U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from GEO Profiles

    • Showing Current items.

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

    Gene ID: 13018, updated on 3-Dec-2024

    Summary

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    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

    Expression

    • Project title: 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Variation

    Alleles

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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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 constitutive 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

    Preferred Names
    transcriptional repressor CTCF
    Names
    11-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.

    mRNA and Protein(s)

    1. NM_001358924.2NP_001345853.1  transcriptional repressor CTCF isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC127419, AC152826
      UniProtKB/TrEMBL
      Q3UYZ8
      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
    2. NM_001403723.1NP_001390652.1  transcriptional repressor CTCF isoform 1

      Status: VALIDATED

      Source sequence(s)
      AC127419, AC152826
      UniProtKB/Swiss-Prot
      Q61164
      UniProtKB/TrEMBL
      Q3UYZ8
    3. NM_001403724.1NP_001390653.1  transcriptional repressor CTCF isoform 1

      Status: VALIDATED

      Source sequence(s)
      AC127419, AC152826
      UniProtKB/Swiss-Prot
      Q61164
      UniProtKB/TrEMBL
      Q3UYZ8
    4. NM_001403725.1NP_001390654.1  transcriptional repressor CTCF isoform 1

      Status: VALIDATED

      Source sequence(s)
      AC127419, AC152826
      UniProtKB/Swiss-Prot
      Q61164
      UniProtKB/TrEMBL
      Q3UYZ8
    5. NM_001403726.1NP_001390655.1  transcriptional repressor CTCF isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC127419, AC152826
      UniProtKB/TrEMBL
      Q3UYZ8
    6. NM_001403727.1NP_001390656.1  transcriptional repressor CTCF isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC127419, AC152826
      UniProtKB/TrEMBL
      Q3UYZ8
    7. NM_001403728.1NP_001390657.1  transcriptional repressor CTCF isoform 2

      Status: VALIDATED

      Source sequence(s)
      AC127419, AC152826
      UniProtKB/TrEMBL
      Q3UYZ8
    8. NM_001403729.1NP_001390658.1  transcriptional repressor CTCF isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC127419, AC152826
      UniProtKB/TrEMBL
      Q3USR8
    9. NM_001403730.1NP_001390659.1  transcriptional repressor CTCF isoform 3

      Status: VALIDATED

      Source sequence(s)
      AC127419, AC152826
      UniProtKB/TrEMBL
      Q3USR8
    10. NM_001403731.1NP_001390660.1  transcriptional repressor CTCF isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC127419, AC152826
      UniProtKB/TrEMBL
      Q3USR8
    11. NM_001403732.1NP_001390661.1  transcriptional repressor CTCF isoform 4

      Status: VALIDATED

      Source sequence(s)
      AC127419, AC152826
      UniProtKB/TrEMBL
      Q3USR8
    12. NM_181322.4NP_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: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_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_030243283.2XP_030099143.1  transcriptional repressor CTCF isoform X5

      UniProtKB/Swiss-Prot
      Q61164
      UniProtKB/TrEMBL
      Q3UYZ8
      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_006530646.5XP_006530709.1  transcriptional repressor CTCF isoform X3

      UniProtKB/TrEMBL
      Q3USR8
      Conserved Domains (4) summary
      COG5048
      Location:375509
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:277297
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:289314
      zf-H2C2_2; Zinc-finger double domain
      pfam13909
      Location:360384
      zf-H2C2_5; C2H2-type zinc-finger domain
    3. XM_006530647.4XP_006530710.1  transcriptional repressor CTCF isoform X4

      UniProtKB/TrEMBL
      Q3USR8
      Conserved Domains (4) summary
      COG5048
      Location:375509
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:277297
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:289314
      zf-H2C2_2; Zinc-finger double domain
      pfam13909
      Location:360384
      zf-H2C2_5; C2H2-type zinc-finger domain
    4. XM_036153746.1XP_036009639.1  transcriptional repressor CTCF isoform X5

      UniProtKB/Swiss-Prot
      Q61164
      UniProtKB/TrEMBL
      Q3UYZ8
      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
    5. XM_036153749.1XP_036009642.1  transcriptional repressor CTCF isoform X7

      UniProtKB/TrEMBL
      Q3USR8
      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

    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