This term is obsolete.

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

1,192,000 annotations

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

Ancestor chart for GO:0000987
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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

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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