definition
term replaced by
subset_property
synonym_type_property
consider
has_alternative_id
has_broad_synonym
database_cross_reference
has_exact_synonym
has_narrow_synonym
has_obo_format_version
has_obo_namespace
has_related_synonym
has_scope
has_synonym_type
in_subset
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.
sequence
sequence
SO:0000001
region
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
Any extent of continuous biological sequence.
INSDC_feature:misc_feature
INSDC_note:other
INSDC_note:sequence_feature
located_sequence_feature
sequence feature
sequence
located sequence feature
SO:0000110
sequence_feature
Any extent of continuous biological sequence.
LAMHDI:mb
SO:ke
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.
INSDC_feature:regulatory
http://en.wikipedia.org/wiki/Enhancer_(genetics)
INSDC_qualifier:enhancer
sequence
SO:0000165
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.
enhancer
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
http://en.wikipedia.org/wiki/Enhancer_(genetics)
wiki
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.
INSDC_feature:regulatory
http://en.wikipedia.org/wiki/Promoter
INSDC_qualifier:promoter
promoter sequence
sequence
SO:0000167
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.
promoter
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
http://en.wikipedia.org/wiki/Promoter
wiki
A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription.
RNA polymerase B promoter
RNApol II promoter
polymerase II promoter
sequence
pol II promoter
SO:0000170
parent term RNA_polymerase_promoter SO:0001203 was obsoleted in Aug 2020, so term has been moved to eukaryotic_promoter SO:0002221.
RNApol_II_promoter
A DNA sequence in eukaryotic DNA to which RNA polymerase II binds, to begin transcription.
SO:ke
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.
INSDC_feature:regulatory
GC rich promoter region
GC-rich region
INSDC_qualifier:GC_rich_promoter_region
sequence
SO:0000173
GC_rich_promoter_region
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
A transcript that in its initial state requires modification to be functional.
http://en.wikipedia.org/wiki/Primary_transcript
INSDC_feature:precursor_RNA
INSDC_feature:prim_transcript
precursor RNA
primary transcript
sequence
SO:0000185
primary_transcript
http://en.wikipedia.org/wiki/Primary_transcript
wiki
A transcript that in its initial state requires modification to be functional.
SO:ma
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://en.wikipedia.org/wiki/Intron
INSDC_feature:intron
sequence
SO:0000188
This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
intron
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
http://en.wikipedia.org/wiki/Intron
wiki
A primary transcript encoding a small nuclear RNA (SO:0000274).
snRNA primary transcript
sequence
SO:0000231
snRNA_primary_transcript
A primary transcript encoding a small nuclear RNA (SO:0000274).
SO:ke
A primary transcript encoding one or more small nucleolar RNAs (SO:0000275).
snoRNA primary transcript
sequence
SO:0000232
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).
snoRNA_primary_transcript
A primary transcript encoding one or more small nucleolar RNAs (SO:0000275).
SO:ke
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://en.wikipedia.org/wiki/Mature_transcript
mature transcript
sequence
SO:0000233
A processed transcript cannot contain introns.
mature_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.
SO:ke
http://en.wikipedia.org/wiki/Mature_transcript
wiki
Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns.
http://en.wikipedia.org/wiki/MRNA
http://www.gencodegenes.org/gencode_biotypes.html
INSDC_feature:mRNA
messenger RNA
protein_coding_transcript
sequence
SO:0000234
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.
mRNA
Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns.
SO:ma
http://en.wikipedia.org/wiki/MRNA
wiki
http://www.gencodegenes.org/gencode_biotypes.html
GENCODE
A DNA site where a transcription factor binds.
TF binding site
transcription factor binding site
sequence
SO:0000235
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.
TF_binding_site
A DNA site where a transcription factor binds.
SO:ke
rRNA is an RNA component of a ribosome that can provide both structural scaffolding and catalytic activity.
INSDC_qualifier:unknown
http://en.wikipedia.org/wiki/RRNA
INSDC_feature:rRNA
ribosomal RNA
ribosomal ribonucleic acid
sequence
SO:0000252
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
rRNA
rRNA is an RNA component of a ribosome that can provide both structural scaffolding and catalytic activity.
ISBN:0198506732
http://www.insdc.org/files/feature_table.html
http://en.wikipedia.org/wiki/RRNA
wiki
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.
INSDC_qualifier:unknown
http://en.wikipedia.org/wiki/TRNA
INSDC_feature:tRNA
sequence
transfer RNA
transfer ribonucleic acid
SO:0000253
This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
tRNA
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.
ISBN:0198506732
http://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00005
http://en.wikipedia.org/wiki/TRNA
wiki
A small nuclear RNA molecule involved in pre-mRNA splicing and processing.
INSDC_feature:ncRNA
http://en.wikipedia.org/wiki/SnRNA
INSDC_qualifier:snRNA
small nuclear RNA
sequence
SO:0000274
This term is mapped to MGED. Do not obsolete without consulting MGED ontology.
snRNA
A small nuclear RNA molecule involved in pre-mRNA splicing and processing.
PMID:11733745
WB:ems
http://www.insdc.org/files/feature_table.html
http://en.wikipedia.org/wiki/SnRNA
wiki
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.
INSDC_feature:ncRNA
INSDC_qualifier:snoRNA
small nucleolar RNA
sequence
SO:0000275
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.
snoRNA
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
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.
SO:0000649
INSDC_feature:ncRNA
http://en.wikipedia.org/wiki/MiRNA
http://en.wikipedia.org/wiki/StRNA
INSDC_qualifier:miRNA
micro RNA
microRNA
small temporal RNA
stRNA
sequence
SO:0000276
miRNA
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
http://en.wikipedia.org/wiki/MiRNA
wiki
http://en.wikipedia.org/wiki/StRNA
wiki
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://en.wikipedia.org/wiki/Origin_of_replication
INSDC_feature:rep_origin
ori
origin of replication
sequence
SO:0000296
origin_of_replication
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.
NCBI:cf
http://www.insdc.org/files/feature_table.html
http://en.wikipedia.org/wiki/Origin_of_replication
wiki
A modified nucleotide, i.e. a nucleotide other than A, T, C. G.
INSDC_feature:modified_base
modified base site
sequence
SO:0000305
Modified base:<modified_base>.
modified_DNA_base
A modified nucleotide, i.e. a nucleotide other than A, T, C. G.
http://www.insdc.org/files/feature_table.html
The first base where RNA polymerase begins to synthesize the RNA transcript.
INSDC_feature:misc_feature
INSDC_note:transcription_start_site
transcription start site
transcription_start_site
sequence
SO:0000315
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.
TSS
The first base where RNA polymerase begins to synthesize the RNA transcript.
SO:ke
Region of sequence similarity by descent from a common ancestor.
INSDC_feature:misc_feature
http://en.wikipedia.org/wiki/Conserved_region
INSDC_note:conserved_region
conserved region
sequence
SO:0000330
conserved_region
Region of sequence similarity by descent from a common ancestor.
SO:ke
http://en.wikipedia.org/wiki/Conserved_region
wiki
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).
INSDC_feature:gene
http://en.wikipedia.org/wiki/Pseudogene
INSDC_qualifier:pseudo
INSDC_qualifier:unknown
sequence
SO:0000336
pseudogene
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
http://en.wikipedia.org/wiki/Pseudogene
wiki
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).
small regulatory ncRNA
sequence
SO:0000370
small_regulatory_ncRNA
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
Cytosolic 5.8S rRNA is an RNA component of the large subunit of cytosolic ribosomes in eukaryotes.
http://en.wikipedia.org/wiki/5.8S_ribosomal_RNA
cytosolic 5.8S LSU rRNA
cytosolic 5.8S rRNA
cytosolic 5.8S ribosomal RNA
cytosolic rRNA 5 8S
sequence
SO:0000375
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.
cytosolic_5_8S_rRNA
Cytosolic 5.8S rRNA is an RNA component of the large subunit of cytosolic ribosomes in eukaryotes.
https://rfam.xfam.org/family/RF00002
http://en.wikipedia.org/wiki/5.8S_ribosomal_RNA
wiki
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.
BS:00033
http://en.wikipedia.org/wiki/Binding_site
INSDC_feature:misc_binding
binding site
binding_or_interaction_site
sequence
site
SO:0000409
See GO:0005488 : binding.
binding_site
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
http://en.wikipedia.org/wiki/Binding_site
wiki
A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules.
INSDC_feature:protein_bind
protein binding site
sequence
SO:0000410
See GO:0042277 : peptide binding.
protein_binding_site
A binding site that, in the molecule, interacts selectively and non-covalently with polypeptide molecules.
SO:ke
A primary transcript that is never translated into a protein.
nc primary transcript
noncoding primary transcript
sequence
SO:0000483
nc_primary_transcript
A primary transcript that is never translated into a protein.
SO:ke
A region of chromosome where the spindle fibers attach during mitosis and meiosis.
http://en.wikipedia.org/wiki/Centromere
INSDC_feature:centromere
sequence
SO:0000577
centromere
A region of chromosome where the spindle fibers attach during mitosis and meiosis.
SO:ke
http://en.wikipedia.org/wiki/Centromere
wiki
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://en.wikipedia.org/wiki/Group_I_intron
group I intron
sequence
SO:0000587
GO:0000372.
group_I_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://www.sanger.ac.uk/cgi-bin/Rfam/getacc?RF00028
http://en.wikipedia.org/wiki/Group_I_intron
wiki
A self spliced intron.
INSDC_feature:ncRNA
INSDC_qualifier:autocatalytically_spliced_intron
autocatalytically spliced intron
sequence
SO:0000588
autocatalytically_spliced_intron
A self spliced intron.
SO:ke
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'.
C D box snoRNA
C/D box snoRNA
SNORD
box C/D snoRNA
sequence
SO:0000593
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.
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://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html
SNORD
PMID:31828325
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.
H ACA box snoRNA
H/ACA box snoRNA
SNORA
box H/ACA snoRNA
sequence
SO:0000594
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.
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://www.bio.umass.edu/biochem/rna-sequence/Yeast_snoRNA_Database/snoRNA_DataBase.html
SNORA
PMID:31828325
A DNA sequence to which bacterial RNA polymerase binds, to begin transcription.
bacterial RNApol promoter
sequence
SO:0000613
former parent RNA_polymerase_promoter SO:0001203 was merged with promoter SO:0000167 in Aug 2020 as part of GREEKC.
bacterial_RNApol_promoter
A DNA sequence to which bacterial RNA polymerase binds, to begin transcription.
SO:ke
A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end.
http://en.wikipedia.org/wiki/Telomere
INSDC_feature:telomere
telomeric DNA
telomeric sequence
sequence
SO:0000624
telomere
A specific structure at the end of a linear chromosome, required for the integrity and maintenance of the end.
SO:ma
http://en.wikipedia.org/wiki/Telomere
wiki
A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control.
INSDC_feature:regulatory
http://en.wikipedia.org/wiki/Silencer_(DNA)
INSDC_qualifier:silencer
sequence
SO:0000625
silencer
A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control.
SO:ke
http://en.wikipedia.org/wiki/Silencer_(DNA)
wiki
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.
INSDC_feature:regulatory
http://en.wikipedia.org/wiki/Insulator_(genetics)
INSDC_qualifier:insulator
insulator element
sequence
SO:0000627
moved from is_a: SO:0001055 transcriptional_cis_regulatory_region as per request from GREEKC initiative in August 2020.
insulator
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
http://en.wikipedia.org/wiki/Insulator_(genetics)
wiki
Regions of the chromosome that are important for structural elements.
chromosomal structural element
sequence
SO:0000628
chromosomal_structural_element
Antisense RNA is RNA that is transcribed from the coding, rather than the template, strand of DNA. It is therefore complementary to mRNA.
INSDC_feature:ncRNA
http://en.wikipedia.org/wiki/Antisense_RNA
INSDC_qualifier:antisense_RNA
antisense RNA
sequence
SO:0000644
antisense_RNA
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
http://en.wikipedia.org/wiki/Antisense_RNA
wiki
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.
INSDC_feature:ncRNA
http://en.wikipedia.org/wiki/SiRNA
INSDC_qualifier:siRNA
small interfering RNA
sequence
SO:0000646
siRNA
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
http://en.wikipedia.org/wiki/SiRNA
wiki
A primary transcript encoding a micro RNA.
SO:0000648
miRNA primary transcript
micro RNA primary transcript
small temporal RNA primary transcript
stRNA primary transcript
stRNA_primary_transcript
sequence
SO:0000647
miRNA_primary_transcript
A primary transcript encoding a micro RNA.
SO:ke
Cytosolic LSU rRNA is an RNA component of the large subunit of cytosolic ribosomes.
cytosolic LSU RNA
cytosolic LSU rRNA
cytosolic large subunit rRNA
sequence
SO:0000651
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.
cytosolic_LSU_rRNA
Cytosolic LSU rRNA is an RNA component of the large subunit of cytosolic ribosomes.
SO:ke
An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product.
INSDC_qualifier:other
http://en.wikipedia.org/wiki/NcRNA
http://www.gencodegenes.org/gencode_biotypes.html
known_ncrna
noncoding RNA
sequence
SO:0000655
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.
ncRNA
An RNA transcript that does not encode for a protein rather the RNA molecule is the gene product.
SO:ke
http://en.wikipedia.org/wiki/NcRNA
wiki
http://www.gencodegenes.org/gencode_biotypes.html
GENCODE
A region of sequence containing one or more repeat units.
INSDC_feature:repeat_region
INSDC_qualifier:other
repeat region
sequence
SO:0000657
repeat_region
A region of sequence containing one or more repeat units.
SO:ke
An RNA synthesized on a DNA or RNA template by an RNA polymerase.
INSDC_feature:misc_RNA
http://en.wikipedia.org/wiki/RNA
sequence
SO:0000673
Added relationship overlaps SO:0002300 unit_of_gene_expression with Mejia-Almonte et.al PMID:32665585 Aug 5, 2020.
transcript
An RNA synthesized on a DNA or RNA template by an RNA polymerase.
SO:ma
http://en.wikipedia.org/wiki/RNA
wiki
A sequence_feature with an extent of zero.
boundary
breakpoint
sequence
SO:0000699
A junction is a boundary between regions. A boundary has an extent of zero.
junction
A sequence_feature with an extent of zero.
SO:ke
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://en.wikipedia.org/wiki/Gene
INSDC_feature:gene
sequence
SO:0000704
This term is mapped to MGED. Do not obsolete without consulting MGED ontology. A gene may be considered as a unit of inheritance.
gene
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
http://en.wikipedia.org/wiki/Gene
wiki
A motif that is active in the DNA form of the sequence.
http://en.wikipedia.org/wiki/DNA_motif
DNA motif
sequence
SO:0000713
DNA_motif
A motif that is active in the DNA form of the sequence.
SO:ke
http://en.wikipedia.org/wiki/DNA_motif
wiki
A region of nucleotide sequence corresponding to a known motif.
INSDC_feature:misc_feature
INSDC_note:nucleotide_motif
nucleotide motif
sequence
SO:0000714
nucleotide_motif
A region of nucleotide sequence corresponding to a known motif.
SO:ke
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.
CRM
TF module
cis regulatory module
transcription factor module
sequence
SO:0000727
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.
cis_regulatory_module
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
A region of a chromosome.
chromosomal region
chromosomal_region
chromosome part
sequence
SO:0000830
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.
chromosome_part
A region of a chromosome.
SO:ke
A region of a gene.
gene member region
sequence
SO:0000831
A manufactured term used to allow the parts of a gene to have an is_a path to the root.
gene_member_region
A region of a gene.
SO:ke
A region of a transcript.
transcript region
sequence
SO:0000833
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.
transcript_region
A region of a transcript.
SO:ke
A region of a mature transcript.
mature transcript region
sequence
SO:0000834
A manufactured term to collect together the parts of a mature transcript and give them an is_a path to the root.
mature_transcript_region
A region of a mature transcript.
SO:ke
A part of a primary transcript.
primary transcript region
sequence
SO:0000835
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.
primary_transcript_region
A part of a primary transcript.
SO:ke
A region of an mRNA.
mRNA region
sequence
SO:0000836
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.
mRNA_region
A region of an mRNA.
SO:cb
A region of UTR.
UTR region
sequence
SO:0000837
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.
UTR_region
A region of UTR.
SO:ke
Biological sequence region that can be assigned to a specific subsequence of a polypeptide.
BS:00124
BS:00331
region
site
sequence
positional
positional polypeptide feature
region or site annotation
SO:0000839
Added to allow the polypeptide regions to have is_a paths back to the root.
polypeptide_region
Biological sequence region that can be assigned to a specific subsequence of a polypeptide.
SO:GAR
SO:ke
region
uniprot:feature_type
site
uniprot:feature_type
A region of a gene that has a specific function.
gene component region
sequence
SO:0000842
gene_component_region
An mRNA that is capped.
capped mRNA
sequence
SO:0000862
capped_mRNA
An mRNA that is capped.
SO:xp
An mRNA that is polyadenylated.
polyadenylated mRNA
sequence
SO:0000871
polyadenylated_mRNA
An mRNA that is polyadenylated.
SO:xp
A small non coding RNA, part of a silencing system that prevents the spreading of selfish genetic elements.
INSDC_feature:ncRNA
http://en.wikipedia.org/wiki/PiRNA
INSDC_qualifier:piRNA
piwi-associated RNA
sequence
SO:0001035
piRNA
A small non coding RNA, part of a silencing system that prevents the spreading of selfish genetic elements.
SO:ke
http://en.wikipedia.org/wiki/PiRNA
wiki
A regulatory_region that modulates the transcription of a gene or genes.
INSDC_feature:regulatory
INSDC_qualifier:transcriptional_cis_regulatory_region
transcription-control region
transcriptional cis regulatory region
sequence
SO:0001055
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.
transcriptional_cis_regulatory_region
A regulatory_region that modulates the transcription of a gene or genes.
PMID:9679020
SO:regcreative
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.).
BS:00032
motif
polypeptide motif
sequence
SO:0001067
Range.
polypeptide_motif
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
motif
uniprot:feature_type
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.
BS:00052
http://en.wikipedia.org/wiki/Post_translational_modification
mod_res
modified residue
post_translational_modification
sequence
SO:0001089
Discrete.
post_translationally_modified_region
mod_res
uniprot:feature_type
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
http://en.wikipedia.org/wiki/Post_translational_modification
wiki
A gene that codes for an RNA that can be translated into a protein.
protein coding gene
sequence
SO:0001217
protein_coding_gene
A base is a sequence feature that corresponds to a single unit of a nucleotide polymer.
http://en.wikipedia.org/wiki/Nucleobase
sequence
SO:0001236
base
A base is a sequence feature that corresponds to a single unit of a nucleotide polymer.
SO:ke
http://en.wikipedia.org/wiki/Nucleobase
wiki
The region of a gene from the 5' most TSS to the 3' TSS.
SO:0000167
TSS region
sequence
SO:0001240
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
TSS_region
true
The region of a gene from the 5' most TSS to the 3' TSS.
BBOP:nw
A part of an miRNA primary_transcript.
miRNA primary transcript region
sequence
SO:0001243
miRNA_primary_transcript_region
A part of an miRNA primary_transcript.
SO:ke
The 60-70 nucleotide region remain after Drosha processing of the primary transcript, that folds back upon itself to form a hairpin structure.
pre-miRNA
sequence
SO:0001244
pre_miRNA
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
A gene that encodes a non-coding RNA.
ncRNA gene
non-coding RNA gene
sequence
SO:0001263
ncRNA_gene
A region which is the result of some arbitrary experimental procedure. The procedure may be carried out with biological material or inside a computer.
experimental output artefact
experimental_output_artefact
sequence
analysis feature
SO:0001410
experimental_feature
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
A region defined by its disposition to be involved in a biological process.
INSDC_misc_feature
INSDC_note:biological_region
biological region
sequence
SO:0001411
biological_region
A region defined by its disposition to be involved in a biological process.
SO:cb
A DNA region within which self-interaction occurs more often than expected by chance because of DNA-looping.
topologically defined region
sequence
SO:0001412
topologically_defined_region
A DNA region within which self-interaction occurs more often than expected by chance because of DNA-looping.
PMID:32782014
SO:cb
A measurable sequence feature that varies within a population.
kareneilbeck
2010-05-28T02:33:07Z
sequence
genetic marker
SO:0001645
genetic_marker
A measurable sequence feature that varies within a population.
SO:db
A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues.
kareneilbeck
2010-08-03T12:26:05Z
sequence
nucleotide to protein binding site
SO:0001654
nucleotide_to_protein_binding_site
A binding site that, in the nucleotide molecule, interacts selectively and non-covalently with polypeptide residues.
SO:ke
An element that can exist within the promoter region of a gene.
kareneilbeck
2010-10-01T11:48:32Z
promoter element
sequence
SO:0001659
Mmoved from is_a: SO:0001055 transcriptional_cis_regulatory_region as per request from GREEKC initiative in August 2020.
promoter_element
The minimal portion of the promoter required to properly initiate transcription in RNA polymerase II transcribed genes.
kareneilbeck
2010-10-01T03:13:41Z
RNApol II core promoter
sequence
SO:0001669
RNApol_II_core_promoter
The minimal portion of the promoter required to properly initiate transcription in RNA polymerase II transcribed genes.
PMID:16858867
A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance.
kareneilbeck
2010-10-14T04:13:22Z
http://en.wikipedia.org/wiki/Sequence_motif
sequence
sequence motif
SO:0001683
sequence_motif
A sequence motif is a nucleotide or amino-acid sequence pattern that may have biological significance.
http://en.wikipedia.org/wiki/Sequence_motif
http://en.wikipedia.org/wiki/Sequence_motif
wikipedia
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.
kareneilbeck
2010-03-31T10:22:08Z
histone modification
sequence
histone modification site
SO:0001700
histone_modification
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
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.
kareneilbeck
2010-03-27T12:02:29Z
sequence
epigenetically modified region
SO:0001720
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.
epigenetically_modified_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.
SO:ke
http://en.wikipedia.org/wiki/Epigenetics
A conserved region within the central region of a modular centromere, where the kinetochore is formed.
kareneilbeck
2011-05-31T12:56:30Z
regional centromere central core
sequence
SO:0001796
regional_centromere_central_core
A conserved region within the central region of a modular centromere, where the kinetochore is formed.
SO:vw
A repeat region found within the modular centromere.
kareneilbeck
2011-05-31T12:59:27Z
INSDC_feature:repeat_region
INSDC_qualifier:centromeric_repeat
centromeric repeat
sequence
SO:0001797
centromeric_repeat
A repeat region found within the modular centromere.
SO:ke
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.
kareneilbeck
2011-05-31T01:01:08Z
lmr repeat
lmr1L
lmr1R
regional centromere inner repeat region
sequence
SO:0001798
regional_centromere_inner_repeat_region
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
A primary transcript encoding a tasiRNA.
kareneilbeck
2011-05-31T03:27:35Z
tasiRNA primary transcript
sequence
SO:0001801
tasiRNA_primary_transcript
A primary transcript encoding a tasiRNA.
PMID:16145017
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.
kareneilbeck
2012-02-14T05:18:01Z
INSDC_feature:ncRNA
http://www.gencodegenes.org/gencode_biotypes.html
INSDC_qualifier:lncRNA
lncRNA_transcript
long non-coding RNA
sequence
SO:0001877
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
lncRNA
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
PMID:33353982
http://www.gencodegenes.org/gencode_biotypes.html
GENCODE
A DNA motif that is found in eukaryotic rDNA repeats, and is a site of replication fork pausing.
kareneilbeck
2012-06-11T02:55:02Z
DNA spacer replication fork barrier
RFB
RTS1 barrier
RTS1 element
rDNA replication fork barrier
sequence
SO:0001914
Requested by Midori - June 2012.
rDNA_replication_fork_barrier
A DNA motif that is found in eukaryotic rDNA repeats, and is a site of replication fork pausing.
PMID:14645529
A non-coding transcript derived from the transcript of the telomere.
kareneilbeck
2012-10-31T01:42:15Z
telomeric transcript
sequence
SO:0001927
telomeric_transcript
A non-coding transcript derived from the transcript of the telomere.
PMID:22139915
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.
kareneilbeck
2014-01-05T07:02:01Z
sequence
SO:0001997
subtelomere
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
A primary transcript encoding a lncRNA.
kareneilbeck
2015-01-09T15:23:03Z
lncRNA primary transcript
sequence
SO:0002035
lncRNA_primary_transcript
A primary transcript encoding a lncRNA.
SO:ke
An origin of replication that initiates early in S phase.
nicole
2016-09-15T15:53:36Z
early origin
early origin of replication
early replication origin
sequence
SO:0002140
early_origin_of_replication
An origin of replication that initiates early in S phase.
PMID:23348837
PMID:9115207
An origin of replication that initiates late in S phase.
nicole
2016-09-15T15:56:07Z
late origin
late origin of replication
late replication origin
sequence
SO:0002141
late_origin_of_replication
An origin of replication that initiates late in S phase.
PMID:23348837
PMID:9115207
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.
david
2019-07-31T14:01:20Z
Eukaryotic promoter
sequence
SO:0002221
eukaryotic_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.
david
2019-07-31T14:02:26Z
Prokaryotic promoter
sequence
SO:0002222
prokaryotic_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.
PMID:32665585
A cis-acting element involved in RNA stability found in the 3' UTR of some RNA (consensus UGUAAAUA).
david
2020-04-14T10:40:30Z
PRE binding RNA
pumilio response element
sequence
SO:0002234
Added as per request by Val Wood GitHub issue #455 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/455)
pumilio_response_element
A cis-acting element involved in RNA stability found in the 3' UTR of some RNA (consensus UGUAAAUA).
PMID:30601114
A non-coding RNA less than 200 nucleotides in length.
david
2020-05-13T11:07:30Z
Small noncoding RNA
sequence
SO:0002247
Added as per request from GitHub Issue #485 (https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/485)
sncRNA
A non-coding RNA less than 200 nucleotides in length.
PMID:30069443
An instance of a self-interacting DNA region flanked by left and right TAD boundaries.
david
2020-08-12T14:01:30Z
TAD
topologically associated domain
sequence
SO:0002304
Added by Dave to be consistent with other ontologies updated with GREEKC initiative.
topologically_associated_domain
An instance of a self-interacting DNA region flanked by left and right TAD boundaries.
GREEKC:cl
PMID:32782014
A DNA region enriched in DNA loop anchors and across which DNA loops occur less often than expected by chance.
david
2020-08-12T14:01:30Z
TAD boundary
TAD_boundary
topologically associated domain boundary
sequence
SO:0002305
Added by Dave to be consistent with other ontologies updated with GREEKC initiative.
topologically_associated_domain_boundary
A DNA region enriched in DNA loop anchors and across which DNA loops occur less often than expected by chance.
GREEKC:cl
PMID:32782014
A region of DNA between two loop anchor positions that are held in close physical proximity.
david
2020-08-12T14:01:30Z
DNA loop
sequence
SO:0002307
Added by Dave to be consistent with other ontologies updated with GREEKC initiative. DS updated defintion Feb 16, 2021. See GitHub Issue #534.
DNA_loop
A region of DNA between two loop anchor positions that are held in close physical proximity.
GREEKC:cl
PMID:32782014
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.
david
2020-08-12T14:01:30Z
DNA loop anchor
sequence
SO:0002308
Added by Dave to be consistent with other ontologies updated with GREEKC initiative. DS updated defintion Feb 16, 2021. See GitHub Issue #534.
DNA_loop_anchor
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
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.
david
2020-08-12T14:01:30Z
core promoter element
sequence
SO:0002309
Added by Dave to be consistent with other ontologies updated with GREEKC initiative.
core_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.
GREEKC:rl
Cytosolic rRNA is an RNA component of the small or large subunits of cytosolic ribosomes.
david
2021-06-10T16:45:30Z
cytosolic rRNA
cytosolic ribosomal RNA
sequence
SO:0002343
Added as a request from EBI. See GitHub Issue #493
cytosolic_rRNA
Cytosolic rRNA is an RNA component of the small or large subunits of cytosolic ribosomes.
PMID:3044395
A region of sequence that is involved in the control of a biological process.
INSDC_feature:regulatory
http://en.wikipedia.org/wiki/Regulatory_region
INSDC_qualifier:other
regulatory region
sequence
SO:0005836
regulatory_region
A region of sequence that is involved in the control of a biological process.
SO:ke
http://en.wikipedia.org/wiki/Regulatory_region
wiki
A region of a peptide that is involved in a biochemical function.
biochemical motif
biochemical region of peptide
sequence
biochemical_region
SO:0100001
Range.
biochemical_region_of_peptide
A region of a peptide that is involved in a biochemical function.
EBIBS:GAR
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.
polypeptide conserved region
sequence
SO:0100021
polypeptide_conserved_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.
EBIBS:GAR
A gene component region which acts as a recombinational unit of a gene whose functional form is generated through somatic recombination.
gene segment
sequence
SO:3000000
Requested by tracker 2021594, July 2008, by Alex.
gene_segment
A gene component region which acts as a recombinational unit of a gene whose functional form is generated through somatic recombination.
GOC:add