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

    Gene ID: 13018, updated on 19-Mar-2019

    Summary

    Official Symbol
    Ctcfprovided by MGI
    Official Full Name
    CCCTC-binding factorprovided by MGI
    Primary source
    MGI:MGI:109447
    See related
    Ensembl:ENSMUSG00000005698
    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
     
    DNA-binding transcription repressor activity, RNA polymerase II-specific 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 
    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, ENSMUST00000005841.15
      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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