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

Summary

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, Nov 2024]
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

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_000068.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
CTCFL expression is associated with cerebral vascular abnormalities.
Title: CTCFL expression is associated with cerebral vascular abnormalities.
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.
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.
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.
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.
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.
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.
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.
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)

Endonuclease-mediated (2)
Targeted (3) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D10Mit157.2 (e-PCR), detects polymorphism
- UniSTS:126061

Ctcfl (e-PCR), detects polymorphism
- UniSTS:547205

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	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	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 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
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	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	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 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
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	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in nuclear body	IEA Inferred from Electronic Annotation 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)

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
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

NC_000068.8 Reference GRCm39 C57BL/6J

Range

172935402..172961318 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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