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

    Gene ID: 10664, updated on 17-Jun-2024

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See CTCF in Genome Data Viewer
    Location:
    16q22.1
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (67562526..67639185)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (73357293..73433954)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (67596429..67673088)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC100505942 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10970 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10971 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10972 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10973 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7608 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7609 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7610 Neighboring gene RHO family interacting cell polarization regulator 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7611 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:67571987-67572608 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10975 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7613 Neighboring gene Sharpr-MPRA regulatory region 14438 Neighboring gene uncharacterized LOC124903703 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:67586099-67586600 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:67586601-67587100 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10977 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10978 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:67596785-67597647 Neighboring gene CTCF divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7616 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:67687361-67687893 Neighboring gene capping protein regulator and myosin 1 linker 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:67693493-67694076 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7617 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7618 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 Functions

    What's a GeneRIF?

    Phenotypes

    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

    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 PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    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 IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in epigenetic regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in genomic imprinting IDA
    Inferred from Direct Assay
    more info
    PubMed 
    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 IBA
    Inferred from Biological aspect of Ancestor
    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 IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    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 
    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

    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)

    NEW Try the new Transcript table

    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
      5120..81771
      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
      UniProtKB/TrEMBL
      A0A2R8Y595, A0A2R8YFL0
      Related
      ENSP00000495218.1, ENST00000645306.1
      Conserved Domains (4) summary
      COG5048
      Location:366500
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:268288
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:280305
      zf-H2C2_2; Zinc-finger double domain
      pfam13909
      Location:351375
      zf-H2C2_5; C2H2-type zinc-finger 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
      B5MC38, P49711, Q53XI7, Q59EL8
      UniProtKB/TrEMBL
      A0A2R8Y595
      Related
      ENSP00000264010.4, ENST00000264010.10
      Conserved Domains (4) summary
      COG5048
      Location:366500
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:268288
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:280305
      zf-H2C2_2; Zinc-finger double domain
      pfam13909
      Location:351375
      zf-H2C2_5; C2H2-type zinc-finger domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000016.10 Reference GRCh38.p14 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

      UniProtKB/TrEMBL
      A0A2R8Y595, A0A2R8YFL0
      Related
      ENSP00000494443.1, ENST00000646771.1
      Conserved Domains (4) summary
      COG5048
      Location:366500
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:268288
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:280305
      zf-H2C2_2; Zinc-finger double domain
      pfam13909
      Location:351375
      zf-H2C2_5; C2H2-type zinc-finger domain
    2. XM_017022868.2XP_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:366500
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:268288
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:280305
      zf-H2C2_2; Zinc-finger double domain
      pfam13909
      Location:351375
      zf-H2C2_5; C2H2-type zinc-finger domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      73357293..73433954
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

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

      UniProtKB/TrEMBL
      A0A2R8Y595, A0A2R8YFL0
    2. XM_054379398.1XP_054235373.1  transcriptional repressor CTCF isoform X1

      UniProtKB/Swiss-Prot
      B5MC38, P49711, Q53XI7, Q59EL8
      UniProtKB/TrEMBL
      A0A2R8Y595