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    CTCF CCCTC-binding factor [ Gallus gallus (chicken) ]

    Gene ID: 396274, updated on 9-Apr-2024

    Summary

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    Symbol
    CTCFprovided by CGNC
    Full Name
    CCCTC-binding factorprovided by CGNC
    Primary source
    CGNC:49729
    See related
    Ensembl:ENSGALG00010022627
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Gallus gallus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Archelosauria; Archosauria; Dinosauria; Saurischia; Theropoda; Coelurosauria; Aves; Neognathae; Galloanserae; Galliformes; Phasianidae; Phasianinae; Gallus
    Also known as
    CTCFL
    Orthologs
    human mouse all
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    Genomic context

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    See CTCF in Genome Data Viewer
    Location:
    chromosome: 11
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    106 current bGalGal1.mat.broiler.GRCg7b (GCF_016699485.2) 11 NC_052542.1 (1129378..1159386)
    106 current bGalGal1.pat.whiteleghornlayer.GRCg7w (GCF_016700215.2) 11 NC_052583.1 (1301852..1331831)

    Chromosome 11 - NC_052542.1Genomic Context describing neighboring genes Neighboring gene uncharacterized oxidoreductase-like Neighboring gene C-factor-like Neighboring gene family with sequence similarity 65 member A Neighboring gene uncharacterized LOC107052159 Neighboring gene RGD motif, leucine rich repeats, tropomodulin domain and proline-rich containing Neighboring gene uncharacterized LOC100857820 Neighboring gene uncharacterized LOC101748539 Neighboring gene adrenocortical dysplasia homolog

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Bibliography

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    Related articles in PubMed

    1. CTCF demarcates chicken embryonic α-globin gene autonomous silencing and contributes to adult stage-specific gene expression. Valdes-Quezada C, et al. Epigenetics, 2013 Aug. PMID 23880533, Free PMC Article
    2. A CTCF-dependent silencer located in the differentially methylated area may regulate expression of a housekeeping gene overlapping a tissue-specific gene domain. Klochkov D, et al. Mol Cell Biol, 2006 Mar. PMID 16478981, Free PMC Article
    3. CTCF, a conserved nuclear factor required for optimal transcriptional activity of the chicken c-myc gene, is an 11-Zn-finger protein differentially expressed in multiple forms. Klenova EM, et al. Mol Cell Biol, 1993 Dec. PMID 8246978, Free PMC Article
    4. Transcription factors CTCF and Pax6 are segregated to different cell types during retinal cell differentiation. Canto-Soler MV, et al. Dev Dyn, 2008 Mar. PMID 18224715, Free PMC Article
    5. The 5'-HS4 chicken beta-globin insulator is a CTCF-dependent nuclear matrix-associated element. Yusufzai TM, et al. Proc Natl Acad Sci U S A, 2004 Jun 8. PMID 15169959, Free PMC Article

    See all (9) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. CTCF is contributing to a specific chromatin configuration that is necessary for differential alpha-globin gene expression during development.
      Title: CTCF demarcates chicken embryonic α-globin gene autonomous silencing and contributes to adult stage-specific gene expression.
    2. study shows CTCF & Pax6 segregate to different retinal cell types; as retina laminates Pax6 restricted to ganglion & amacrine cells & CTCF to bipolar/Muller cell layer & outer nuclear layer; immature & differentiated photoreceptors are CTCF (+)/ Pax6 (-)
      Title: Transcription factors CTCF and Pax6 are segregated to different cell types during retinal cell differentiation.
    3. CTCF blocks the binding of YB-1 to its DNA recognition sequences in vitro, thus providing a possible mechanism of regulation of YB-1 activation of the 5-HTT VNTR by CTCF.
      Title: YB-1 and CTCF differentially regulate the 5-HTT polymorphic intron 2 enhancer which predisposes to a variety of neurological disorders.
    4. CTCF-dependent silencer stabilizes the level of ggPRX gene transcription in erythroid cells
      Title: A CTCF-dependent silencer located in the differentially methylated area may regulate expression of a housekeeping gene overlapping a tissue-specific gene domain.
    5. a DNA sequence element, HS4, at the 5' end of the beta-globin locus, contains a binding site for CTCF that is necessary and sufficient for insulator action
      Title: The 5'-HS4 chicken beta-globin insulator is a CTCF-dependent nuclear matrix-associated element.
    Submit: New GeneRIF Correction

    General gene information

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    Homology

    Gene Ontology Provided by RefSeq

    Function Evidence Code Pubs
    enables DNA-binding transcription factor activity, RNA polymerase II-specific IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    transcriptional repressor CTCF
    Names
    11-zinc finger protein
    CCCTC-binding factor (zinc finger protein)
    CCCTC-binding factor like
    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)

    1. NM_205332.6 → NP_990663.2  transcriptional repressor CTCF

      See identical proteins and their annotated locations for NP_990663.2

      Status: VALIDATED

      Source sequence(s)
      AW773196, BM490841, CR386100, JAENSK010000247, Z22605
      UniProtKB/Swiss-Prot
      Q08705
      UniProtKB/TrEMBL
      F1NFT1
      Related
      ENSGALP00010033306.1, ENSGALT00010055081.1
      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

    RefSeqs of Annotated Genomes: Gallus gallus Annotation Release 106 details...Open this link in a new tab

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

    Reference bGalGal1.mat.broiler.GRCg7b Primary Assembly

    Genomic

    1. NC_052542.1 Reference bGalGal1.mat.broiler.GRCg7b Primary Assembly

      Range
      1129378..1159386
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_015279119.4 → XP_015134605.1  transcriptional repressor CTCF isoform X1

      UniProtKB/TrEMBL
      A0A1D5PYS0, A0A8V0ZR33
      Related
      ENSGALP00010033298.1, ENSGALT00010055070.1
      Conserved Domains (3) summary
      COG5048
      Location:377 → 511
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:279 → 299
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:520 → 545
      zf-H2C2_2; Zinc-finger double domain

    2. XM_046899387.1 → XP_046755343.1  transcriptional repressor CTCF isoform X2

      Related
      ENSGALP00010033304.1, ENSGALT00010055078.1

    3. XM_015279121.4 → XP_015134607.1  transcriptional repressor CTCF isoform X3

      UniProtKB/Swiss-Prot
      Q08705
      UniProtKB/TrEMBL
      F1NFT1
      Related
      ENSGALP00010033302.1, ENSGALT00010055075.1
      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

    4. XM_025154151.3 → XP_025009919.1  transcriptional repressor CTCF isoform X1

      UniProtKB/TrEMBL
      A0A1D5PYS0, A0A8V0ZR33
      Conserved Domains (3) summary
      COG5048
      Location:377 → 511
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:279 → 299
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:520 → 545
      zf-H2C2_2; Zinc-finger double domain

    5. XM_046899388.1 → XP_046755344.1  transcriptional repressor CTCF isoform X3

      UniProtKB/TrEMBL
      F1NFT1

    6. XM_040707013.2 → XP_040562947.1  transcriptional repressor CTCF isoform X3

      UniProtKB/Swiss-Prot
      Q08705
      UniProtKB/TrEMBL
      F1NFT1
      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 bGalGal1.pat.whiteleghornlayer.GRCg7w

    Genomic

    1. NC_052583.1 Alternate bGalGal1.pat.whiteleghornlayer.GRCg7w

      Range
      1301852..1331831
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_046925362.1 → XP_046781318.1  transcriptional repressor CTCF isoform X1

      UniProtKB/TrEMBL
      A0A1D5PYS0

    2. XM_046925364.1 → XP_046781320.1  transcriptional repressor CTCF isoform X2

    3. XM_046925365.1 → XP_046781321.1  transcriptional repressor CTCF isoform X3

      UniProtKB/TrEMBL
      F1NFT1

    4. XM_046925363.1 → XP_046781319.1  transcriptional repressor CTCF isoform X1

      UniProtKB/TrEMBL
      A0A1D5PYS0

    5. XM_046925366.1 → XP_046781322.1  transcriptional repressor CTCF isoform X3

      UniProtKB/TrEMBL
      F1NFT1

    6. XM_046925367.1 → XP_046781323.1  transcriptional repressor CTCF isoform X3

      UniProtKB/TrEMBL
      F1NFT1
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q08705.1 GenPept UniProtKB/Swiss-Prot:Q08705

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