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

Gene ID: 10664, updated on 17-Jun-2019

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
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
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

Genomic context

See CTCF in Genome Data Viewer
Location:
16q22.1
Exon count:
13
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 16 NC_000016.10 (67562526..67639185)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (67596310..67673088)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC100505942 Neighboring gene RHO family interacting cell polarization regulator 1 Neighboring gene uncharacterized LOC107984813 Neighboring gene capping protein regulator and myosin 1 linker 2 Neighboring gene par-6 family cell polarity regulator alpha Neighboring gene ACD shelterin complex subunit and telomerase recruitment factor

Genomic regions, transcripts, and products

Expression

  • Project title: 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

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Mental retardation, autosomal dominant 21
MedGen: C3809686 OMIM: 615502 GeneReviews: Not available
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2018-03-28)

ClinGen Genome Curation Page
Haploinsufficency

Some evidence for dosage pathogenicity (Last evaluated (2018-03-28)

ClinGen Genome Curation PagePubMed

NHGRI GWAS Catalog

Description
Loci influencing lipid levels and coronary heart disease risk in 16 European population cohorts.
NHGRI GWA Catalog

HIV-1 interactions

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

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Process Evidence Code Pubs
DNA methylation IEA
Inferred from Electronic Annotation
more info
 
chromosome segregation IEA
Inferred from Electronic Annotation
more info
 
maintenance of DNA methylation IEA
Inferred from Electronic Annotation
more info
 
negative regulation of cell proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
negative regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
nucleosome positioning IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of gene expression IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription, DNA-templated IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein localization to chromosome, centromeric region IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of centromeric sister chromatid cohesion NAS
Non-traceable Author Statement
more info
PubMed 
regulation of gene expression by genetic imprinting IEA
Inferred from Electronic Annotation
more info
 
regulation of gene expression, epigenetic IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of histone acetylation IEA
Inferred from Electronic Annotation
more info
 
regulation of histone methylation IEA
Inferred from Electronic Annotation
more info
 
regulation of molecular function, epigenetic IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
chromosome, centromeric region IDA
Inferred from Direct Assay
more info
PubMed 
condensed chromosome IDA
Inferred from Direct Assay
more info
PubMed 
nucleolus IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

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)

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

  1. NG_033892.1 RefSeqGene

    Range
    5001..81779
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001191022.2NP_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:38172
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:2545
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:181206
    zf-H2C2_2; Zinc-finger double domain
  2. NM_001363916.1NP_001350845.1  transcriptional repressor CTCF isoform 3

    Status: REVIEWED

    Source sequence(s)
    AC009095, AC027682
    Consensus CDS
    CCDS86536.1
    Conserved Domains (3) summary
    COG5048
    Location:366500
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:268288
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:509534
    zf-H2C2_2; Zinc-finger double domain
  3. NM_006565.4NP_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
    P49711
    Related
    ENSP00000264010.4, ENST00000264010.10
    Conserved Domains (3) summary
    COG5048
    Location:366500
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:268288
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:509534
    zf-H2C2_2; Zinc-finger double domain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p13 Primary Assembly

    Range
    67562526..67639185
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    See identical proteins and their annotated locations for XP_005255832.1

    Related
    ENSP00000494443.1, ENST00000646771.1
    Conserved Domains (3) summary
    COG5048
    Location:366500
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:268288
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:509534
    zf-H2C2_2; Zinc-finger double domain
  2. XM_017022868.1XP_016878357.1  transcriptional repressor CTCF isoform X1

    UniProtKB/Swiss-Prot
    P49711
    Related
    ENSP00000493495.1, ENST00000644753.1
    Conserved Domains (3) summary
    COG5048
    Location:366500
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:268288
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:509534
    zf-H2C2_2; Zinc-finger double domain
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