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

Gene ID: 664799, updated on 4-Feb-2026
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 genomic 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, Jul 2025]
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
all
Try the new Gene page
Try the new Transcripts and proteins table
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

Go to nucleotide: Graphics FASTA GenBank

  • 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

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)

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (3) 
  • Targeted (3)  1 citation
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables DNA binding ISO
Inferred from Sequence Orthology
more info
  
enables DNA-binding transcription activator activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
  
enables DNA-binding transcription activator activity, RNA polymerase II-specific IEA
Inferred from Electronic Annotation
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 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 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 IEA
Inferred from Electronic Annotation
more info
  
enables sequence-specific DNA binding ISO
Inferred from Sequence Orthology
more info
  
enables transcription cis-regulatory region binding IEA
Inferred from Electronic Annotation
more info
  
enables transcription cis-regulatory region binding ISO
Inferred from Sequence Orthology
more info
  
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in chromatin organization IEA
Inferred from Electronic Annotation
more info
  
involved_in establishment of protein localization to chromatin 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 IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of DNA-templated transcription ISO
Inferred from Sequence Orthology
more info
  
involved_in positive regulation of gene expression IEA
Inferred from Electronic Annotation
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 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 regulation of gene expression IEA
Inferred from Electronic Annotation
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 IEA
Inferred from Electronic Annotation
more info
  
involved_in transcription initiation-coupled chromatin remodeling ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
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 
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  
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)

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_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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