloned_genomic http://purl.obolibrary.org/obo/SO_0000792 cloned_cDNA http://purl.obolibrary.org/obo/SO_0000793 engineered_DNA http://purl.obolibrary.org/obo/SO_0000916 edit_operation http://purl.obolibrary.org/obo/SO_0000937 vertebrate_immune_system_feature http://purl.obolibrary.org/obo/SO_0000968 sequence_replication_mode http://purl.obolibrary.org/obo/SO_0000969 rolling_circle http://purl.obolibrary.org/obo/SO_0000970 theta_replication http://purl.obolibrary.org/obo/SO_0000971 DNA_replication_mode http://purl.obolibrary.org/obo/SO_0000972 RNA_replication_mode http://purl.obolibrary.org/obo/SO_0001020 sequence_variant_affecting_copy_number http://purl.obolibrary.org/obo/SO_0001051 nested_region http://purl.obolibrary.org/obo/SO_0001052 nested_repeat http://purl.obolibrary.org/obo/SO_0001053 nested_transposon http://purl.obolibrary.org/obo/SO_0001057 enhanceosome http://purl.obolibrary.org/obo/SO_0001432 sequence_variant_affecting_polyadenylation http://purl.obolibrary.org/obo/SO_0001579 transcript_sequence_variant http://purl.obolibrary.org/obo/SO_0002057 intronic_splicing_enhancer http://purl.obolibrary.org/obo/SO_0002117 http://purl.obolibrary.org/obo/SO_1000079 sequence_variation_affecting_transcript_sequence http://purl.obolibrary.org/obo/SO_1000080 sequence_variant_increasing_rate_of_transcription http://purl.obolibrary.org/obo/SO_1000094 sequence_variant_causing_conservative_amino_acid_substitution http://purl.obolibrary.org/obo/SO_1000095 sequence_variant_causing_nonconservative_amino_acid_substitution http://purl.obolibrary.org/obo/SO_1000102 sequence_variant_affecting_level_of_translational_product http://purl.obolibrary.org/obo/SO_1000103 sequence_variant_decreasing_level_of_translation_product http://purl.obolibrary.org/obo/SO_1000104 sequence_variant_increasing_level_of_translation_product http://purl.obolibrary.org/obo/SO_1000105 sequence_variant_affecting_polypeptide_amino_acid_sequence http://purl.obolibrary.org/obo/SO_1000106 mutation_causing_inframe_polypeptide_N_terminal_elongation http://purl.obolibrary.org/obo/SO_1000107 mutation_causing_out_of_frame_polypeptide_N_terminal_elongation http://purl.obolibrary.org/obo/SO_1000108 mutaton_causing_inframe_polypeptide_C_terminal_elongation http://purl.obolibrary.org/obo/SO_1000109 mutation_causing_out_of_frame_polypeptide_C_terminal_elongation http://purl.obolibrary.org/obo/SO_1000112 sequence_variant_causing_no_3D_structural_change http://purl.obolibrary.org/obo/SO_1000115 sequence_variant_causing_complex_3D_structural_change http://purl.obolibrary.org/obo/SO_1000116 sequence_variant_causing_conformational_change http://purl.obolibrary.org/obo/SO_1000117 sequence_variant_affecting_polypeptide_function http://purl.obolibrary.org/obo/SO_1000118 sequence_variant_causing_loss_of_function_of_polypeptide http://purl.obolibrary.org/obo/SO_1000119 sequence_variant_causing_inactive_ligand_binding_site http://purl.obolibrary.org/obo/SO_1000120 sequence_variant_causing_inactive_catalytic_site http://purl.obolibrary.org/obo/SO_1000121 sequence_variant_causing_polypeptide_localization_change http://purl.obolibrary.org/obo/SO_1000122 sequence_variant_causing_polypeptide_post_translational_processing_change http://purl.obolibrary.org/obo/SO_1000123 polypeptide_post_translational_processing_affected http://purl.obolibrary.org/obo/SO_1000124 sequence_variant_causing_partial_loss_of_function_of_polypeptide http://purl.obolibrary.org/obo/SO_1000125 sequence_variant_causing_gain_of_function_of_polypeptide http://purl.obolibrary.org/obo/SO_1000127 sequence_variant_causing_compensatory_transcript_secondary_structure_mutation http://purl.obolibrary.org/obo/SO_1000134 sequence_variant_causing_polypeptide_fusion http://purl.obolibrary.org/obo/SO_1000186 sequence_variant_causing_cryptic_splice_donor_activation http://purl.obolibrary.org/obo/SO_1001186 sequence_variant_causing_cryptic_splice_acceptor_activation http://purl.obolibrary.org/obo/SO_1001194 alternatively_spliced_gene_encoding_greater_than_1_polypeptide_coding_regions_overlapping http://purl.obolibrary.org/obo/SO_1001244 alternatively_spliced_transcript_encoding_greater_than_1_polypeptide_different_start_codon_different_stop_codon_coding_regions_non_overlapping http://purl.obolibrary.org/obo/SO_1001255 status_of_coding_sequence http://purl.obolibrary.org/obo/SO_1001266 stop_codon_redefinition_as_selenocysteine http://purl.obolibrary.org/obo/SO_1001267 stop_codon_readthrough http://purl.obolibrary.org/obo/SO_1001270 stop_codon_redefinition_as_pyrrolysine http://purl.obolibrary.org/obo/so#complete_evidence_for_feature complete_evidence_for_feature http://purl.obolibrary.org/obo/so#evidence_for_feature evidence_for_feature B is complete_evidence_for_feature A if the extent (5' and 3' boundaries) and internal boundaries of B fully support the extent and internal boundaries of A. http://purl.obolibrary.org/obo/so#has_integral_part has_integral_part http://purl.obolibrary.org/obo/so#has_part has_part X has_integral_part Y if and only if: X has_part Y and Y part_of X. http://purl.obolibrary.org/obo/so#integral_part_of integral_part_of http://purl.obolibrary.org/obo/so#part_of part_of X integral_part_of Y if and only if: X part_of Y and Y has_part X. http://purl.obolibrary.org/obo/so#non_functional_homolog_of non_functional_homolog_of http://purl.obolibrary.org/obo/so#homologous_to homologous_to A relationship between a pseudogenic feature and its functional ancestor. http://purl.obolibrary.org/obo/so#partial_evidence_for_feature partial_evidence_for_feature http://purl.obolibrary.org/obo/so#evidence_for_feature evidence_for_feature B is partial_evidence_for_feature A if the extent of B supports part_of but not all of A. http://purl.obolibrary.org/obo/so#orthologous_to orthologous_to http://purl.obolibrary.org/obo/so#homologous_to homologous_to http://purl.obolibrary.org/obo/so#paralogous_to paralogous_to http://purl.obolibrary.org/obo/so#homologous_to homologous_to http://purl.obolibrary.org/obo/so#member_of member_of http://purl.obolibrary.org/obo/so#part_of part_of http://purl.obolibrary.org/obo/so#homologous_to homologous_to http://purl.obolibrary.org/obo/so#similar_to similar_to http://purl.obolibrary.org/obo/so#has_part has_part Inverse of part_of. http://purl.obolibrary.org/obo/so#adjacent_to adjacent_to A geometric operator, specified in Egenhofer 1989. Two features meet if they share a junction on the sequence. X adjacent_to Y iff X and Y share a boundary but do not overlap. http://purl.obolibrary.org/obo/so#connects_on connects_on X connects_on Y, Z, R iff whenever Z is on a R, X is adjacent to a Y and adjacent to a Z. http://purl.obolibrary.org/obo/so#contained_by contained_by X contained_by Y iff X starts after start of Y and X ends before end of Y. http://purl.obolibrary.org/obo/so#contains contains The inverse of contained_by. http://purl.obolibrary.org/obo/so#disconnected_from disconnected_from X is disconnected_from Y iff it is not the case that X overlaps Y. http://purl.obolibrary.org/obo/so#evidence_for_feature evidence_for_feature B is evidence_for_feature A, if an instance of B supports the existence of A. http://purl.obolibrary.org/obo/so#exemplar_of exemplar_of X is exemplar of Y if X is the best evidence for Y. http://purl.obolibrary.org/obo/so#finished_by finished_by Xy is finished_by Y if Y part of X, and X and Y share a 3' boundary. http://purl.obolibrary.org/obo/so#finishes finishes X finishes Y if X is part_of Y and X and Y share a 3' or C terminal boundary. http://purl.obolibrary.org/obo/so#gained gained X gained Y if X is a variant_of X' and Y part of X but not X'. http://purl.obolibrary.org/obo/so#is_consecutive_sequence_of is_consecutive_sequence_of R is_consecutive_sequence_of R iff every instance of R is equivalent to a collection of instances of U:u1, u2, un, such that no pair of ux uy is overlapping and for all ux, it is adjacent to ux-1 and ux+1, with the exception of the initial and terminal u1,and un (which may be identical). http://purl.obolibrary.org/obo/so#lost lost X lost Y if X is a variant_of X' and Y part of X' but not X. http://purl.obolibrary.org/obo/so#maximally_overlaps maximally_overlaps A maximally_overlaps X iff all parts of A (including A itself) overlap both A and Y. http://purl.obolibrary.org/obo/so#overlaps overlaps X overlaps Y iff there exists some Z such that Z contained_by X and Z contained_by Y. http://purl.obolibrary.org/obo/so#part_of part_of X part_of Y if X is a subregion of Y. http://purl.obolibrary.org/obo/so#processed_from processed_from Inverse of processed_into. http://purl.obolibrary.org/obo/so#processed_into processed_into X is processed_into Y if a region X is modified to create Y. http://purl.obolibrary.org/obo/so#started_by started_by X is strted_by Y if Y is part_of X and X and Y share a 5' boundary. http://purl.obolibrary.org/obo/so#starts starts X starts Y if X is part of Y, and A and Y share a 5' or N-terminal boundary. http://purl.obolibrary.org/obo/so#transcribed_from transcribed_from X is transcribed_from Y if X is synthesized from template Y. http://purl.obolibrary.org/obo/so#transcribed_to transcribed_to Inverse of transcribed_from. http://purl.obolibrary.org/obo/so#translates_to translates_to Inverse of translation _of. http://purl.obolibrary.org/obo/so#translation_of translation_of X is translation of Y if Y is translated by ribosome to create X. http://purl.obolibrary.org/obo/so#variant_of variant_of A' is a variant (mutation) of A = definition every instance of A' is either an immediate mutation of some instance of A, or there is a chain of immediate mutation processes linking A' to some instance of A. http://purl.obolibrary.org/obo/so#associated_with associated_with http://purl.obolibrary.org/obo/so#derives_from derives_from http://purl.obolibrary.org/obo/so#edited_from edited_from http://purl.obolibrary.org/obo/so#edited_to edited_to http://purl.obolibrary.org/obo/so#genome_of genome_of http://purl.obolibrary.org/obo/so#guided_by guided_by http://purl.obolibrary.org/obo/so#guides guides http://purl.obolibrary.org/obo/so#has_origin has_origin http://purl.obolibrary.org/obo/so#has_quality has_quality http://purl.obolibrary.org/obo/so#position_of position_of http://purl.obolibrary.org/obo/so#recombined_from recombined_from http://purl.obolibrary.org/obo/so#recombined_to recombined_to http://purl.obolibrary.org/obo/so#sequence_of sequence_of http://purl.obolibrary.org/obo/so#similar_to similar_to http://purl.obolibrary.org/obo/so#trans_spliced_from trans_spliced_from http://purl.obolibrary.org/obo/so#trans_spliced_to trans_spliced_to