Ctcf CCCTC-binding factor [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Ctcfprovided by MGI
Official Full Name: CCCTC-binding factorprovided by MGI
Primary source: MGI:MGI:109447
See related: Ensembl:ENSMUSG00000005698 AllianceGenome:MGI:109447
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Summary: Enables chromatin binding activity and cis-regulatory region sequence-specific DNA binding activity. Involved in chromatin looping; negative regulation of gene expression; and positive regulation of gene expression. Acts upstream of or within several processes, including cardiac muscle cell development; epigenetic regulation of gene expression; and negative regulation of transcription by RNA polymerase II. Located in male germ cell nucleus. Is expressed in several structures, including alimentary system; central nervous system; early conceptus; genitourinary system; and limb. Human ortholog(s) of this gene implicated in autosomal dominant intellectual developmental disorder 21; basal cell carcinoma; female breast cancer; skin melanoma; and skin squamous cell carcinoma. Orthologous to human CTCF (CCCTC-binding factor). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Ubiquitous expression in CNS E11.5 (RPKM 18.2), thymus adult (RPKM 13.4) and 27 other tissues See more
Orthologs: human all
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Genomic context

Location:: 8 D3; 8 53.04 cM

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	8	NC_000074.7 (106351135..106409554)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	8	NC_000074.6 (105636474..105682922)

Chromosome 8 - NC_000074.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

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Expression

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See details

Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

A CTCF-binding site in the Mdm1-Il22-Ifng locus shapes cytokine expression profiles and plays a critical role in early Th1 cell fate specification.
Title: A CTCF-binding site in the Mdm1-Il22-Ifng locus shapes cytokine expression profiles and plays a critical role in early Th1 cell fate specification.
CTCF mutation at R567 causes developmental disorders via 3D genome rearrangement and abnormal neurodevelopment.
Title: CTCF mutation at R567 causes developmental disorders via 3D genome rearrangement and abnormal neurodevelopment.
Transcriptional regulation of FACT involves Coordination of chromatin accessibility and CTCF binding.
Title: Transcriptional regulation of FACT involves Coordination of chromatin accessibility and CTCF binding.
Systematic assessment of ISWI subunits shows that NURF creates local accessibility for CTCF.
Title: Systematic assessment of ISWI subunits shows that NURF creates local accessibility for CTCF.
ADNP modulates SINE B2-derived CTCF-binding sites during blastocyst formation in mice.
Title: ADNP modulates SINE B2-derived CTCF-binding sites during blastocyst formation in mice.
CCCTC-binding factor: the specific transcription factor of beta-galactoside alpha-2,6-sialyltransferase 1 that upregulates the sialylation of anti-citrullinated protein antibodies in rheumatoid arthritis.
Title: CCCTC-binding factor: the specific transcription factor of β-galactoside α-2,6-sialyltransferase 1 that upregulates the sialylation of anti-citrullinated protein antibodies in rheumatoid arthritis.
Outward-oriented sites within clustered CTCF boundaries are key for intra-TAD chromatin interactions and gene regulation.
Title: Outward-oriented sites within clustered CTCF boundaries are key for intra-TAD chromatin interactions and gene regulation.
CTCF coordinates cell fate specification via orchestrating regulatory hubs with pioneer transcription factors.
Title: CTCF coordinates cell fate specification via orchestrating regulatory hubs with pioneer transcription factors.
Sequential and directional insulation by conserved CTCF sites underlies the Hox timer in stembryos.
Title: Sequential and directional insulation by conserved CTCF sites underlies the Hox timer in stembryos.
SATB1 regulates 3D genome architecture in T cells by constraining chromatin interactions surrounding CTCF-binding sites.
Title: SATB1 regulates 3D genome architecture in T cells by constraining chromatin interactions surrounding CTCF-binding sites.

Submit: New GeneRIF Correction See all GeneRIFs (184)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (5) 1 citation
Targeted (9) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

CTCF_3772 (e-PCR)
- UniSTS:462131

U51037 (e-PCR)
- UniSTS:125764

AW108038 (e-PCR)
- UniSTS:179805

Ctcf (e-PCR), detects polymorphism
- UniSTS:141440

BF389170 (e-PCR)
- UniSTS:245397

10.MMHAP67FRD7.seq (e-PCR)
- UniSTS:123043

MARC_20750-20751:1025022208:1 (e-PCR)
- UniSTS:268474

BE692055 (e-PCR)
- UniSTS:208320

NoName (e-PCR)
- UniSTS:224221

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription factor activity	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor binding	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription repressor activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription repressor activity, RNA polymerase II-specific	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables chromatin insulator sequence binding	IEA Inferred from Electronic Annotation more info
enables chromatin insulator sequence binding	ISO Inferred from Sequence Orthology more info
enables chromatin loop anchoring activity	IEA Inferred from Electronic Annotation more info
enables chromatin loop anchoring activity	ISO Inferred from Sequence Orthology more info
enables cis-regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables sequence-specific double-stranded DNA binding	ISO Inferred from Sequence Orthology more info
enables transcription cis-regulatory region binding	ISO Inferred from Sequence Orthology more info
enables transcription coregulator binding	IEA Inferred from Electronic Annotation more info
enables transcription coregulator binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within DNA methylation-dependent constitutive heterochromatin formation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cardiac muscle cell development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cardiac muscle cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in chromatin looping	IDA Inferred from Direct Assay more info	PubMed
involved_in chromatin looping	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in chromatin looping	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within chromatin organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in chromosome segregation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within epigenetic regulation of gene expression	IDA Inferred from Direct Assay more info	PubMed
involved_in epigenetic regulation of gene expression	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within genomic imprinting	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within genomic imprinting	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within heart development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within in utero embryonic development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within mitochondrion organization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of cell population proliferation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of cell population proliferation	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of gene expression via chromosomal CpG island methylation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of miRNA transcription	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in protein localization to chromosome, centromeric region	ISO Inferred from Sequence Orthology more info
involved_in protein localization to chromosome, centromeric region	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within random inactivation of X chromosome	TAS Traceable Author Statement more info	PubMed
acts_upstream_of_or_within regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in chromosome, centromeric region	ISO Inferred from Sequence Orthology more info
located_in chromosome, centromeric region	ISS Inferred from Sequence or Structural Similarity more info
located_in condensed chromosome	IEA Inferred from Electronic Annotation more info
located_in condensed chromosome	ISO Inferred from Sequence Orthology more info
located_in dense fibrillar component	ISO Inferred from Sequence Orthology more info
located_in granular component	ISO Inferred from Sequence Orthology more info
located_in male germ cell nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleolus	IEA Inferred from Electronic Annotation more info
located_in nucleolus	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: transcriptional repressor CTCF

Names: 11-zinc finger protein; CTCFL paralog

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001358924.2 → NP_001345853.1 transcriptional repressor CTCF isoform 2

Status: VALIDATED

Source sequence(s)

AC127419, AC152826

UniProtKB/TrEMBL

Q3UYZ8

Conserved Domains (3) summary

COG5048
Location:366 → 500

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:268 → 288

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam13465
Location:509 → 534

zf-H2C2_2; Zinc-finger double domain
NM_001403723.1 → NP_001390652.1 transcriptional repressor CTCF isoform 1

Status: VALIDATED

Source sequence(s)

AC127419, AC152826

UniProtKB/Swiss-Prot

Q61164
NM_001403724.1 → NP_001390653.1 transcriptional repressor CTCF isoform 1

Status: VALIDATED

Source sequence(s)

AC127419, AC152826

UniProtKB/Swiss-Prot

Q61164
NM_001403725.1 → NP_001390654.1 transcriptional repressor CTCF isoform 1

Status: VALIDATED

Source sequence(s)

AC127419, AC152826

UniProtKB/Swiss-Prot

Q61164
NM_001403726.1 → NP_001390655.1 transcriptional repressor CTCF isoform 2

Status: VALIDATED

Source sequence(s)

AC127419, AC152826
NM_001403727.1 → NP_001390656.1 transcriptional repressor CTCF isoform 2

Status: VALIDATED

Source sequence(s)

AC127419, AC152826
NM_001403728.1 → NP_001390657.1 transcriptional repressor CTCF isoform 2

Status: VALIDATED

Source sequence(s)

AC127419, AC152826
NM_001403729.1 → NP_001390658.1 transcriptional repressor CTCF isoform 3

Status: VALIDATED

Source sequence(s)

AC127419, AC152826
NM_001403730.1 → NP_001390659.1 transcriptional repressor CTCF isoform 3

Status: VALIDATED

Source sequence(s)

AC127419, AC152826
NM_001403731.1 → NP_001390660.1 transcriptional repressor CTCF isoform 4

Status: VALIDATED

Source sequence(s)

AC127419, AC152826
NM_001403732.1 → NP_001390661.1 transcriptional repressor CTCF isoform 4

Status: VALIDATED

Source sequence(s)

AC127419, AC152826
NM_181322.4 → NP_851839.1 transcriptional repressor CTCF isoform 1

See identical proteins and their annotated locations for NP_851839.1

Status: VALIDATED

Source sequence(s)

AC127419, AC152826

Consensus CDS

CCDS22606.1

UniProtKB/Swiss-Prot

Q61164

UniProtKB/TrEMBL

Q3UYZ8

Related

ENSMUSP00000005841.10, ENSMUST00000005841.16

Conserved Domains (4) summary

COG5048
Location:366 → 500

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:268 → 288

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam13465
Location:280 → 305

zf-H2C2_2; Zinc-finger double domain

pfam13909
Location:351 → 375

zf-H2C2_5; C2H2-type zinc-finger domain

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCm39 C57BL/6J

Genomic

NC_000074.7 Reference GRCm39 C57BL/6J

Range

106351135..106409554

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_030243283.2 → XP_030099143.1 transcriptional repressor CTCF isoform X5

UniProtKB/Swiss-Prot

Q61164

UniProtKB/TrEMBL

Q3UYZ8

Conserved Domains (4) summary

COG5048
Location:366 → 500

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:268 → 288

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam13465
Location:280 → 305

zf-H2C2_2; Zinc-finger double domain

pfam13909
Location:351 → 375

zf-H2C2_5; C2H2-type zinc-finger domain
XM_006530646.5 → XP_006530709.1 transcriptional repressor CTCF isoform X3

UniProtKB/TrEMBL

Q3USR8

Conserved Domains (4) summary

COG5048
Location:375 → 509

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:277 → 297

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam13465
Location:289 → 314

zf-H2C2_2; Zinc-finger double domain

pfam13909
Location:360 → 384

zf-H2C2_5; C2H2-type zinc-finger domain
XM_006530647.4 → XP_006530710.1 transcriptional repressor CTCF isoform X4

UniProtKB/TrEMBL

Q3USR8

Conserved Domains (4) summary

COG5048
Location:375 → 509

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:277 → 297

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam13465
Location:289 → 314

zf-H2C2_2; Zinc-finger double domain

pfam13909
Location:360 → 384

zf-H2C2_5; C2H2-type zinc-finger domain
XM_036153746.1 → XP_036009639.1 transcriptional repressor CTCF isoform X5

UniProtKB/Swiss-Prot

Q61164

UniProtKB/TrEMBL

Q3UYZ8

Conserved Domains (4) summary

COG5048
Location:366 → 500

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:268 → 288

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam13465
Location:280 → 305

zf-H2C2_2; Zinc-finger double domain

pfam13909
Location:351 → 375

zf-H2C2_5; C2H2-type zinc-finger domain
XM_036153749.1 → XP_036009642.1 transcriptional repressor CTCF isoform X7

UniProtKB/TrEMBL

Q3USR8

Conserved Domains (4) summary

COG5048
Location:366 → 500

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:268 → 288

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam13465
Location:280 → 305

zf-H2C2_2; Zinc-finger double domain

pfam13909
Location:351 → 375

zf-H2C2_5; C2H2-type zinc-finger domain