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

Gene ID: 13018, updated on 10-Jan-2023

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 sequence-specific DNA binding activity. Involved in regulation of gene expression and regulation of histone modification. Acts upstream of or within DNA metabolic process and regulation of gene expression. Located in 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 non-syndromic intellectual disability 21. Orthologous to human CTCF (CCCTC-binding factor). [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in CNS E11.5 (RPKM 18.2), thymus adult (RPKM 13.4) and 27 other tissues See more
Orthologs
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Genomic context

See Ctcf in Genome Data Viewer
Location:
8; 8 D3
Exon count:
15
Annotation release Status Assembly Chr Location
109 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 microRNA 1966 Neighboring gene predicted gene 5914 Neighboring gene myosin light polypeptide 6-like Neighboring gene predicted gene, 33578 Neighboring gene capping protein regulator and myosin 1 linker 2 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)
  • Targeted (7)  1 citation
  • Endonuclease-mediated (2) 

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

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
PubMed 
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 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
PubMed 
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 ISO
Inferred from Sequence Orthology
more info
 
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 transcription cis-regulatory region binding ISO
Inferred from Sequence Orthology
more info
 
enables transcription coregulator binding ISO
Inferred from Sequence Orthology
more info
 
Process Evidence Code Pubs
acts_upstream_of_or_within DNA methylation IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within DNA methylation IMP
Inferred from Mutant Phenotype
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 IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within chromosome segregation IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within dosage compensation by inactivation of X chromosome TAS
Traceable Author Statement
more info
PubMed 
involved_in epigenetic regulation of gene expression ISO
Inferred from Sequence Orthology
more info
 
involved_in genomic imprinting ISO
Inferred from Sequence Orthology
more info
 
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 gene expression IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within negative regulation of gene expression via chromosomal DNA cytosine 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 protein localization to chromosome, centromeric region ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within regulation of gene expression by genomic imprinting IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within regulation of gene expression by genomic imprinting IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
located_in chromosome IEA
Inferred from Electronic Annotation
more info
 
located_in chromosome, centromeric region ISO
Inferred from Sequence Orthology
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 ISO
Inferred from Sequence Orthology
more info
 
located_in nucleoplasm ISO
Inferred from Sequence Orthology
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)

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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_001358924.2NP_001345853.1  transcriptional repressor CTCF isoform 2

    Status: VALIDATED

    Source sequence(s)
    AC127419, AC152826
    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
    A0A8C6HB84
  3. NM_001403724.1NP_001390653.1  transcriptional repressor CTCF isoform 1

    Status: VALIDATED

    Source sequence(s)
    AC127419, AC152826
    UniProtKB/Swiss-Prot
    Q61164
    UniProtKB/TrEMBL
    A0A8C6HB84
  4. NM_001403725.1NP_001390654.1  transcriptional repressor CTCF isoform 1

    Status: VALIDATED

    Source sequence(s)
    AC127419, AC152826
    UniProtKB/Swiss-Prot
    Q61164
    UniProtKB/TrEMBL
    A0A8C6HB84
  5. NM_001403726.1NP_001390655.1  transcriptional repressor CTCF isoform 2

    Status: VALIDATED

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

    Status: VALIDATED

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

    Status: VALIDATED

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

    Status: VALIDATED

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

    Status: VALIDATED

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

    Status: VALIDATED

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

    Status: VALIDATED

    Source sequence(s)
    AC127419, AC152826
  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
    A0A8C6HB84
    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: Mus musculus Annotation Release 109 details...Open this link in a new tab

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
    A0A8C6HB84
    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_036153747.1XP_036009640.1  transcriptional repressor CTCF isoform X6

    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
  3. XM_036153748.1XP_036009641.1  transcriptional repressor CTCF isoform X7

    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
  4. XM_030243280.2XP_030099140.1  transcriptional repressor CTCF isoform X1

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

    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
  6. XM_030243282.2XP_030099142.1  transcriptional repressor CTCF isoform X2

    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
  7. XM_006530647.4XP_006530710.1  transcriptional repressor CTCF isoform X4

    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
  8. XM_036153746.1XP_036009639.1  transcriptional repressor CTCF isoform X5

    UniProtKB/Swiss-Prot
    Q61164
    UniProtKB/TrEMBL
    A0A8C6HB84
    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
  9. XM_036153749.1XP_036009642.1  transcriptional repressor CTCF isoform X7

    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
  10. XM_006530648.2XP_006530711.1  transcriptional repressor CTCF isoform X5

    UniProtKB/Swiss-Prot
    Q61164
    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