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

    Gene ID: 664799, updated on 5-Mar-2024

    Summary

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    Official Symbol
    Ctcflprovided by MGI
    Official Full Name
    CCCTC-binding factor likeprovided by MGI
    Primary source
    MGI:MGI:3652571
    See related
    Ensembl:ENSMUSG00000070495 AllianceGenome:MGI:3652571
    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
    Boris
    Summary
    Enables histone binding activity and sequence-specific DNA binding activity. Involved in DNA methylation involved in gamete generation; histone methylation; and regulation of gene expression by genetic imprinting. Located in cytoplasm and nucleus. Is expressed in eye and nervous system. Orthologous to human CTCFL (CCCTC-binding factor like). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in subcutaneous fat pad adult (RPKM 1.3), genital fat pad adult (RPKM 1.1) and 11 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Ctcfl in Genome Data Viewer
    Location:
    2 H3; 2 95.74 cM
    Exon count:
    12
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 2 NC_000068.8 (172935402..172961318, complement)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 2 NC_000068.7 (173093609..173119525, complement)

    Chromosome 2 - NC_000068.8Genomic Context describing neighboring genes Neighboring gene CapStarr-seq enhancer MGSCv37_chr2:172879441-172879628 Neighboring gene predicted gene, 36337 Neighboring gene predicted gene, 36462 Neighboring gene predicted gene, 36417 Neighboring gene STARR-seq mESC enhancer starr_06608 Neighboring gene CapStarr-seq enhancer MGSCv37_chr2:172908254-172908455 Neighboring gene STARR-positive B cell enhancer ABC_E2064 Neighboring gene VISTA enhancer mm1693 Neighboring gene STARR-positive B cell enhancer ABC_E8953 Neighboring gene predicted gene, 40011 Neighboring gene STARR-positive B cell enhancer ABC_E4527 Neighboring gene CCCTC-binding factor like, opposite strand Neighboring gene predicted gene, 36691 Neighboring gene predicted gene, 36749

    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
    • 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. Boris knockout eliminates AOM/DSS-induced in situ colorectal cancer by suppressing DNA damage repair and inflammation. Zuo BW, et al. Cancer Sci, 2023 May. PMID 36692143, Free PMC Article
    2. The combined action of CTCF and its testis-specific paralog BORIS is essential for spermatogenesis. Rivero-Hinojosa S, et al. Nat Commun, 2021 Jun 22. PMID 34158481, Free PMC Article
    3. CTCFL expression is associated with cerebral vascular abnormalities. Sati L, et al. Tissue Cell, 2021 Oct. PMID 33756271
    4. Testis-specific transcriptional regulators selectively occupy BORIS-bound CTCF target regions in mouse male germ cells. Rivero-Hinojosa S, et al. Sci Rep, 2017 Feb 1. PMID 28145452, Free PMC Article
    5. Expression of the CTCFL Gene during Mouse Embryogenesis Causes Growth Retardation, Postnatal Lethality, and Dysregulation of the Transforming Growth Factor β Pathway. Sati L, et al. Mol Cell Biol, 2015 Oct. PMID 26169830, Free PMC Article

    See all (25) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Boris knockout eliminates AOM/DSS-induced in situ colorectal cancer by suppressing DNA damage repair and inflammation.
      Title: Boris knockout eliminates AOM/DSS-induced in situ colorectal cancer by suppressing DNA damage repair and inflammation.
    2. CTCFL expression is associated with cerebral vascular abnormalities.
      Title: CTCFL expression is associated with cerebral vascular abnormalities.
    3. The combined action of CTCF and its testis-specific paralog BORIS is essential for spermatogenesis.
      Title: The combined action of CTCF and its testis-specific paralog BORIS is essential for spermatogenesis.
    4. Defining the relative and combined contribution of CTCF and CTCFL to genomic regulation.
      Title: Defining the relative and combined contribution of CTCF and CTCFL to genomic regulation.
    5. CTCF and BORIS cooperate with additional Testis-specific transcriptional regulators to regulate gene expression in developing male gametes.
      Title: Testis-specific transcriptional regulators selectively occupy BORIS-bound CTCF target regions in mouse male germ cells.
    6. The TGFB pathway as most affected by embryonic Ctcfl expression.
      Title: Expression of the CTCFL Gene during Mouse Embryogenesis Causes Growth Retardation, Postnatal Lethality, and Dysregulation of the Transforming Growth Factor β Pathway.
    7. down-regulation of endogenous BORIS by specific shRNAs inhibited both RNA transcription and cell cycle progression. The results altogether suggest a role for BORIS in coordinating S phase events with mitosis.
      Title: A cell cycle role for the epigenetic factor CTCF-L/BORIS.
    8. Rb2 coimmunolocalizes with the chromatin insulator CCCTC-binding factor (CTCF) and BORIS in T-antigen-positive but not in T-antigen-negative cells.
      Title: Integrating role of T antigen, Rb2/p130, CTCF and BORIS in mediating non-canonical endoplasmic reticulum-dependent death pathways triggered by chronic ER stress in mouse medulloblastoma.
    9. These findings show that BORIS expression is more widespread than previously believed, and suggest a role for BORIS in nucleolar function.
      Title: Widespread expression of BORIS/CTCFL in normal and cancer cells.
    10. findings indicate that BORIS-induced expression of TSP50 is governed by accessibility and binding of BORIS to the promoter
      Title: Transcription factor BORIS (Brother of the Regulator of Imprinted Sites) directly induces expression of a cancer-testis antigen, TSP50, through regulated binding of BORIS to the promoter.
    Submit: New GeneRIF Correction See all GeneRIFs (14)

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Targeted (3)  1 citation
    • Endonuclease-mediated (2) 

    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 ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables DNA-binding transcription activator activity, RNA polymerase II-specific ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables RNA polymerase II cis-regulatory region sequence-specific DNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables chromatin insulator sequence binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables histone 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 transcription cis-regulatory region binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within chromatin organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in establishment of protein localization to chromatin ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in genomic imprinting IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of gene expression ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in transcription initiation-coupled chromatin remodeling ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    is_active_in chromosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nuclear body ISO
    Inferred from Sequence Orthology
    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 

    General protein information

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    Preferred Names
    transcriptional repressor CTCFL
    Names
    BORIS
    Brother of the regulator of imprinted sites
    CCCTC-binding factor (zinc finger protein)-like
    CTCF paralog
    CTCF-like protein
    likely orthologue of H. sapiens CCCTC-binding factor-like protein (CTCFL)

    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_001081387.2 → NP_001074856.1  transcriptional repressor CTCFL isoform 2

      See identical proteins and their annotated locations for NP_001074856.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame 3' splice junction compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AL837509, AL928599
      Consensus CDS
      CCDS38349.1
      UniProtKB/Swiss-Prot
      A2APF3, B9EKP6, Q3Y6S0
      Related
      ENSMUSP00000091845.4, ENSMUST00000094287.10
      Conserved Domains (3) summary
      COG5048
      Location:256 → 491
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:344 → 364
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:385 → 409
      zf-H2C2_2; Zinc-finger double domain

    2. NM_001355185.1 → NP_001342114.1  transcriptional repressor CTCFL isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AL837509, AL928599
      Conserved Domains (2) summary
      COG5048
      Location:256 → 491
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:344 → 364
      ZF_C2H2; C2H2 Zn finger [structural motif]

    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_000068.8 Reference GRCm39 C57BL/6J

      Range
      172935402..172961318 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017319167.2 → XP_017174656.1  transcriptional repressor CTCFL isoform X1

      Conserved Domains (4) summary
      COG5048
      Location:19 → 81
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:25 → 45
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam13465
      Location:66 → 90
      zf-H2C2_2; Zinc-finger double domain
      pfam13909
      Location:167 → 191
      zf-H2C2_5; C2H2-type zinc-finger domain
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    A2APF3.1 GenPept UniProtKB/Swiss-Prot:A2APF3

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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