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

Gene ID: 13018, updated on 2-Oct-2018

Summary

Official Symbol
Ctcfprovided by MGI
Official Full Name
CCCTC-binding factorprovided by MGI
Primary source
MGI:MGI:109447
See related
Ensembl:ENSMUSG00000005698 Vega:OTTMUSG00000017298
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
Also known as
AW108038
Expression
Ubiquitous expression in CNS E11.5 (RPKM 18.2), thymus adult (RPKM 13.4) and 27 other tissues See more
Orthologs

Genomic context

See Ctcf in Genome Data Viewer
Location:
8; 8 D3
Exon count:
14
Annotation release Status Assembly Chr Location
106 current GRCm38.p4 (GCF_000001635.24) 8 NC_000074.6 (105636538..105682922)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 8 NC_000074.5 (108160438..108206822)

Chromosome 8 - NC_000074.6Genomic Context describing neighboring genes Neighboring gene 40S ribosomal protein S2 pseudogene Neighboring gene RHO family interacting cell polarization regulator 1 Neighboring gene microRNA 1966 Neighboring gene predicted gene 5914 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 FunctionsWhat's a GeneRIF?

Variation

Alleles

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

Pathways from BioSystems

  • Mecp2 and Associated Rett Syndrome, organism-specific biosystem (from WikiPathways)
    Mecp2 and Associated Rett Syndrome, organism-specific biosystemMecp2 is in many mammals an important regulator of neuronal function and development. It affects all cell types, especially neurons but also astrocytes, oligodendrocytes, and glial cells. Mecp2 plays...
  • PluriNetWork, organism-specific biosystem (from WikiPathways)
    PluriNetWork, organism-specific biosystemThe aim of the PluriNetWork is to give an overview of specific mechanisms associated with pluripotency in mouse. Each node represents a gene and its corresponding protein product. As stated, we inten...
  • SIDS Susceptibility Pathways, organism-specific biosystem (from WikiPathways)
    SIDS Susceptibility Pathways, organism-specific biosystemIn this model, we provide an integrated view of Sudden Infant Death Syndrome (SIDS) at the level of implicated tissues, signaling networks and genetics. The purpose of this model is to serve as an ov...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
DNA-binding transcription activator activity, RNA polymerase II-specific IDA
Inferred from Direct Assay
more info
PubMed 
DNA-binding transcription factor activity ISO
Inferred from Sequence Orthology
more info
 
RNA polymerase II proximal promoter sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
 
chromatin binding IDA
Inferred from Direct Assay
more info
PubMed 
chromatin insulator sequence binding ISO
Inferred from Sequence Orthology
more info
 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
nucleic acid binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
proximal promoter DNA-binding transcription repressor activity, RNA polymerase II-specific ISO
Inferred from Sequence Orthology
more info
 
sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
 
transcription regulatory region DNA binding ISO
Inferred from Sequence Orthology
more info
 
Process Evidence Code Pubs
DNA methylation IDA
Inferred from Direct Assay
more info
PubMed 
DNA methylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
chromatin organization IEA
Inferred from Electronic Annotation
more info
 
chromosome segregation IEA
Inferred from Electronic Annotation
more info
 
dosage compensation by inactivation of X chromosome TAS
Traceable Author Statement
more info
PubMed 
maintenance of DNA methylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of cell proliferation ISO
Inferred from Sequence Orthology
more info
 
negative regulation of gene expression IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
negative regulation of transcription, DNA-templated ISO
Inferred from Sequence Orthology
more info
 
nucleosome positioning ISO
Inferred from Sequence Orthology
more info
 
positive regulation of gene expression IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of gene expression ISO
Inferred from Sequence Orthology
more info
 
positive regulation of pri-miRNA transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
positive regulation of transcription, DNA-templated ISO
Inferred from Sequence Orthology
more info
 
protein localization to chromosome, centromeric region ISO
Inferred from Sequence Orthology
more info
 
regulation of gene expression by genetic imprinting IDA
Inferred from Direct Assay
more info
PubMed 
regulation of gene expression by genetic imprinting IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of gene expression, epigenetic ISO
Inferred from Sequence Orthology
more info
 
regulation of histone acetylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of histone methylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of molecular function, epigenetic ISO
Inferred from Sequence Orthology
more info
 
regulation of transcription, DNA-templated IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
chromosome IEA
Inferred from Electronic Annotation
more info
 
chromosome, centromeric region ISO
Inferred from Sequence Orthology
more info
 
condensed chromosome ISO
Inferred from Sequence Orthology
more info
 
nucleolus ISO
Inferred from Sequence Orthology
more info
 
nucleoplasm ISO
Inferred from Sequence Orthology
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
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)

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_001358924.1NP_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_181322.3NP_851839.1  transcriptional repressor CTCF isoform 1

    See identical proteins and their annotated locations for NP_851839.1

    Status: VALIDATED

    Source sequence(s)
    AC127419, BC049131
    Consensus CDS
    CCDS22606.1
    UniProtKB/Swiss-Prot
    Q61164
    Related
    ENSMUSP00000005841.9, OTTMUSP00000018870, ENSMUST00000005841.15, OTTMUST00000041960
    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

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 106

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

Reference GRCm38.p4 C57BL/6J

Genomic

  1. NC_000074.6 Reference GRCm38.p4 C57BL/6J

    Range
    105636538..105682922
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017312557.1XP_017168046.1  transcriptional repressor CTCF isoform X6

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

    See identical proteins and their annotated locations for XP_006530711.1

    UniProtKB/Swiss-Prot
    Q61164
    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
  3. XM_006530647.2XP_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]
    pfam06750
    Location:447492
    DiS_P_DiS; Bacterial Peptidase A24 N-terminal domain
    pfam13465
    Location:403427
    zf-H2C2_2; Zinc-finger double domain
  4. XM_006530644.2XP_006530707.1  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]
    pfam06750
    Location:447492
    DiS_P_DiS; Bacterial Peptidase A24 N-terminal domain
    pfam13465
    Location:403427
    zf-H2C2_2; Zinc-finger double domain
  5. XM_006530646.3XP_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]
    pfam06750
    Location:447492
    DiS_P_DiS; Bacterial Peptidase A24 N-terminal domain
    pfam13465
    Location:403427
    zf-H2C2_2; Zinc-finger double domain
  6. XM_006530645.3XP_006530708.1  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]
    pfam06750
    Location:447492
    DiS_P_DiS; Bacterial Peptidase A24 N-terminal domain
    pfam13465
    Location:403427
    zf-H2C2_2; Zinc-finger double domain
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