GO:0000987
JSON
cis-regulatory region sequence-specific DNA binding
Molecular Function
Definition (GO:0000987 GONUTS page)
Binding to a specific upstream regulatory DNA sequence (transcription factor recognition sequence or binding site, located in cis relative to the transcription start site (i.e., on the same strand of DNA) of a gene transcribed by some RNA polymerase. Cis-regulatory sites are often referred to as a sequence motifs, enhancers, or silencers.
Secondary IDs
GO:0000986, GO:0001150, GO:0001158, GO:0001159, GO:0035326
Synonyms
Synonyms are alternative words or phrases closely related in meaning to the term name, with indication of the relationship between the name and synonym given by the synonym scope.
Synonym | Type |
---|---|
promoter proximal region sequence-specific DNA binding | narrow |
enhancer binding | related |
proximal promoter sequence-specific DNA binding | narrow |
enhancer sequence-specific DNA binding | related |
core promoter proximal region sequence-specific DNA binding | narrow |
core promoter proximal region DNA binding | narrow |
cis-regulatory region binding | related |
bacterial-type RNA polymerase upstream activating sequence (UAS) sequence-specific DNA binding | narrow |
bacterial-type RNA polymerase core promoter proximal region sequence-specific DNA binding | narrow |
bacterial-type RNA polymerase enhancer sequence-specific DNA binding | narrow |
Ancestor Chart
Child Terms
This table lists all terms that are direct descendants (child terms) of GO:0000987
Child Term | Relationship to GO:0000987 |
---|---|
RNA polymerase III cis-regulatory region sequence-specific DNA binding
|
is_a |
RNA polymerase II cis-regulatory region sequence-specific DNA binding
|
is_a |
Annotation Guidance
Usage of this term is subject to the following annotation guidelines:
Binding term considerations | Link |
Considerations when annotating from ChiP assay results | Link |
Annotation Blacklist
This list aims to correct incorrect annotations to UniProtKB accessions inferred from electronic annotation (IEA) methods that are supplied by the UniProt-GOA project to the GO Consortium:
Category | Entity Type | Entity ID | Taxon ID | Entity Name | Ancestor GO ID | Reason | Rule/Method ID |
---|---|---|---|---|---|---|---|
IEA Review | protein | P40999 | 284812 | PMT1M_SCHPO | GO:0003677 | To remove over-annotation from InterPro entries IPR001525 and IPR018117; for this particular C5-methyltransferase family member, there is a Ser residue in the active site that may be responsible. Reported by InterPro on 19-10-2012 | |
NOT-qualified manual | protein | A0A0G2K0G0 | 10116 | A0A0G2K0G0_RAT | GO:0003677 | 1 NOT-qualified manual annotation exists with evidence code ECO:0000266 from this reference: GO_REF:0000096 | |
NOT-qualified manual | protein | A0A0G2K6Q9 | 10116 | A0A0G2K6Q9_RAT | GO:0003690 | 1 NOT-qualified manual annotation exists with evidence code ECO:0000266 from this reference: GO_REF:0000096 | |
NOT-qualified manual | protein | A0A1B0GWQ8 | 10116 | A0A1B0GWQ8_RAT | GO:0003677 | 1 NOT-qualified manual annotation exists with evidence code ECO:0000266 from this reference: GO_REF:0000096 | |
NOT-qualified manual | protein | A0A1D8PIK2 | 237561 | A0A1D8PIK2_CANAL | GO:0000976 | 1 NOT-qualified manual annotation exists with evidence code ECO:0000314 from this reference: PMID:20008550 | |
NOT-qualified manual | protein | A0A8I5Y5Z6 | 10116 | A0A8I5Y5Z6_RAT | GO:0003677 | 1 NOT-qualified manual annotation exists with evidence code ECO:0000266 from this reference: GO_REF:0000096 | |
NOT-qualified manual | protein | A0A8I5ZKC5 | 10116 | A0A8I5ZKC5_RAT | GO:0003677 | 1 NOT-qualified manual annotation exists with evidence code ECO:0000266 from this reference: GO_REF:0000096 | |
NOT-qualified manual | protein | A0A8I6A2T0 | 10116 | A0A8I6A2T0_RAT | GO:0003677 | 1 NOT-qualified manual annotation exists with evidence code ECO:0000266 from this reference: GO_REF:0000096 | |
NOT-qualified manual | protein | A0A8I6A7B9 | 10116 | A0A8I6A7B9_RAT | GO:0003677 | 1 NOT-qualified manual annotation exists with evidence code ECO:0000266 from this reference: GO_REF:0000096 | |
NOT-qualified manual | protein | A0A8I6AB42 | 10116 | A0A8I6AB42_RAT | GO:0003677 | 1 NOT-qualified manual annotation exists with evidence code ECO:0000266 from this reference: GO_REF:0000096 |
Cross-references
Database | ID | Description |
---|---|---|
InterPro | IPR026262 | Antitoxin DinJ |
InterPro | IPR033897 | MADS SRF-like |
Co-occurring Terms
These tables show the number of times the term listed in the table has been co-annotated.
No co-occurrence statistics for GO:0000987 based on ALL annotations
The top 100 of 2,855 co-occurring terms
Co-occurring Term | PR | S% | #Together | #Compared |
---|---|---|---|---|
cis-regulatory region sequence-specific DNA binding
|
5,377.63 | 100.00 | 36,848 | 36,848 |
toxic substance binding
|
2,030.65 | 10.13 | 4,483 | 11,872 |
single-species biofilm formation
|
1,337.63 | 8.91 | 4,489 | 18,047 |
snRNA transcription by RNA polymerase II
|
1,251.36 | 8.45 | 4,317 | 18,552 |
transcription elongation factor complex
|
840.16 | 7.18 | 4,317 | 27,632 |
positive regulation of transcription elongation by RNA polymerase II
|
526.49 | 5.63 | 4,315 | 44,074 |
anatomical structure formation involved in morphogenesis
|
2,106.29 | 5.25 | 2,108 | 5,382 |
neuron fate specification
|
2,201.78 | 5.07 | 2,014 | 4,919 |
eye development
|
1,072.62 | 4.31 | 1,922 | 9,636 |
sequence-specific double-stranded DNA binding
|
308.92 | 3.88 | 3,923 | 68,292 |
Totals | 176350 | 6273885 |
No co-occurrence statistics for GO:0000987 based on MANUAL annotations
The top 100 of 2,390 co-occurring terms
Co-occurring Term | PR | S% | #Together | #Compared |
---|---|---|---|---|
cis-regulatory region sequence-specific DNA binding
|
636.97 | 100.00 | 2,216 | 2,216 |
DNA-binding transcription activator activity
|
275.14 | 9.41 | 238 | 551 |
protein-DNA complex
|
97.23 | 6.85 | 245 | 1,605 |
regulation of DNA-templated transcription
|
33.71 | 5.09 | 1,265 | 23,906 |
ligand-modulated transcription factor activity
|
535.06 | 4.70 | 105 | 125 |
snRNA transcription by RNA polymerase II
|
148.73 | 3.90 | 99 | 424 |
positive regulation of DNA-templated transcription
|
29.33 | 3.82 | 406 | 8,816 |
transcription elongation factor complex
|
79.52 | 3.40 | 99 | 793 |
sequence-specific double-stranded DNA binding
|
41.84 | 3.30 | 138 | 2,101 |
negative regulation of gene expression
|
41.65 | 3.19 | 130 | 1,988 |
Totals | 11832 | 492159 |
Change Log
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- Definition / Synonyms
- Definition / Synonyms
- Relationships
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- Cross-references
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Timestamp | Action | Category | Detail |
---|---|---|---|
2024-01-15 | Deleted | DEFINITION | Binding to a specific upstream regulatory DNA sequence (transcription factor recognition sequence or binding site, located in cis relative to the transcription start site (i.e., on the same strand of DNA) of a gene transcribed by some RNA polymerase. Cis-regulatory sites are often referred to as a sequence motifs, enhancers, or silencers. |
2024-01-15 | Added | DEFINITION | Binding to a specific upstream regulatory DNA sequence (transcription factor recognition sequence or binding site, located in cis relative to the transcription start site (i.e., on the same strand of DNA) of a gene transcribed by some RNA polymerase. Cis-regulatory sites are often referred to as a sequence motifs, enhancers, or silencers. |
2023-08-04 | Added | DEFINITION | Binding to a specific upstream regulatory DNA sequence (transcription factor recognition sequence or binding site, located in cis relative to the transcription start site (i.e., on the same strand of DNA) of a gene transcribed by some RNA polymerase. Cis-regulatory sites are often referred to as a sequence motifs, enhancers, or silencers. |
2023-08-04 | Deleted | DEFINITION | Binding to a specific upstream regulatory DNA sequence (transcription factor recognition sequence or binding site) located in cis relative to the transcription start site (i.e., on the same strand of DNA) of a gene transcribed by some RNA polymerase. The proximal promoter is in cis with and relatively close to the core promoter. |
2021-09-14 | Added | SYNONYM | bacterial-type proximal promoter sequence-specific DNA binding |
2021-09-14 | Added | SECONDARY | GO:0001150 (bacterial-type RNA polymerase enhancer sequence-specific DNA binding) |
2021-09-14 | Added | SYNONYM | bacterial-type RNA polymerase upstream activating sequence (UAS) sequence-specific DNA binding |
2021-09-14 | Added | SYNONYM | bacterial-type RNA polymerase core promoter proximal region sequence-specific DNA binding |
2021-09-14 | Added | SYNONYM | bacterial-type RNA polymerase enhancer sequence-specific DNA binding |
2021-09-14 | Added | SYNONYM | eubacterial-type RNA polymerase regulatory transcription factor sequence-specific DNA binding |
Timestamp | Action | Category | Detail |
---|---|---|---|
2019-11-01 | Updated | TERM | cis-regulatory region sequence-specific DNA binding |
2017-11-03 | Updated | TERM | proximal promoter sequence-specific DNA binding |
2011-01-27 | Updated | TERM | core promoter proximal region sequence-specific DNA binding |
2010-09-03 | Added | TERM | regulatory transcription factor site sequence-specific DNA binding |
Timestamp | Action | Category | Detail |
---|---|---|---|
2024-01-15 | Deleted | DEFINITION | Binding to a specific upstream regulatory DNA sequence (transcription factor recognition sequence or binding site, located in cis relative to the transcription start site (i.e., on the same strand of DNA) of a gene transcribed by some RNA polymerase. Cis-regulatory sites are often referred to as a sequence motifs, enhancers, or silencers. |
2024-01-15 | Added | DEFINITION | Binding to a specific upstream regulatory DNA sequence (transcription factor recognition sequence or binding site, located in cis relative to the transcription start site (i.e., on the same strand of DNA) of a gene transcribed by some RNA polymerase. Cis-regulatory sites are often referred to as a sequence motifs, enhancers, or silencers. |
2023-08-04 | Added | DEFINITION | Binding to a specific upstream regulatory DNA sequence (transcription factor recognition sequence or binding site, located in cis relative to the transcription start site (i.e., on the same strand of DNA) of a gene transcribed by some RNA polymerase. Cis-regulatory sites are often referred to as a sequence motifs, enhancers, or silencers. |
2023-08-04 | Deleted | DEFINITION | Binding to a specific upstream regulatory DNA sequence (transcription factor recognition sequence or binding site) located in cis relative to the transcription start site (i.e., on the same strand of DNA) of a gene transcribed by some RNA polymerase. The proximal promoter is in cis with and relatively close to the core promoter. |
2021-09-14 | Added | SYNONYM | bacterial-type proximal promoter sequence-specific DNA binding |
2021-09-14 | Added | SYNONYM | bacterial-type RNA polymerase upstream activating sequence (UAS) sequence-specific DNA binding |
2021-09-14 | Added | SYNONYM | bacterial-type RNA polymerase core promoter proximal region sequence-specific DNA binding |
2021-09-14 | Added | SYNONYM | bacterial-type RNA polymerase enhancer sequence-specific DNA binding |
2021-09-14 | Added | SYNONYM | eubacterial-type RNA polymerase regulatory transcription factor sequence-specific DNA binding |
2021-09-14 | Added | SYNONYM | bacterial-type cis-regulatory region sequence-specific DNA binding |
2021-05-24 | Added | DEFINITION | Binding to a specific upstream regulatory DNA sequence (transcription factor recognition sequence or binding site) located in cis relative to the transcription start site (i.e., on the same strand of DNA) of a gene transcribed by some RNA polymerase. The proximal promoter is in cis with and relatively close to the core promoter. |
2021-05-24 | Deleted | DEFINITION | Interacting selectively and non-covalently with a specific upstream regulatory DNA sequence (transcription factor recognition sequence or binding site) located in cis relative to the transcription start site (i.e., on the same strand of DNA) of a gene transcribed by some RNA polymerase. The proximal promoter is in cis with and relatively close to the core promoter. |
2020-04-29 | Added | SYNONYM | cis-regulatory region binding |
2020-04-29 | Added | SYNONYM | enhancer binding |
2019-11-01 | Added | SYNONYM | proximal promoter sequence-specific DNA binding |
2019-11-01 | Added | SYNONYM | enhancer sequence-specific DNA binding |
2019-11-01 | Added | SYNONYM | core promoter proximal region sequence-specific DNA binding |
2019-11-01 | Deleted | SYNONYM | core promoter proximal region DNA binding |
2019-11-01 | Deleted | SYNONYM | core promoter proximal region sequence-specific DNA binding |
2019-11-01 | Added | SYNONYM | promoter proximal region sequence-specific DNA binding |
2019-11-01 | Added | SYNONYM | core promoter proximal region DNA binding |
2019-11-01 | Added | DEFINITION | Interacting selectively and non-covalently with a specific upstream regulatory DNA sequence (transcription factor recognition sequence or binding site) located in cis relative to the transcription start site (i.e., on the same strand of DNA) of a gene transcribed by some RNA polymerase. The proximal promoter is in cis with and relatively close to the core promoter. |
2019-11-01 | Deleted | DEFINITION | Interacting selectively and non-covalently with a specific upstream regulatory DNA sequence (transcription factor recognition sequence or binding site) located in the proximal promoter. The proximal promoter is in cis with and relatively close to the core promoter. |
2019-11-01 | Deleted | SYNONYM | promoter proximal region sequence-specific DNA binding |
2017-11-03 | Deleted | DEFINITION | Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to the core promoter. The transcribed region might be described as a gene, cistron, or operon. |
2017-11-03 | Added | DEFINITION | Interacting selectively and non-covalently with a specific upstream regulatory DNA sequence (transcription factor recognition sequence or binding site) located in the proximal promoter. The proximal promoter is in cis with and relatively close to the core promoter. |
2017-11-03 | Added | SYNONYM | core promoter proximal region DNA binding |
2017-11-03 | Added | SYNONYM | promoter proximal region sequence-specific DNA binding |
2017-11-03 | Added | SYNONYM | core promoter proximal region sequence-specific DNA binding |
2011-01-27 | Added | DEFINITION | Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to the core promoter. The transcribed region might be described as a gene, cistron, or operon. |
2011-01-27 | Deleted | DEFINITION | Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to the core promoter, but which is bound by a regulatory transcription factor rather than by a basal transcription factor. The transcribed region might be described as a gene, cistron, or operon. |
2010-09-03 | Added | DEFINITION | Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to the core promoter, but which is bound by a regulatory transcription factor rather than by a basal transcription factor. The transcribed region might be described as a gene, cistron, or operon. |
Timestamp | Action | Category | Detail |
---|---|---|---|
2020-04-29 | Deleted | RELATION | is a GO:0035326 (cis-regulatory region binding) |
2019-11-01 | Added | RELATION | is a GO:0035326 (cis-regulatory region binding) |
2017-11-03 | Deleted | RELATION | is a GO:0001159 (core promoter proximal region DNA binding) |
2011-01-30 | Added | RELATION | is a GO:0001159 (core promoter proximal region DNA binding) |
2010-09-03 | Added | RELATION | is a GO:0000976 (transcription cis-regulatory region binding) |
Timestamp | Action | Category | Detail |
---|
Timestamp | Action | Category | Detail |
---|---|---|---|
2021-09-14 | Added | SECONDARY | GO:0001150 (bacterial-type RNA polymerase enhancer sequence-specific DNA binding) |
2021-09-14 | Added | SECONDARY | GO:0000986 (bacterial-type cis-regulatory region sequence-specific DNA binding) |
2020-04-29 | Added | SECONDARY | GO:0035326 (cis-regulatory region binding) |
2019-11-01 | Added | SECONDARY | GO:0001158 (enhancer sequence-specific DNA binding) |
2017-11-03 | Added | SECONDARY | GO:0001159 (core promoter proximal region DNA binding) |
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