FB2026_03 , released September 17, 2026

CV Term Report

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General Information

Term

cis-regulatory region sequence-specific DNA binding

ID (Ontology)

GO:0000987 (Gene Ontology)

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.

Comment

Links to External Ontologies

QuickGO data AmiGO data

Annotations

Records annotated with this term OR any of its CHILD TERMS

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Direct annotations: records annotated with this exact term (child terms are NOT included)

Data Class	Field	Direct annotations
Genes (FBgn)	GO_MOLECULAR_FUNCTION

Full annotation statements including this term (annotations to child terms are NOT included), and relevant FlyBase records

Full annotation statements	Relevant FlyBase reports
Full annotation statements	Genes
cis-regulatory region sequence-specific DNA binding (all annotations which use CV term, excluding "NOT" statements)
enables \| cis-regulatory region sequence-specific DNA binding

Spanning Tree (Parents/Children)

transcription regulatory region nucleic acid binding__
sequence-specific double-stranded DNA binding_________|
                                                      transcription cis-regulatory region binding
                                                       |__cis-regulatory region sequence-specific DNA binding  395 rec.
                                                           |__RNA polymerase II cis-regulatory region sequence-specific DNA binding 386 rec.
                                                           |   |__cAMP response element binding 2 rec.
                                                           |   |__carbohydrate response element binding
                                                           |   |__E-box binding 11 rec.
                                                           |   |__estrogen response element binding 5 rec.
                                                           |   |__GC-box binding
                                                           |   |__juvenile hormone response element binding 2 rec.
                                                           |   |__N-box binding
                                                           |   |__retinoic acid-responsive element binding
                                                           |   |__RNA polymerase II cis-regulatory region sequence-specific DNA binding, bending
                                                           |   |__serum response element binding
                                                           |   |__sterol response element binding
                                                           |   |__vitamin D response element binding
                                                           |__RNA polymerase III cis-regulatory region sequence-specific DNA binding 8 rec.
                                                               |__RNA polymerase III hybrid type promoter sequence-specific DNA binding
                                                               |__RNA polymerase III type 1 promoter sequence-specific DNA binding 1 rec.
                                                               |__RNA polymerase III type 2 promoter sequence-specific DNA binding 1 rec.
                                                               |__RNA polymerase III type 3 promoter sequence-specific DNA binding 6 rec.

Spanning Tree View Settings
Parents/Children View Depth	Show hierarchy levels: for parents, for children
Relationships
Is a	transcription cis-regulatory region binding
Part of
Synonyms & Secondary IDs
Synonyms
	"bacterial-type cis-regulatory region sequence-specific DNA binding" NARROW "bacterial-type proximal promoter 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 "bacterial-type RNA polymerase upstream activating sequence (UAS) sequence-specific DNA binding" NARROW "cis-regulatory region binding" RELATED "core promoter proximal region DNA binding" NARROW "core promoter proximal region sequence-specific DNA binding" NARROW "enhancer binding" RELATED "enhancer sequence-specific DNA binding" RELATED "eubacterial-type RNA polymerase regulatory transcription factor sequence-specific DNA binding" NARROW "promoter proximal region sequence-specific DNA binding" NARROW "proximal promoter sequence-specific DNA binding" NARROW
Secondary IDs

External Crossreferences & Linkouts