format-version: 1.2 data-version: go/releases/2023-02-28/imports/so_import.owl ontology: go/imports/so_import [Term] id: SO:0000001 name: region namespace: sequence def: "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." [SO:ke] subset: SOFA synonym: "sequence" EXACT [] is_a: SO:0000110 ! sequence_feature [Term] id: SO:0000110 name: sequence_feature namespace: sequence def: "Any extent of continuous biological sequence." [LAMHDI:mb, SO:ke] subset: SOFA synonym: "INSDC_feature:misc_feature" EXACT [] synonym: "INSDC_note:other" EXACT [] synonym: "INSDC_note:sequence_feature" EXACT [] synonym: "located sequence feature" RELATED [] synonym: "located_sequence_feature" EXACT [] synonym: "sequence feature" EXACT [] [Term] id: SO:0000165 name: enhancer namespace: sequence def: "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://www.insdc.org/files/feature_table.html] comment: An enhancer may participate in an enhanceosome GO:0034206. A protein-DNA complex formed by the association of a distinct set of general and specific transcription factors with a region of enhancer DNA. The cooperative assembly of an enhanceosome confers specificity of transcriptional regulation. This comment is a place holder should we start to make cross products with GO. subset: SOFA synonym: "INSDC_feature:regulatory" BROAD [] synonym: "INSDC_qualifier:enhancer" EXACT [] xref: http://en.wikipedia.org/wiki/Enhancer_(genetics) "wiki" is_a: SO:0000727 ! cis_regulatory_module [Term] id: SO:0000167 name: promoter namespace: sequence def: "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." [SO:regcreative] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. The region on a DNA molecule involved in RNA polymerase binding to initiate transcription. Moved from is_a: SO:0001055 transcriptional_cis_regulatory_region as per request from GREEKC initiative in August 2020. Merged with RNA_polymerase_promoter (SO:0001203) Aug 2020. Moved up one level from is_a CRM (SO:0000727) to is_a transcriptional_cis_regulatory_region (SO:0001055) as part of the GREEKC work January 2021. Pascale Gaudet from Gene Ontology pointed out that CRM can be located upstream of the promoter and therefore cannot include the promoter. subset: SOFA synonym: "INSDC_feature:regulatory" BROAD [] synonym: "INSDC_qualifier:promoter" EXACT [] synonym: "promoter sequence" EXACT [] xref: http://en.wikipedia.org/wiki/Promoter "wiki" is_a: SO:0000842 ! gene_component_region is_a: SO:0001055 ! transcriptional_cis_regulatory_region [Term] id: SO:0000170 name: RNApol_II_promoter namespace: sequence def: "A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription." [SO:ke] comment: parent term RNA_polymerase_promoter SO:0001203 was obsoleted in Aug 2020, so term has been moved to eukaryotic_promoter SO:0002221. synonym: "pol II promoter" RELATED [] synonym: "polymerase II promoter" EXACT [] synonym: "RNA polymerase B promoter" EXACT [] synonym: "RNApol II promoter" EXACT [] is_a: SO:0002221 ! eukaryotic_promoter [Term] id: SO:0000173 name: GC_rich_promoter_region namespace: sequence def: "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://www.insdc.org/files/feature_table.html] synonym: "GC rich promoter region" EXACT [] synonym: "GC-rich region" EXACT [] synonym: "INSDC_feature:regulatory" BROAD [] synonym: "INSDC_qualifier:GC_rich_promoter_region" EXACT [] is_a: SO:0001659 ! promoter_element [Term] id: SO:0000185 name: primary_transcript namespace: sequence def: "A transcript that in its initial state requires modification to be functional." [SO:ma] subset: SOFA synonym: "INSDC_feature:precursor_RNA" EXACT [] synonym: "INSDC_feature:prim_transcript" EXACT [] synonym: "precursor RNA" EXACT [] synonym: "primary transcript" EXACT [] xref: http://en.wikipedia.org/wiki/Primary_transcript "wiki" is_a: SO:0000673 ! transcript [Term] id: SO:0000188 name: intron namespace: sequence def: "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://www.insdc.org/files/feature_table.html] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA synonym: "INSDC_feature:intron" EXACT [] xref: http://en.wikipedia.org/wiki/Intron "wiki" is_a: SO:0000835 ! primary_transcript_region [Term] id: SO:0000231 name: snRNA_primary_transcript namespace: sequence def: "A primary transcript encoding a small nuclear RNA (SO:0000274)." [SO:ke] synonym: "snRNA primary transcript" EXACT [] is_a: SO:0000483 ! nc_primary_transcript [Term] id: SO:0000232 name: snoRNA_primary_transcript namespace: sequence def: "A primary transcript encoding one or more small nucleolar RNAs (SO:0000275)." [SO:ke] comment: This definition was broadened 26 Jan 2021 to reflect that a single transcript can encode one or more snoRNAs. Brought to our attention by FlyBase. GitHub Issue #520 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/520). synonym: "snoRNA primary transcript" EXACT [] is_a: SO:0000483 ! nc_primary_transcript [Term] id: SO:0000233 name: mature_transcript namespace: sequence def: "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." [SO:ke] comment: A processed transcript cannot contain introns. subset: SOFA synonym: "mature transcript" EXACT [] xref: http://en.wikipedia.org/wiki/Mature_transcript "wiki" is_a: SO:0000673 ! transcript [Term] id: SO:0000234 name: mRNA namespace: sequence def: "Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:ma] comment: An mRNA does not contain introns as it is a processed_transcript. The equivalent kind of primary_transcript is protein_coding_primary_transcript (SO:0000120) which may contain introns. This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA synonym: "INSDC_feature:mRNA" EXACT [] synonym: "messenger RNA" EXACT [] synonym: "protein_coding_transcript" EXACT [] xref: http://en.wikipedia.org/wiki/MRNA "wiki" xref: http://www.gencodegenes.org/gencode_biotypes.html "GENCODE" is_a: SO:0000233 ! mature_transcript [Term] id: SO:0000235 name: TF_binding_site namespace: sequence def: "A DNA site where a transcription factor binds." [SO:ke] comment: Definition updated along with definitions in Mejia-Almonte et.al PMID:32665585. Added relationship part_of SO:0000727 CRM in place of previous CRM relationship has_part TF_binding_site August 2020 in response to requests from GREEKC initiative. Moved from transcription_regulatory_region (SO:0001679) to transcriptional_cis_regulatory_region (SO:0001055) by Dave Sant on Feb 11, 2021 when transcription_regulatory_region was merged into transcriptional_cis_regulatory_region to be consistent with GO and reduce redundancy as part of the GREEKC consortium. See GitHub Issue #527. subset: SOFA synonym: "TF binding site" EXACT [] synonym: "transcription factor binding site" EXACT [] is_a: SO:0001055 ! transcriptional_cis_regulatory_region is_a: SO:0001654 ! nucleotide_to_protein_binding_site [Term] id: SO:0000252 name: rRNA namespace: sequence def: "rRNA is an RNA component of a ribosome that can provide both structural scaffolding and catalytic activity." [http://www.insdc.org/files/feature_table.html, ISBN:0198506732] comment: Definition updated 10 June 2021 as part of restructuring rRNA terms and reforming definitions to have similar structures. Request from EBI. See GitHub Issue #493 subset: SOFA synonym: "INSDC_feature:rRNA" EXACT [] synonym: "INSDC_qualifier:unknown" BROAD [] synonym: "ribosomal ribonucleic acid" EXACT [] synonym: "ribosomal RNA" EXACT [] xref: http://en.wikipedia.org/wiki/RRNA "wiki" is_a: SO:0000655 ! ncRNA [Term] id: SO:0000253 name: tRNA namespace: sequence def: "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://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005, ISBN:0198506732] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA synonym: "INSDC_feature:tRNA" EXACT [] synonym: "INSDC_qualifier:unknown" BROAD [] synonym: "transfer ribonucleic acid" RELATED [] synonym: "transfer RNA" RELATED [] xref: http://en.wikipedia.org/wiki/TRNA "wiki" is_a: SO:0002247 ! sncRNA [Term] id: SO:0000274 name: snRNA namespace: sequence def: "A small nuclear RNA molecule involved in pre-mRNA splicing and processing." [http://www.insdc.org/files/feature_table.html, PMID:11733745, WB:ems] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. subset: SOFA synonym: "INSDC_feature:ncRNA" BROAD [] synonym: "INSDC_qualifier:snRNA" EXACT [] synonym: "small nuclear RNA" EXACT [] xref: http://en.wikipedia.org/wiki/SnRNA "wiki" is_a: SO:0002247 ! sncRNA [Term] id: SO:0000275 name: snoRNA namespace: sequence def: "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." [GOC:kgc, PMID:31828325] comment: Updated the definition of snoRNA (SO:0000275) from "A snoRNA (small nucleolar RNA) is any one of a class of small RNAs that are associated with the eukaryotic nucleus as components of small nucleolar ribonucleoproteins. They participate in the processing or modifications of many RNAs, mostly ribosomal RNAs (rRNAs) though snoRNAs are also known to target other classes of RNA, including spliceosomal RNAs, tRNAs, and mRNAs via a stretch of sequence that is complementary to a sequence in the targeted RNA." to "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." to acknowledge that some snoRNAs functionally localize to other compartments (cytoplasm or even secreted). See GitHub Issue #578. subset: SOFA synonym: "INSDC_feature:ncRNA" BROAD [] synonym: "INSDC_qualifier:snoRNA" EXACT [] synonym: "small nucleolar RNA" EXACT [] is_a: SO:0002247 ! sncRNA [Term] id: SO:0000276 name: miRNA namespace: sequence alt_id: SO:0000649 def: "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." [PMID:11081512, PMID:12592000] subset: SOFA synonym: "INSDC_feature:ncRNA" BROAD [] synonym: "INSDC_qualifier:miRNA" EXACT [] synonym: "micro RNA" EXACT [] synonym: "microRNA" EXACT [] synonym: "small temporal RNA" EXACT [] synonym: "stRNA" EXACT [] xref: http://en.wikipedia.org/wiki/MiRNA "wiki" xref: http://en.wikipedia.org/wiki/StRNA "wiki" is_a: SO:0000370 ! small_regulatory_ncRNA [Term] id: SO:0000296 name: origin_of_replication namespace: sequence def: "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://www.insdc.org/files/feature_table.html, NCBI:cf] subset: SOFA synonym: "INSDC_feature:rep_origin" EXACT [] synonym: "ori" EXACT [] synonym: "origin of replication" EXACT [] xref: http://en.wikipedia.org/wiki/Origin_of_replication "wiki" is_a: SO:0001411 ! biological_region [Term] id: SO:0000305 name: modified_DNA_base namespace: sequence def: "A modified nucleotide, i.e. a nucleotide other than A, T, C. G." [http://www.insdc.org/files/feature_table.html] comment: Modified base:. subset: SOFA synonym: "INSDC_feature:modified_base" EXACT [] synonym: "modified base site" EXACT [] is_a: SO:0001236 ! base is_a: SO:0001720 ! epigenetically_modified_region [Term] id: SO:0000315 name: TSS namespace: sequence def: "The first base where RNA polymerase begins to synthesize the RNA transcript." [SO:ke] comment: Added relationship is_a SO:0002309 core_promoter_element with the creation of core_promoter_element as part of GREEKC initiative August 2020 - Dave Sant. subset: SOFA synonym: "INSDC_feature:misc_feature" BROAD [] synonym: "INSDC_note:transcription_start_site" EXACT [] synonym: "transcription start site" EXACT [] synonym: "transcription_start_site" EXACT [] is_a: SO:0000835 ! primary_transcript_region is_a: SO:0002309 ! core_promoter_element [Term] id: SO:0000330 name: conserved_region namespace: sequence def: "Region of sequence similarity by descent from a common ancestor." [SO:ke] subset: SOFA synonym: "conserved region" EXACT [] synonym: "INSDC_feature:misc_feature" BROAD [] synonym: "INSDC_note:conserved_region" EXACT [] xref: http://en.wikipedia.org/wiki/Conserved_region "wiki" is_a: SO:0001410 ! experimental_feature [Term] id: SO:0000336 name: pseudogene namespace: sequence def: "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://www.ucl.ac.uk/~ucbhjow/b241/glossary.html] subset: Alliance_of_Genome_Resources subset: SOFA synonym: "INSDC_feature:gene" BROAD [] synonym: "INSDC_qualifier:pseudo" EXACT [] synonym: "INSDC_qualifier:unknown" EXACT [] xref: http://en.wikipedia.org/wiki/Pseudogene "wiki" is_a: SO:0001411 ! biological_region [Term] id: SO:0000370 name: small_regulatory_ncRNA namespace: sequence def: "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)." [PMID:28541282, PomBase:al, SO:ma] subset: SOFA synonym: "small regulatory ncRNA" EXACT [] is_a: SO:0002247 ! sncRNA [Term] id: SO:0000375 name: cytosolic_5_8S_rRNA namespace: sequence def: "Cytosolic 5.8S rRNA is an RNA component of the large subunit of cytosolic ribosomes in eukaryotes." [https://rfam.xfam.org/family/RF00002] comment: Dave Sant removed '5_8S rRNA is also found in archaea.' from definition due to lack of references mentioning this on 1 Feb 2021. See GitHub Issue #505. Renamed from rRNA_5_8S to cytosolic_5_8S_rRNA on 10 June 2021 with the restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Requested by EBI. See GitHub Issue #493. subset: SOFA synonym: "cytosolic 5.8S LSU rRNA" EXACT [] synonym: "cytosolic 5.8S ribosomal RNA" EXACT [] synonym: "cytosolic 5.8S rRNA" EXACT [] synonym: "cytosolic rRNA 5 8S" EXACT [] xref: http://en.wikipedia.org/wiki/5.8S_ribosomal_RNA "wiki" is_a: SO:0000651 ! cytosolic_LSU_rRNA [Term] id: SO:0000409 name: binding_site namespace: sequence alt_id: BS:00033 def: "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." [EBIBS:GAR, SO:ke] comment: See GO:0005488 : binding. subset: biosapiens subset: SOFA synonym: "binding site" EXACT [] synonym: "binding_or_interaction_site" EXACT [] synonym: "INSDC_feature:misc_binding" EXACT [] synonym: "site" RELATED [] xref: http://en.wikipedia.org/wiki/Binding_site "wiki" is_a: SO:0001411 ! biological_region [Term] id: SO:0000410 name: protein_binding_site namespace: sequence def: "A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules." [SO:ke] comment: See GO:0042277 : peptide binding. subset: SOFA synonym: "INSDC_feature:protein_bind" EXACT [] synonym: "protein binding site" EXACT [] is_a: SO:0000409 ! binding_site [Term] id: SO:0000483 name: nc_primary_transcript namespace: sequence def: "A primary transcript that is never translated into a protein." [SO:ke] subset: SOFA synonym: "nc primary transcript" EXACT [] synonym: "noncoding primary transcript" EXACT [] is_a: SO:0000185 ! primary_transcript [Term] id: SO:0000577 name: centromere namespace: sequence def: "A region of chromosome where the spindle fibers attach during mitosis and meiosis." [SO:ke] subset: SOFA synonym: "INSDC_feature:centromere" EXACT [] xref: http://en.wikipedia.org/wiki/Centromere "wiki" is_a: SO:0000628 ! chromosomal_structural_element [Term] id: SO:0000587 name: group_I_intron namespace: sequence def: "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://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00028] comment: GO:0000372. subset: SOFA synonym: "group I intron" EXACT [] xref: http://en.wikipedia.org/wiki/Group_I_intron "wiki" is_a: SO:0000588 ! autocatalytically_spliced_intron [Term] id: SO:0000588 name: autocatalytically_spliced_intron namespace: sequence def: "A self spliced intron." [SO:ke] subset: SOFA synonym: "autocatalytically spliced intron" EXACT [] synonym: "INSDC_feature:ncRNA" BROAD [] synonym: "INSDC_qualifier:autocatalytically_spliced_intron" EXACT [] is_a: SO:0000188 ! intron [Term] id: SO:0000593 name: C_D_box_snoRNA namespace: sequence def: "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://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html] comment: Added 'SNORD' as a synonym of C_D_box_snoRNA (SO:0000593) and 'SNORA' as a synonym of H_ACA_box_snoRNA (SO:0000594). See GitHub Issue #577. subset: SOFA synonym: "box C/D snoRNA" EXACT [] synonym: "C D box snoRNA" EXACT [] synonym: "C/D box snoRNA" EXACT [] synonym: "SNORD" EXACT [PMID:31828325] is_a: SO:0000275 ! snoRNA [Term] id: SO:0000594 name: H_ACA_box_snoRNA namespace: sequence def: "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://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html] comment: Added 'SNORD' as a synonym of C_D_box_snoRNA (SO:0000593) and 'SNORA' as a synonym of H_ACA_box_snoRNA (SO:0000594). See GitHub Issue #577. synonym: "box H/ACA snoRNA" EXACT [] synonym: "H ACA box snoRNA" EXACT [] synonym: "H/ACA box snoRNA" EXACT [] synonym: "SNORA" EXACT [PMID:31828325] is_a: SO:0000275 ! snoRNA [Term] id: SO:0000613 name: bacterial_RNApol_promoter namespace: sequence def: "A DNA sequence to which bacterial RNA polymerase binds, to begin transcription." [SO:ke] comment: former parent RNA_polymerase_promoter SO:0001203 was merged with promoter SO:0000167 in Aug 2020 as part of GREEKC. synonym: "bacterial RNApol promoter" EXACT [] is_a: SO:0002222 ! prokaryotic_promoter [Term] id: SO:0000624 name: telomere namespace: sequence def: "A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end." [SO:ma] subset: SOFA synonym: "INSDC_feature:telomere" EXACT [] synonym: "telomeric DNA" EXACT [] synonym: "telomeric sequence" EXACT [] xref: http://en.wikipedia.org/wiki/Telomere "wiki" is_a: SO:0000628 ! chromosomal_structural_element [Term] id: SO:0000625 name: silencer namespace: sequence def: "A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control." [SO:ke] subset: SOFA synonym: "INSDC_feature:regulatory" BROAD [] synonym: "INSDC_qualifier:silencer" EXACT [] xref: http://en.wikipedia.org/wiki/Silencer_(DNA) "wiki" is_a: SO:0000727 ! cis_regulatory_module [Term] id: SO:0000627 name: insulator namespace: sequence def: "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." [NCBI:cf, PMID:12154228, SO:regcreative] comment: moved from is_a: SO:0001055 transcriptional_cis_regulatory_region as per request from GREEKC initiative in August 2020. subset: SOFA synonym: "INSDC_feature:regulatory" BROAD [] synonym: "INSDC_qualifier:insulator" EXACT [] synonym: "insulator element" EXACT [] xref: http://en.wikipedia.org/wiki/Insulator_(genetics) "wiki" is_a: SO:0000727 ! cis_regulatory_module [Term] id: SO:0000628 name: chromosomal_structural_element namespace: sequence def: "Regions of the chromosome that are important for structural elements." [] subset: SOFA synonym: "chromosomal structural element" EXACT [] is_a: SO:0000830 ! chromosome_part [Term] id: SO:0000644 name: antisense_RNA namespace: sequence def: "Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA." [SO:ke] subset: SOFA synonym: "antisense RNA" EXACT [] synonym: "INSDC_feature:ncRNA" BROAD [] synonym: "INSDC_qualifier:antisense_RNA" EXACT [] xref: http://en.wikipedia.org/wiki/Antisense_RNA "wiki" is_a: SO:0000655 ! ncRNA [Term] id: SO:0000646 name: siRNA namespace: sequence def: "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." [PMID:12592000] subset: SOFA synonym: "INSDC_feature:ncRNA" BROAD [] synonym: "INSDC_qualifier:siRNA" EXACT [] synonym: "small interfering RNA" EXACT [] xref: http://en.wikipedia.org/wiki/SiRNA "wiki" is_a: SO:0000370 ! small_regulatory_ncRNA [Term] id: SO:0000647 name: miRNA_primary_transcript namespace: sequence alt_id: SO:0000648 def: "A primary transcript encoding a micro RNA." [SO:ke] synonym: "micro RNA primary transcript" EXACT [] synonym: "miRNA primary transcript" EXACT [] synonym: "small temporal RNA primary transcript" EXACT [] synonym: "stRNA primary transcript" EXACT [] synonym: "stRNA_primary_transcript" EXACT [] is_a: SO:0000483 ! nc_primary_transcript [Term] id: SO:0000651 name: cytosolic_LSU_rRNA namespace: sequence def: "Cytosolic LSU rRNA is an RNA component of the large subunit of cytosolic ribosomes." [SO:ke] comment: Renamed to cytosolic_LSU_rRNA from large_subunit_rRNA on 10 June 2021 as per restructuring of rRNA child terms. Updated definition to be consistent with format of other rRNA definitions. Request from EBI. See GitHub Issue #493. subset: SOFA synonym: "cytosolic large subunit rRNA" EXACT [] synonym: "cytosolic LSU RNA" EXACT [] synonym: "cytosolic LSU rRNA" EXACT [] is_a: SO:0002343 ! cytosolic_rRNA [Term] id: SO:0000655 name: ncRNA namespace: sequence def: "An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product." [SO:ke] comment: A ncRNA is a processed_transcript, so it may not contain parts such as transcribed_spacer_regions that are removed in the act of processing. For the corresponding primary_transcripts, please see term SO:0000483 nc_primary_transcript. subset: SOFA synonym: "INSDC_qualifier:other" BROAD [] synonym: "known_ncrna" EXACT [] synonym: "noncoding RNA" EXACT [] xref: http://en.wikipedia.org/wiki/NcRNA "wiki" xref: http://www.gencodegenes.org/gencode_biotypes.html "GENCODE" is_a: SO:0000233 ! mature_transcript [Term] id: SO:0000657 name: repeat_region namespace: sequence def: "A region of sequence containing one or more repeat units." [SO:ke] subset: SOFA synonym: "INSDC_feature:repeat_region" BROAD [] synonym: "INSDC_qualifier:other" EXACT [] synonym: "repeat region" EXACT [] is_a: SO:0001411 ! biological_region [Term] id: SO:0000673 name: transcript namespace: sequence def: "An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:ma] comment: Added relationship overlaps SO:0002300 unit_of_gene_expression with Mejia-Almonte et.al PMID:32665585 Aug 5, 2020. subset: SOFA synonym: "INSDC_feature:misc_RNA" BROAD [] xref: http://en.wikipedia.org/wiki/RNA "wiki" is_a: SO:0000831 ! gene_member_region [Term] id: SO:0000699 name: junction namespace: sequence def: "A sequence_feature with an extent of zero." [SO:ke] comment: A junction is a boundary between regions. A boundary has an extent of zero. subset: SOFA synonym: "boundary" EXACT [] synonym: "breakpoint" EXACT [] is_a: SO:0000110 ! sequence_feature [Term] id: SO:0000704 name: gene namespace: sequence def: "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." [SO:immuno_workshop] comment: This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A gene may be considered as a unit of inheritance. subset: SOFA synonym: "INSDC_feature:gene" EXACT [] xref: http://en.wikipedia.org/wiki/Gene "wiki" is_a: SO:0001411 ! biological_region [Term] id: SO:0000713 name: DNA_motif namespace: sequence def: "A motif that is active in the DNA form of the sequence." [SO:ke] synonym: "DNA motif" EXACT [] xref: http://en.wikipedia.org/wiki/DNA_motif "wiki" is_a: SO:0000714 ! nucleotide_motif [Term] id: SO:0000714 name: nucleotide_motif namespace: sequence def: "A region of nucleotide sequence corresponding to a known motif." [SO:ke] subset: SOFA synonym: "INSDC_feature:misc_feature" BROAD [] synonym: "INSDC_note:nucleotide_motif" EXACT [] synonym: "nucleotide motif" EXACT [] is_a: SO:0001683 ! sequence_motif [Term] id: SO:0000727 name: cis_regulatory_module namespace: sequence def: "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." [PMID:19660565, SO:SG] comment: Requested by Stephen Grossmann Dec 2004. Changed relationship from has_part SO:0000235 TF_binding site to TF_binding_site is part_of SO:0000727 CRM in response to requests from GREEKC initiative in Aug 2020. Removed 3' from definition because 5' UTRs are included as well, notified by Colin Logie of GREEKC. Nov 9 2020. DS Updated name from 'CRM' to 'cis_regulatory_module' on 08 Feb 2021. See GitHub Issue #526. DS Added final sentence to definition as part of GREEKC Feb 16, 2021. See GitHub Issue #534. subset: SOFA synonym: "cis regulatory module" EXACT [] synonym: "CRM" EXACT [] synonym: "TF module" EXACT [] synonym: "transcription factor module" EXACT [] is_a: SO:0001055 ! transcriptional_cis_regulatory_region [Term] id: SO:0000830 name: chromosome_part namespace: sequence def: "A region of a chromosome." [SO:ke] comment: This is a manufactured term, that serves the purpose of allow the parts of a chromosome to have an is_a path to the root. subset: SOFA synonym: "chromosomal region" EXACT [] synonym: "chromosomal_region" EXACT [] synonym: "chromosome part" EXACT [] is_a: SO:0001411 ! biological_region [Term] id: SO:0000831 name: gene_member_region namespace: sequence def: "A region of a gene." [SO:ke] comment: A manufactured term used to allow the parts of a gene to have an is_a path to the root. subset: SOFA synonym: "gene member region" EXACT [] is_a: SO:0001411 ! biological_region [Term] id: SO:0000833 name: transcript_region namespace: sequence def: "A region of a transcript." [SO:ke] comment: This term was added to provide a grouping term for the region parts of transcript, thus giving them an is_a path back to the root. subset: SOFA synonym: "transcript region" EXACT [] is_a: SO:0001411 ! biological_region [Term] id: SO:0000834 name: mature_transcript_region namespace: sequence def: "A region of a mature transcript." [SO:ke] comment: A manufactured term to collect together the parts of a mature transcript and give them an is_a path to the root. subset: SOFA synonym: "mature transcript region" EXACT [] is_a: SO:0000833 ! transcript_region [Term] id: SO:0000835 name: primary_transcript_region namespace: sequence def: "A part of a primary transcript." [SO:ke] comment: This term was added to provide a grouping term for the region parts of primary_transcript, thus giving them an is_a path back to the root. subset: SOFA synonym: "primary transcript region" EXACT [] is_a: SO:0000833 ! transcript_region [Term] id: SO:0000836 name: mRNA_region namespace: sequence def: "A region of an mRNA." [SO:cb] comment: This term was added to provide a grouping term for the region parts of mRNA, thus giving them an is_a path back to the root. subset: SOFA synonym: "mRNA region" EXACT [] is_a: SO:0000834 ! mature_transcript_region [Term] id: SO:0000837 name: UTR_region namespace: sequence def: "A region of UTR." [SO:ke] comment: A region of UTR. This term is a grouping term to allow the parts of UTR to have an is_a path to the root. subset: SOFA synonym: "UTR region" EXACT [] is_a: SO:0000836 ! mRNA_region [Term] id: SO:0000839 name: polypeptide_region namespace: sequence alt_id: BS:00124 alt_id: BS:00331 def: "Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke] comment: Added to allow the polypeptide regions to have is_a paths back to the root. subset: biosapiens subset: SOFA synonym: "positional" RELATED [] synonym: "positional polypeptide feature" RELATED [] synonym: "region" NARROW [uniprot:feature_type] synonym: "region or site annotation" RELATED [] synonym: "site" NARROW [uniprot:feature_type] is_a: SO:0001411 ! biological_region [Term] id: SO:0000842 name: gene_component_region namespace: sequence def: "A region of a gene that has a specific function." [] subset: SOFA synonym: "gene component region" EXACT [] is_a: SO:0001411 ! biological_region [Term] id: SO:0000862 name: capped_mRNA namespace: sequence def: "An mRNA that is capped." [SO:xp] synonym: "capped mRNA" EXACT [] is_a: SO:0000234 ! mRNA [Term] id: SO:0000871 name: polyadenylated_mRNA namespace: sequence def: "An mRNA that is polyadenylated." [SO:xp] synonym: "polyadenylated mRNA" EXACT [] is_a: SO:0000234 ! mRNA [Term] id: SO:0001035 name: piRNA namespace: sequence def: "A small non coding RNA, part of a silencing system that prevents the spreading of selfish genetic elements." [SO:ke] synonym: "INSDC_feature:ncRNA" BROAD [] synonym: "INSDC_qualifier:piRNA" EXACT [] synonym: "piwi-associated RNA" EXACT [] xref: http://en.wikipedia.org/wiki/PiRNA "wiki" is_a: SO:0000370 ! small_regulatory_ncRNA [Term] id: SO:0001055 name: transcriptional_cis_regulatory_region namespace: sequence def: "A regulatory_region that modulates the transcription of a gene or genes." [PMID:9679020, SO:regcreative] comment: Previous parent term transcription_regulatory_region (SO:0001067) has been merged with this term on 11 Feb 2021 as part of the GREEKC consortium. See GitHub Issue #527. subset: SOFA synonym: "INSDC_feature:regulatory" BROAD [] synonym: "INSDC_qualifier:transcriptional_cis_regulatory_region" EXACT [] synonym: "transcription-control region" EXACT [] synonym: "transcriptional cis regulatory region" EXACT [] is_a: SO:0005836 ! regulatory_region [Term] id: SO:0001067 name: polypeptide_motif namespace: sequence alt_id: BS:00032 def: "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.)." [EBIBS:GAR, UniProt:curation_manual] comment: Range. subset: biosapiens synonym: "motif" BROAD [uniprot:feature_type] synonym: "polypeptide motif" EXACT [] is_a: SO:0100021 ! polypeptide_conserved_region [Term] id: SO:0001089 name: post_translationally_modified_region namespace: sequence alt_id: BS:00052 def: "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." [EBIBS:GAR, UniProt:curation_manual] comment: Discrete. subset: biosapiens synonym: "mod_res" EXACT [uniprot:feature_type] synonym: "modified residue" EXACT [] synonym: "post_translational_modification" EXACT [] xref: http://en.wikipedia.org/wiki/Post_translational_modification "wiki" is_a: SO:0100001 ! biochemical_region_of_peptide [Term] id: SO:0001217 name: protein_coding_gene namespace: sequence def: "A gene that codes for an RNA that can be translated into a protein." [] subset: Alliance_of_Genome_Resources synonym: "protein coding gene" EXACT [] is_a: SO:0000704 ! gene [Term] id: SO:0001236 name: base namespace: sequence def: "A base is a sequence feature that corresponds to a single unit of a nucleotide polymer." [SO:ke] subset: SOFA xref: http://en.wikipedia.org/wiki/Nucleobase "wiki" is_a: SO:0001411 ! biological_region [Term] id: SO:0001240 name: TSS_region namespace: sequence def: "The region of a gene from the 5' most TSS to the 3' TSS." [BBOP:nw] comment: Merged into promoter (SO:0000167) on 11 Feb 2021 by Dave Sant. GREEKC had asked us to merge these terms to reduce redundancy. See GitHub Issue #528 synonym: "TSS region" EXACT [] is_obsolete: true replaced_by: SO:0000167 [Term] id: SO:0001243 name: miRNA_primary_transcript_region namespace: sequence def: "A part of an miRNA primary_transcript." [SO:ke] synonym: "miRNA primary transcript region" EXACT [] is_a: SO:0000835 ! primary_transcript_region [Term] id: SO:0001244 name: pre_miRNA namespace: sequence def: "The 60-70 nucleotide region remain after Drosha processing of the primary transcript, that folds back upon itself to form a hairpin structure." [SO:ke] synonym: "pre-miRNA" EXACT [] is_a: SO:0001243 ! miRNA_primary_transcript_region [Term] id: SO:0001263 name: ncRNA_gene namespace: sequence def: "A gene that encodes a non-coding RNA." [] subset: Alliance_of_Genome_Resources synonym: "ncRNA gene" EXACT [] synonym: "non-coding RNA gene" EXACT [] is_a: SO:0000704 ! gene [Term] id: SO:0001410 name: experimental_feature namespace: sequence def: "A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer." [SO:cb] subset: SOFA synonym: "analysis feature" RELATED [] synonym: "experimental output artefact" EXACT [] synonym: "experimental_output_artefact" EXACT [] is_a: SO:0000001 ! region [Term] id: SO:0001411 name: biological_region namespace: sequence def: "A region defined by its disposition to be involved in a biological process." [SO:cb] subset: SOFA synonym: "biological region" EXACT [] synonym: "INSDC_misc_feature" BROAD [] synonym: "INSDC_note:biological_region" EXACT [] is_a: SO:0000001 ! region [Term] id: SO:0001412 name: topologically_defined_region namespace: sequence def: "A DNA region within which self-interaction occurs more often than expected by chance because of DNA-looping." [PMID:32782014, SO:cb] subset: SOFA synonym: "topologically defined region" EXACT [] is_a: SO:0000001 ! region [Term] id: SO:0001645 name: genetic_marker namespace: sequence def: "A measurable sequence feature that varies within a population." [SO:db] synonym: "genetic marker" RELATED [] is_a: SO:0001411 ! biological_region created_by: kareneilbeck creation_date: 2010-05-28T02:33:07Z [Term] id: SO:0001654 name: nucleotide_to_protein_binding_site namespace: sequence def: "A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues." [SO:ke] subset: SOFA synonym: "nucleotide to protein binding site" RELATED [] is_a: SO:0000410 ! protein_binding_site created_by: kareneilbeck creation_date: 2010-08-03T12:26:05Z [Term] id: SO:0001659 name: promoter_element namespace: sequence def: "An element that can exist within the promoter region of a gene." [] comment: Mmoved from is_a: SO:0001055 transcriptional_cis_regulatory_region as per request from GREEKC initiative in August 2020. synonym: "promoter element" EXACT [] is_a: SO:0000713 ! DNA_motif created_by: kareneilbeck creation_date: 2010-10-01T11:48:32Z [Term] id: SO:0001669 name: RNApol_II_core_promoter namespace: sequence def: "The minimal portion of the promoter required to properly initiate transcription in RNA polymerase II transcribed genes." [PMID:16858867] synonym: "RNApol II core promoter" EXACT [] is_a: SO:0000170 ! RNApol_II_promoter created_by: kareneilbeck creation_date: 2010-10-01T03:13:41Z [Term] id: SO:0001683 name: sequence_motif namespace: sequence def: "A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance." [http://en.wikipedia.org/wiki/Sequence_motif] subset: SOFA synonym: "sequence motif" RELATED [] xref: http://en.wikipedia.org/wiki/Sequence_motif "wikipedia" is_a: SO:0001411 ! biological_region created_by: kareneilbeck creation_date: 2010-10-14T04:13:22Z [Term] id: SO:0001700 name: histone_modification namespace: sequence def: "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:en.wikipedia.org/wiki/Histone] synonym: "histone modification" EXACT [] synonym: "histone modification site" RELATED [] is_a: SO:0001089 ! post_translationally_modified_region is_a: SO:0001720 ! epigenetically_modified_region created_by: kareneilbeck creation_date: 2010-03-31T10:22:08Z [Term] id: SO:0001720 name: epigenetically_modified_region namespace: sequence def: "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://en.wikipedia.org/wiki/Epigenetics, SO:ke] comment: Moved from is_a biological_region (SO:0001411) to is_a regulatory_region (SO:0005836) on 11 Feb 2021. GREEKC members pointed out that this would be a more appropriate location. See GitHub Issue #530. 11 Feb 2021 updated definition along with addition of epigenomically_modified_region (SO:0002332). Epigenetically modified region is now not inherited while epigenomically modified region is not annotated as inherited. See GitHub Issue #532 and issue #534. subset: SOFA synonym: "epigenetically modified region" RELATED [] is_a: SO:0005836 ! regulatory_region created_by: kareneilbeck creation_date: 2010-03-27T12:02:29Z [Term] id: SO:0001796 name: regional_centromere_central_core namespace: sequence def: "A conserved region within the central region of a modular centromere, where the kinetochore is formed." [SO:vw] synonym: "regional centromere central core" EXACT [] is_a: SO:0000330 ! conserved_region created_by: kareneilbeck creation_date: 2011-05-31T12:56:30Z [Term] id: SO:0001797 name: centromeric_repeat namespace: sequence def: "A repeat region found within the modular centromere." [SO:ke] synonym: "centromeric repeat" EXACT [] synonym: "INSDC_feature:repeat_region" BROAD [] synonym: "INSDC_qualifier:centromeric_repeat" EXACT [] is_a: SO:0000657 ! repeat_region created_by: kareneilbeck creation_date: 2011-05-31T12:59:27Z [Term] id: SO:0001798 name: regional_centromere_inner_repeat_region namespace: sequence def: "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." [SO:vw] synonym: "lmr repeat" EXACT [] synonym: "lmr1L" EXACT [] synonym: "lmr1R" EXACT [] synonym: "regional centromere inner repeat region" EXACT [] is_a: SO:0001797 ! centromeric_repeat created_by: kareneilbeck creation_date: 2011-05-31T01:01:08Z [Term] id: SO:0001801 name: tasiRNA_primary_transcript namespace: sequence def: "A primary transcript encoding a tasiRNA." [PMID:16145017] synonym: "tasiRNA primary transcript" EXACT [] is_a: SO:0000483 ! nc_primary_transcript created_by: kareneilbeck creation_date: 2011-05-31T03:27:35Z [Term] id: SO:0001877 name: lncRNA namespace: sequence def: "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." [HGNC:mw] {comment="PMID:33353982"} comment: Updated the definition of lncRNA (SO:0001877) from "A non-coding RNA over 200nucleotides in length." to "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." See GitHub Issue #575 synonym: "INSDC_feature:ncRNA" BROAD [] synonym: "INSDC_qualifier:lncRNA" EXACT [] synonym: "lncRNA_transcript" EXACT [] synonym: "long non-coding RNA" EXACT [] xref: http://www.gencodegenes.org/gencode_biotypes.html "GENCODE" is_a: SO:0000655 ! ncRNA created_by: kareneilbeck creation_date: 2012-02-14T05:18:01Z [Term] id: SO:0001914 name: rDNA_replication_fork_barrier namespace: sequence def: "A DNA motif that is found in eukaryotic rDNA repeats, and is a site of replication fork pausing." [PMID:14645529] comment: Requested by Midori - June 2012. synonym: "DNA spacer replication fork barrier" EXACT [] synonym: "rDNA replication fork barrier" EXACT [] synonym: "RFB" EXACT [] synonym: "RTS1 barrier" EXACT [] synonym: "RTS1 element" EXACT [] is_a: SO:0000713 ! DNA_motif created_by: kareneilbeck creation_date: 2012-06-11T02:55:02Z [Term] id: SO:0001927 name: telomeric_transcript namespace: sequence def: "A non-coding transcript derived from the transcript of the telomere." [PMID:22139915] synonym: "telomeric transcript" EXACT [] is_a: SO:0000655 ! ncRNA created_by: kareneilbeck creation_date: 2012-10-31T01:42:15Z [Term] id: SO:0001997 name: subtelomere namespace: sequence def: "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." [POMBE:al] is_a: SO:0000628 ! chromosomal_structural_element created_by: kareneilbeck creation_date: 2014-01-05T07:02:01Z [Term] id: SO:0002035 name: lncRNA_primary_transcript namespace: sequence def: "A primary transcript encoding a lncRNA." [SO:ke] synonym: "lncRNA primary transcript" EXACT [] is_a: SO:0000483 ! nc_primary_transcript created_by: kareneilbeck creation_date: 2015-01-09T15:23:03Z [Term] id: SO:0002140 name: early_origin_of_replication namespace: sequence def: "An origin of replication that initiates early in S phase." [PMID:23348837, PMID:9115207] synonym: "early origin" EXACT [] synonym: "early origin of replication" EXACT [] synonym: "early replication origin" EXACT [] is_a: SO:0000296 ! origin_of_replication created_by: nicole creation_date: 2016-09-15T15:53:36Z [Term] id: SO:0002141 name: late_origin_of_replication namespace: sequence def: "An origin of replication that initiates late in S phase." [PMID:23348837, PMID:9115207] synonym: "late origin" EXACT [] synonym: "late origin of replication" EXACT [] synonym: "late replication origin" EXACT [] is_a: SO:0000296 ! origin_of_replication created_by: nicole creation_date: 2016-09-15T15:56:07Z [Term] id: SO:0002221 name: eukaryotic_promoter namespace: sequence def: "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." [] synonym: "Eukaryotic promoter" EXACT [] is_a: SO:0000167 ! promoter created_by: david creation_date: 2019-07-31T14:01:20Z [Term] id: SO:0002222 name: prokaryotic_promoter namespace: sequence def: "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." [PMID:32665585] synonym: "Prokaryotic promoter" EXACT [] is_a: SO:0000167 ! promoter created_by: david creation_date: 2019-07-31T14:02:26Z [Term] id: SO:0002234 name: pumilio_response_element namespace: sequence def: "A cis-acting element involved in RNA stability found in the 3' UTR of some RNA (consensus UGUAAAUA)." [PMID:30601114] comment: Added as per request by Val Wood GitHub issue #455 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/455) synonym: "PRE binding RNA" EXACT [] synonym: "pumilio response element" EXACT [] is_a: SO:0000837 ! UTR_region created_by: david creation_date: 2020-04-14T10:40:30Z [Term] id: SO:0002247 name: sncRNA namespace: sequence def: "A non-coding RNA less than 200 nucleotides in length." [PMID:30069443] comment: Added as per request from GitHub Issue #485 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/485) synonym: "Small noncoding RNA" EXACT [] is_a: SO:0000655 ! ncRNA created_by: david creation_date: 2020-05-13T11:07:30Z [Term] id: SO:0002304 name: topologically_associated_domain namespace: sequence def: "An instance of a self-interacting DNA region flanked by left and right TAD boundaries." [GREEKC:cl, PMID:32782014] comment: Added by Dave to be consistent with other ontologies updated with GREEKC initiative. synonym: "TAD" EXACT [] synonym: "topologically associated domain" EXACT [] is_a: SO:0001412 ! topologically_defined_region created_by: david creation_date: 2020-08-12T14:01:30Z [Term] id: SO:0002305 name: topologically_associated_domain_boundary namespace: sequence def: "A DNA region enriched in DNA loop anchors and across which DNA loops occur less often than expected by chance." [GREEKC:cl, PMID:32782014] comment: Added by Dave to be consistent with other ontologies updated with GREEKC initiative. synonym: "TAD boundary" EXACT [] synonym: "TAD_boundary" EXACT [] synonym: "topologically associated domain boundary" EXACT [] is_a: SO:0000699 ! junction created_by: david creation_date: 2020-08-12T14:01:30Z [Term] id: SO:0002307 name: DNA_loop namespace: sequence def: "A region of DNA between two loop anchor positions that are held in close physical proximity." [GREEKC:cl, PMID:32782014] comment: Added by Dave to be consistent with other ontologies updated with GREEKC initiative. DS updated defintion Feb 16, 2021. See GitHub Issue #534. synonym: "DNA loop" EXACT [] is_a: SO:0000830 ! chromosome_part created_by: david creation_date: 2020-08-12T14:01:30Z [Term] id: SO:0002308 name: DNA_loop_anchor namespace: sequence def: "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." [GREEKC:cl, PMID:32782014] comment: Added by Dave to be consistent with other ontologies updated with GREEKC initiative. DS updated defintion Feb 16, 2021. See GitHub Issue #534. synonym: "DNA loop anchor" EXACT [] is_a: SO:0000727 ! cis_regulatory_module created_by: david creation_date: 2020-08-12T14:01:30Z [Term] id: SO:0002309 name: core_promoter_element namespace: sequence def: "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." [GREEKC:rl] comment: Added by Dave to be consistent with other ontologies updated with GREEKC initiative. synonym: "core promoter element" EXACT [] is_a: SO:0001659 ! promoter_element created_by: david creation_date: 2020-08-12T14:01:30Z [Term] id: SO:0002343 name: cytosolic_rRNA namespace: sequence def: "Cytosolic rRNA is an RNA component of the small or large subunits of cytosolic ribosomes." [PMID:3044395] comment: Added as a request from EBI. See GitHub Issue #493 synonym: "cytosolic ribosomal RNA" EXACT [] synonym: "cytosolic rRNA" EXACT [] is_a: SO:0000252 ! rRNA created_by: david creation_date: 2021-06-10T16:45:30Z [Term] id: SO:0005836 name: regulatory_region namespace: sequence def: "A region of sequence that is involved in the control of a biological process." [SO:ke] subset: SOFA synonym: "INSDC_feature:regulatory" BROAD [] synonym: "INSDC_qualifier:other" EXACT [] synonym: "regulatory region" EXACT [] xref: http://en.wikipedia.org/wiki/Regulatory_region "wiki" is_a: SO:0000831 ! gene_member_region [Term] id: SO:0100001 name: biochemical_region_of_peptide namespace: sequence def: "A region of a peptide that is involved in a biochemical function." [EBIBS:GAR] comment: Range. subset: biosapiens synonym: "biochemical motif" EXACT [] synonym: "biochemical region of peptide" EXACT [] synonym: "biochemical_region" RELATED [] is_a: SO:0001067 ! polypeptide_motif [Term] id: SO:0100021 name: polypeptide_conserved_region namespace: sequence def: "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." [EBIBS:GAR] subset: biosapiens synonym: "polypeptide conserved region" EXACT [] is_a: SO:0000839 ! polypeptide_region [Term] id: SO:3000000 name: gene_segment namespace: sequence def: "A gene component region which acts as a recombinational unit of a gene whose functional form is generated through somatic recombination." [GOC:add] comment: Requested by tracker 2021594, July 2008, by Alex. synonym: "gene segment" EXACT [] is_a: SO:0000842 ! gene_component_region