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

    Gene ID: 10664, updated on 10-Dec-2017
    Official Symbol
    CTCFprovided by HGNC
    Official Full Name
    CCCTC-binding factorprovided by HGNC
    Primary source
    HGNC:HGNC:13723
    See related
    Ensembl:ENSG00000102974 MIM:604167; Vega:OTTHUMG00000137539
    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
    Location:
    16q22.1
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 16 NC_000016.10 (67562407..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

    • 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 Jun 15 11:32:44 2016

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Associated conditions

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

    NHGRI GWAS Catalog

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

    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

    Products Interactant Other Gene Complex Source Pubs Description

    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
     
    covalent chromatin modification 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 from RNA polymerase II promoter 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 from RNA polymerase II promoter IEA
    Inferred from Electronic Annotation
    more info
     
    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 
    transcription from RNA polymerase II promoter IEA
    Inferred from Electronic Annotation
    more info
     
    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 IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Preferred Names
    transcriptional repressor CTCF
    Names
    11 zinc finger transcriptional repressor
    11-zinc finger protein
    CCCTC-binding factor (zinc finger protein)
    CTCFL paralog

    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_001191022.1NP_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, OTTHUMP00000197610, ENST00000401394.5, OTTHUMT00000318525
      Conserved Domains (4) summary
      COG5048
      Location:38172
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:2545
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam06750
      Location:110155
      DiS_P_DiS; Bacterial Peptidase A24 N-terminal domain
      pfam13465
      Location:6690
      zf-H2C2_2; Zinc-finger double domain
    2. NM_006565.3NP_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, OTTHUMP00000174843, ENST00000264010.8, OTTHUMT00000268870
      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 108

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000016.10 Reference GRCh38.p7 Primary Assembly

      Range
      67562407..67639185
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005255775.3XP_005255832.1  transcriptional repressor CTCF isoform X2

      See identical proteins and their annotated locations for XP_005255832.1

      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]
      pfam06750
      Location:438483
      DiS_P_DiS; Bacterial Peptidase A24 N-terminal domain
      pfam13465
      Location:394418
      zf-H2C2_2; Zinc-finger double domain
    2. XM_017022868.1XP_016878357.1  transcriptional repressor CTCF isoform X1

      UniProtKB/Swiss-Prot
      P49711
      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. XM_017022869.1XP_016878358.1  transcriptional repressor CTCF isoform X2

      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]
      pfam06750
      Location:438483
      DiS_P_DiS; Bacterial Peptidase A24 N-terminal domain
      pfam13465
      Location:394418
      zf-H2C2_2; Zinc-finger double domain

    Alternate CHM1_1.1

    Genomic

    1. NC_018927.2 Alternate CHM1_1.1

      Range
      69003654..69080781
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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