CTCF CCCTC-binding factor [Homo sapiens (human)] - Gene

Summary

Official Symbol: CTCFprovided by HGNC
Official Full Name: CCCTC-binding factorprovided by HGNC
Primary source: HGNC:HGNC:13723
See related: Ensembl:ENSG00000102974 MIM:604167; AllianceGenome:HGNC:13723
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: MRD21; FAP108; CFAP108
Summary: This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger (ZF) domains. This nuclear protein is able to use different combinations of the ZF domains to bind different DNA target sequences and proteins. Depending upon the context of the site, the protein can bind a histone acetyltransferase (HAT)-containing complex and function as a transcriptional activator or bind a histone deacetylase (HDAC)-containing complex and function as a transcriptional repressor. If the protein is bound to a transcriptional insulator element, it can block communication between enhancers and upstream promoters, thereby regulating imprinted expression. Mutations in this gene have been associated with invasive breast cancers, prostate cancers, and Wilms' tumors. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2010]
Expression: Ubiquitous expression in lymph node (RPKM 18.3), spleen (RPKM 14.7) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 16q22.1

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	16	NC_000016.10 (67562526..67639185)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	16	NC_060940.1 (73357293..73433954)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	16	NC_000016.9 (67596429..67673088)

Chromosome 16 - NC_000016.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

METTL3 aggravates cell damage induced by Streptococcus pneumoniae via the NEAT1/CTCF/MUC19 axis.
Title: METTL3 aggravates cell damage induced by Streptococcus pneumoniae via the NEAT1/CTCF/MUC19 axis.
CTCF and BORIS-mediated autophagy regulation via alternative splicing of BNIP3L in breast cancer.
Title: CTCF and BORIS-mediated autophagy regulation via alternative splicing of BNIP3L in breast cancer.
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.
Single-molecule imaging reveals a direct role of CTCF's zinc fingers in SA interaction and cluster-dependent RNA recruitment.
Title: Single-molecule imaging reveals a direct role of CTCF's zinc fingers in SA interaction and cluster-dependent RNA recruitment.
CCCTC-binding factor suppresses alpha-2-macroglobulin transcription to improve vascular endothelial cell functions in lower extremity arteriosclerosis obliterans.
Title: CCCTC-binding factor suppresses alpha-2-macroglobulin transcription to improve vascular endothelial cell functions in lower extremity arteriosclerosis obliterans.
The N-terminal dimerization domains of human and Drosophila CTCF have similar functionality.
Title: The N-terminal dimerization domains of human and Drosophila CTCF have similar functionality.
RPL35A drives ovarian cancer progression by promoting the binding of YY1 to CTCF promoter.
Title: RPL35A drives ovarian cancer progression by promoting the binding of YY1 to CTCF promoter.
Identification of DNA methylation episignature for the intellectual developmental disorder, autosomal dominant 21 syndrome, caused by variants in the CTCF gene.
Title: Identification of DNA methylation episignature for the intellectual developmental disorder, autosomal dominant 21 syndrome, caused by variants in the CTCF gene.
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.
Host-encoded CTCF regulates human cytomegalovirus latency via chromatin looping.
Title: Host-encoded CTCF regulates human cytomegalovirus latency via chromatin looping.

Submit: New GeneRIF Correction See all GeneRIFs (328)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Intellectual disability-feeding difficulties-developmental delay-microcephaly syndrome MedGen: C3809686 OMIM: 615502 GeneReviews: CTCF-Related Disorder	Compare labs

Copy number response

Description
Copy number response Triplosensitivity No evidence available (Last evaluated 2021-09-22) ClinGen Genome Curation Page Haploinsufficency Sufficient evidence for dosage pathogenicity (Last evaluated 2021-09-22) ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Description
Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
retropepsin	gag-pol	Positional proteomics analysis identifies the cleavage of human CCCTC-binding factor (zinc finger protein) (CTCF) at amino acid residues 360-361 by the HIV-1 protease	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-152529 (e-PCR)
- UniSTS:183061

SHGC-3332 (e-PCR)
- UniSTS:78365

RH68791 (e-PCR)
- UniSTS:30498

CTCF_3772 (e-PCR)
- UniSTS:462131

D16S3085 (e-PCR), detects polymorphism
- UniSTS:49742

SHGC-151259 (e-PCR)
- UniSTS:173660

WI-21064 (e-PCR)
- UniSTS:72035

SHGC-60657 (e-PCR)
- UniSTS:1900

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

RH80821 (e-PCR)
- UniSTS:87978

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA-binding transcription factor activity	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription factor activity	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription repressor activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info	PubMed
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	IDA Inferred from Direct Assay more info	PubMed
enables chromatin insulator sequence binding	IDA Inferred from Direct Assay more info	PubMed
enables chromatin loop anchoring activity	IMP Inferred from Mutant Phenotype more info	PubMed
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 double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables transcription cis-regulatory region binding	IDA Inferred from Direct Assay more info	PubMed
enables transcription coregulator binding	IPI Inferred from Physical Interaction more info	PubMed
enables zinc ion binding	TAS Traceable Author Statement more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA methylation-dependent constitutive heterochromatin formation	IEA Inferred from Electronic Annotation more info
involved_in cardiac muscle cell development	IEA Inferred from Electronic Annotation more info
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 chromosome segregation	IEA Inferred from Electronic Annotation more info
involved_in epigenetic regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in gene expression	IEA Inferred from Electronic Annotation more info
involved_in genomic imprinting	IDA Inferred from Direct Assay more info	PubMed
involved_in in utero embryonic development	IEA Inferred from Electronic Annotation more info
involved_in mitochondrion organization	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of cell population proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of gene expression via chromosomal CpG island methylation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of DNA-templated transcription	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in protein localization to chromosome, centromeric region	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of centromeric sister chromatid cohesion	NAS Non-traceable Author Statement 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	IDA Inferred from Direct Assay more info	PubMed
located_in condensed chromosome	IDA Inferred from Direct Assay more info	PubMed
located_in male germ cell nucleus	IEA Inferred from Electronic Annotation more info
located_in nucleolus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: transcriptional repressor CTCF

Names: 11 zinc finger transcriptional repressor; 11-zinc finger protein; CCCTC-binding factor (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.

Genomic

NG_033892.1 RefSeqGene

Range

5120..81771

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001191022.2 → NP_001177951.1 transcriptional repressor CTCF isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks internal two consecutive exons, resulting in a downstream AUG start codon, as compared to variant 1. The resulting isoform (2) has a shorter N-terminus, as compared to isoform 1.

Source sequence(s)

AA814313, AB209793, DB229066

Consensus CDS

CCDS54029.1

UniProtKB/Swiss-Prot

P49711

Related

ENSP00000384707.1, ENST00000401394.6

Conserved Domains (3) summary

COG5048
Location:38 → 172

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

sd00017
Location:25 → 45

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam13465
Location:181 → 206

zf-H2C2_2; Zinc-finger double domain
NM_001363916.1 → NP_001350845.1 transcriptional repressor CTCF isoform 3

Status: REVIEWED

Source sequence(s)

AC009095, AC027682

Consensus CDS

CCDS86536.1

UniProtKB/TrEMBL

A0A2R8Y595, A0A2R8YFL0

Related

ENSP00000495218.1, ENST00000645306.1

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
NM_006565.4 → NP_006556.1 transcriptional repressor CTCF isoform 1

See identical proteins and their annotated locations for NP_006556.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) is the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AA814313, BC014267, DB229066

Consensus CDS

CCDS10841.1

UniProtKB/Swiss-Prot

B5MC38, P49711, Q53XI7, Q59EL8

UniProtKB/TrEMBL

A0A2R8Y595

Related

ENSP00000264010.4, ENST00000264010.10

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_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000016.10 Reference GRCh38.p14 Primary Assembly

Range

67562526..67639185

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005255775.4 → XP_005255832.1 transcriptional repressor CTCF isoform X2

See identical proteins and their annotated locations for XP_005255832.1

UniProtKB/TrEMBL

A0A2R8Y595, A0A2R8YFL0

Related

ENSP00000494443.1, ENST00000646771.1

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_017022868.2 → XP_016878357.1 transcriptional repressor CTCF isoform X1

UniProtKB/Swiss-Prot

B5MC38, P49711, Q53XI7, Q59EL8

UniProtKB/TrEMBL

A0A2R8Y595

Related

ENSP00000493495.1, ENST00000644753.1

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

Alternate T2T-CHM13v2.0

Genomic

NC_060940.1 Alternate T2T-CHM13v2.0

Range

73357293..73433954

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054379399.1 → XP_054235374.1 transcriptional repressor CTCF isoform X2

UniProtKB/TrEMBL

A0A2R8YFL0
XM_054379398.1 → XP_054235373.1 transcriptional repressor CTCF isoform X1

UniProtKB/Swiss-Prot

B5MC38, P49711, Q53XI7, Q59EL8