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Ctcf CCCTC-binding factor [ Mus musculus (house mouse) ]

Gene ID: 13018, updated on 2-Nov-2024

Summary

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Official Symbol
Ctcfprovided by MGI
Official Full Name
CCCTC-binding factorprovided by MGI
Primary source
MGI:MGI:109447
See related
Ensembl:ENSMUSG00000005698 AllianceGenome:MGI:109447
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Summary
Enables chromatin binding activity and cis-regulatory region sequence-specific DNA binding activity. Involved in chromatin looping; negative regulation of gene expression; and positive regulation of gene expression. Acts upstream of or within several processes, including cardiac muscle cell development; epigenetic regulation of gene expression; and negative regulation of transcription by RNA polymerase II. Located in male germ cell nucleus. Is expressed in several structures, including alimentary system; central nervous system; early conceptus; genitourinary system; and limb. Human ortholog(s) of this gene implicated in autosomal dominant intellectual developmental disorder 21; basal cell carcinoma; female breast cancer; skin melanoma; and skin squamous cell carcinoma. Orthologous to human CTCF (CCCTC-binding factor). [provided by Alliance of Genome Resources, Nov 2024]
Expression
Ubiquitous expression in CNS E11.5 (RPKM 18.2), thymus adult (RPKM 13.4) and 27 other tissues See more
Orthologs
human all
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Genomic context

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See Ctcf in Genome Data Viewer
Location:
8 D3; 8 53.04 cM
Exon count:
15
Annotation release Status Assembly Chr Location
RS_2024_02 current GRCm39 (GCF_000001635.27) 8 NC_000074.7 (106351135..106409554)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 8 NC_000074.6 (105636474..105682922)

Chromosome 8 - NC_000074.7Genomic Context describing neighboring genes Neighboring gene predicted gene 45855 Neighboring gene RHO family interacting cell polarization regulator 1 Neighboring gene CapStarr-seq enhancer MGSCv37_chr8:108146466-108146676 Neighboring gene CapStarr-seq enhancer MGSCv37_chr8:108147057-108147307 Neighboring gene microRNA 1966 Neighboring gene predicted gene 5914 Neighboring gene myosin light polypeptide 6-like Neighboring gene STARR-positive B cell enhancer ABC_E5037 Neighboring gene predicted gene, 33578 Neighboring gene capping protein regulator and myosin 1 linker 2 Neighboring gene STARR-positive B cell enhancer ABC_E3798 Neighboring gene par-6 family cell polarity regulator alpha Neighboring gene adrenocortical dysplasia

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
  • Description: RNA profiling data sets generated by the Mouse ENCODE project.
  • BioProject: PRJNA66167
  • Publication: PMID 25409824
  • Analysis date: n/a

Bibliography

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Related articles in PubMed

  1. Epigenomic signatures underpin the axonal regenerative ability of dorsal root ganglia sensory neurons. Palmisano I, et al. Nat Neurosci, 2019 Nov. PMID 31591560
  2. Inducible podocyte-specific deletion of CTCF drives progressive kidney disease and bone abnormalities. Christov M, et al. JCI Insight, 2018 Feb 22. PMID 29467330, Free PMC Article
  3. Orientation-dependent Dxz4 contacts shape the 3D structure of the inactive X chromosome. Bonora G, et al. Nat Commun, 2018 Apr 13. PMID 29654302, Free PMC Article
  4. Remote Memory and Cortical Synaptic Plasticity Require Neuronal CCCTC-Binding Factor (CTCF). Kim S, et al. J Neurosci, 2018 May 30. PMID 29712785, Free PMC Article
  5. Computational prediction of CTCF/cohesin-based intra-TAD loops that insulate chromatin contacts and gene expression in mouse liver. Matthews BJ, et al. Elife, 2018 May 14. PMID 29757144, Free PMC Article

See all (263) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. A CTCF-binding site in the Mdm1-Il22-Ifng locus shapes cytokine expression profiles and plays a critical role in early Th1 cell fate specification.
    Title: A CTCF-binding site in the Mdm1-Il22-Ifng locus shapes cytokine expression profiles and plays a critical role in early Th1 cell fate specification.
  2. CTCF mutation at R567 causes developmental disorders via 3D genome rearrangement and abnormal neurodevelopment.
    Title: CTCF mutation at R567 causes developmental disorders via 3D genome rearrangement and abnormal neurodevelopment.
  3. Transcriptional regulation of FACT involves Coordination of chromatin accessibility and CTCF binding.
    Title: Transcriptional regulation of FACT involves Coordination of chromatin accessibility and CTCF binding.
  4. Systematic assessment of ISWI subunits shows that NURF creates local accessibility for CTCF.
    Title: Systematic assessment of ISWI subunits shows that NURF creates local accessibility for CTCF.
  5. ADNP modulates SINE B2-derived CTCF-binding sites during blastocyst formation in mice.
    Title: ADNP modulates SINE B2-derived CTCF-binding sites during blastocyst formation in mice.
  6. CCCTC-binding factor: the specific transcription factor of beta-galactoside alpha-2,6-sialyltransferase 1 that upregulates the sialylation of anti-citrullinated protein antibodies in rheumatoid arthritis.
    Title: CCCTC-binding factor: the specific transcription factor of β-galactoside α-2,6-sialyltransferase 1 that upregulates the sialylation of anti-citrullinated protein antibodies in rheumatoid arthritis.
  7. Outward-oriented sites within clustered CTCF boundaries are key for intra-TAD chromatin interactions and gene regulation.
    Title: Outward-oriented sites within clustered CTCF boundaries are key for intra-TAD chromatin interactions and gene regulation.
  8. CTCF coordinates cell fate specification via orchestrating regulatory hubs with pioneer transcription factors.
    Title: CTCF coordinates cell fate specification via orchestrating regulatory hubs with pioneer transcription factors.
  9. Sequential and directional insulation by conserved CTCF sites underlies the Hox timer in stembryos.
    Title: Sequential and directional insulation by conserved CTCF sites underlies the Hox timer in stembryos.
  10. SATB1 regulates 3D genome architecture in T cells by constraining chromatin interactions surrounding CTCF-binding sites.
    Title: SATB1 regulates 3D genome architecture in T cells by constraining chromatin interactions surrounding CTCF-binding sites.
Submit: New GeneRIF Correction See all GeneRIFs (184)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables DNA-binding transcription activator activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
  
enables DNA-binding transcription factor activity ISO
Inferred from Sequence Orthology
more info
  
enables DNA-binding transcription factor binding ISO
Inferred from Sequence Orthology
more info
  
enables DNA-binding transcription repressor activity, RNA polymerase II-specific IEA
Inferred from Electronic Annotation
more info
  
enables DNA-binding transcription repressor activity, RNA polymerase II-specific ISO
Inferred from Sequence Orthology
more info
  
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
  
enables chromatin binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables chromatin insulator sequence binding IEA
Inferred from Electronic Annotation
more info
  
enables chromatin insulator sequence binding ISO
Inferred from Sequence Orthology
more info
  
enables chromatin loop anchoring activity IEA
Inferred from Electronic Annotation
more info
  
enables chromatin loop anchoring activity ISO
Inferred from Sequence Orthology
more info
  
enables cis-regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
  
enables sequence-specific double-stranded DNA binding ISO
Inferred from Sequence Orthology
more info
  
enables transcription cis-regulatory region binding ISO
Inferred from Sequence Orthology
more info
  
enables transcription coregulator binding IEA
Inferred from Electronic Annotation
more info
  
enables transcription coregulator binding ISO
Inferred from Sequence Orthology
more info
  
Process Evidence Code Pubs
acts_upstream_of_or_within DNA methylation-dependent heterochromatin formation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within cardiac muscle cell development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within cardiac muscle cell differentiation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
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 chromatin looping ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within chromatin organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in chromosome segregation IEA
Inferred from Electronic Annotation
more info
  
acts_upstream_of_or_within epigenetic regulation of gene expression IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in epigenetic regulation of gene expression ISO
Inferred from Sequence Orthology
more info
  
acts_upstream_of_or_within gene expression IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within genomic imprinting IDA
Inferred from Direct Assay
more info
 PubMed 
acts_upstream_of_or_within genomic imprinting IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within heart development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within in utero embryonic development IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within mitochondrion organization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of DNA-templated transcription ISO
Inferred from Sequence Orthology
more info
  
involved_in negative regulation of cell population proliferation ISO
Inferred from Sequence Orthology
more info
  
involved_in negative regulation of cell population proliferation ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in negative regulation of gene expression IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within negative regulation of gene expression via chromosomal CpG island methylation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
  
involved_in positive regulation of DNA-templated transcription ISO
Inferred from Sequence Orthology
more info
  
involved_in positive regulation of gene expression IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of gene expression ISO
Inferred from Sequence Orthology
more info
  
involved_in positive regulation of miRNA transcription ISO
Inferred from Sequence Orthology
more info
  
involved_in positive regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
  
involved_in protein localization to chromosome, centromeric region ISO
Inferred from Sequence Orthology
more info
  
involved_in protein localization to chromosome, centromeric region ISS
Inferred from Sequence or Structural Similarity
more info
  
acts_upstream_of_or_within random inactivation of X chromosome TAS
Traceable Author Statement
more info
 PubMed 
acts_upstream_of_or_within regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in chromosome, centromeric region ISO
Inferred from Sequence Orthology
more info
  
located_in chromosome, centromeric region ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in condensed chromosome IEA
Inferred from Electronic Annotation
more info
  
located_in condensed chromosome ISO
Inferred from Sequence Orthology
more info
  
located_in dense fibrillar component ISO
Inferred from Sequence Orthology
more info
  
located_in granular component ISO
Inferred from Sequence Orthology
more info
  
located_in male germ cell nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleolus IEA
Inferred from Electronic Annotation
more info
  
located_in nucleolus ISO
Inferred from Sequence Orthology
more info
  
located_in nucleoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus ISO
Inferred from Sequence Orthology
more info
  

General protein information

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Preferred Names
transcriptional repressor CTCF
Names
11-zinc finger protein
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_001358924.2 → NP_001345853.1  transcriptional repressor CTCF isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC127419, AC152826
    UniProtKB/TrEMBL
    Q3UYZ8
    Conserved Domains (3) 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:509 → 534
    zf-H2C2_2; Zinc-finger double domain

  2. NM_001403723.1 → NP_001390652.1  transcriptional repressor CTCF isoform 1

    Status: VALIDATED

    Source sequence(s)
    AC127419, AC152826
    UniProtKB/Swiss-Prot
    Q61164

  3. NM_001403724.1 → NP_001390653.1  transcriptional repressor CTCF isoform 1

    Status: VALIDATED

    Source sequence(s)
    AC127419, AC152826
    UniProtKB/Swiss-Prot
    Q61164

  4. NM_001403725.1 → NP_001390654.1  transcriptional repressor CTCF isoform 1

    Status: VALIDATED

    Source sequence(s)
    AC127419, AC152826
    UniProtKB/Swiss-Prot
    Q61164

  5. NM_001403726.1 → NP_001390655.1  transcriptional repressor CTCF isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC127419, AC152826

  6. NM_001403727.1 → NP_001390656.1  transcriptional repressor CTCF isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC127419, AC152826

  7. NM_001403728.1 → NP_001390657.1  transcriptional repressor CTCF isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC127419, AC152826

  8. NM_001403729.1 → NP_001390658.1  transcriptional repressor CTCF isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC127419, AC152826

  9. NM_001403730.1 → NP_001390659.1  transcriptional repressor CTCF isoform 3

    Status: VALIDATED

    Source sequence(s)
    AC127419, AC152826

  10. NM_001403731.1 → NP_001390660.1  transcriptional repressor CTCF isoform 4

    Status: VALIDATED

    Source sequence(s)
    AC127419, AC152826

  11. NM_001403732.1 → NP_001390661.1  transcriptional repressor CTCF isoform 4

    Status: VALIDATED

    Source sequence(s)
    AC127419, AC152826

  12. NM_181322.4 → NP_851839.1  transcriptional repressor CTCF isoform 1

    See identical proteins and their annotated locations for NP_851839.1

    Status: VALIDATED

    Source sequence(s)
    AC127419, AC152826
    Consensus CDS
    CCDS22606.1
    UniProtKB/Swiss-Prot
    Q61164
    UniProtKB/TrEMBL
    Q3UYZ8
    Related
    ENSMUSP00000005841.10, ENSMUST00000005841.16
    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: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000074.7 Reference GRCm39 C57BL/6J

    Range
    106351135..106409554
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_030243283.2 → XP_030099143.1  transcriptional repressor CTCF isoform X5

    UniProtKB/Swiss-Prot
    Q61164
    UniProtKB/TrEMBL
    Q3UYZ8
    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

  2. XM_006530646.5 → XP_006530709.1  transcriptional repressor CTCF isoform X3

    UniProtKB/TrEMBL
    Q3USR8
    Conserved Domains (4) summary
    COG5048
    Location:375 → 509
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:277 → 297
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:289 → 314
    zf-H2C2_2; Zinc-finger double domain
    pfam13909
    Location:360 → 384
    zf-H2C2_5; C2H2-type zinc-finger domain

  3. XM_006530647.4 → XP_006530710.1  transcriptional repressor CTCF isoform X4

    UniProtKB/TrEMBL
    Q3USR8
    Conserved Domains (4) summary
    COG5048
    Location:375 → 509
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:277 → 297
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam13465
    Location:289 → 314
    zf-H2C2_2; Zinc-finger double domain
    pfam13909
    Location:360 → 384
    zf-H2C2_5; C2H2-type zinc-finger domain

  4. XM_036153746.1 → XP_036009639.1  transcriptional repressor CTCF isoform X5

    UniProtKB/Swiss-Prot
    Q61164
    UniProtKB/TrEMBL
    Q3UYZ8
    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

  5. XM_036153749.1 → XP_036009642.1  transcriptional repressor CTCF isoform X7

    UniProtKB/TrEMBL
    Q3USR8
    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

RNA

  1. XR_004934760.1 RNA Sequence

  2. XR_004934757.1 RNA Sequence

  3. XR_004934759.1 RNA Sequence

  4. XR_004934758.1 RNA Sequence

Nucleotide Protein Strain
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q61164.2 GenPept UniProtKB/Swiss-Prot:Q61164

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