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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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