Ctcf CCCTC-binding factor [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Ctcfprovided by RGD
Official Full Name: CCCTC-binding factorprovided by RGD
Primary source: RGD:621344
See related: EnsemblRapid:ENSRNOG00000017674 AllianceGenome:RGD:621344
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Enables DNA-binding transcription factor binding activity. Involved in positive regulation of miRNA transcription. Located in dense fibrillar component and granular component. Human ortholog(s) of this gene implicated in autosomal dominant intellectual developmental disorder 21; basal cell carcinoma; female breast cancer; skin melanoma; and skin squamous cell carcinoma. Orthologous to human CTCF (CCCTC-binding factor). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Thymus (RPKM 380.9), Spleen (RPKM 217.9) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 19q12

Exon count:: 13

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	19	NC_086037.1 (50431478..50481013)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	19	NC_051354.1 (33521726..33571124)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	19	NC_005118.4 (37600151..37649674)

Chromosome 19 - NC_086037.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

CCCTC-binding factor suppresses alpha-2-macroglobulin transcription to improve vascular endothelial cell functions in lower extremity arteriosclerosis obliterans.
Title: CCCTC-binding factor suppresses alpha-2-macroglobulin transcription to improve vascular endothelial cell functions in lower extremity arteriosclerosis obliterans.
miR-383-5p Regulated by the Transcription Factor CTCF Affects Neuronal Impairment in Cerebral Ischemia by Mediating Deacetylase HDAC9 Activity.
Title: miR-383-5p Regulated by the Transcription Factor CTCF Affects Neuronal Impairment in Cerebral Ischemia by Mediating Deacetylase HDAC9 Activity.
Up-regulation of SNHG16 induced by CTCF accelerates cardiac hypertrophy by targeting miR-182-5p/IGF1 axis.
Title: Up-regulation of SNHG16 induced by CTCF accelerates cardiac hypertrophy by targeting miR-182-5p/IGF1 axis.
Our results propose that a broad pattern of astrocyte responses to dopamine specifically relies on CTCF-dependent gene networks
Title: Dopamine Triggers CTCF-Dependent Morphological and Genomic Remodeling of Astrocytes.

Submit: New GeneRIF Correction

General gene information

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Markers

CTCF_3772 (e-PCR)
- UniSTS:462131

D19Got22 (e-PCR)
- UniSTS:114742

U51037 (e-PCR)
- UniSTS:125764

WI-21064 (e-PCR)
- UniSTS:72035

Ctcf (e-PCR), detects polymorphism
- UniSTS:141440

BF389170 (e-PCR)
- UniSTS:245397

MARC_20750-20751:1025022208:1 (e-PCR)
- UniSTS:268474

Gene Ontology Provided by RGD

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	TAS Traceable Author Statement more info	PubMed
enables DNA-binding transcription factor activity	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription factor activity	ISO Inferred from Sequence Orthology more info
enables DNA-binding transcription factor activity	TAS Traceable Author Statement more info	PubMed
enables DNA-binding transcription factor binding	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription repressor activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
enables DNA-binding transcription repressor 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 chromatin binding	ISO Inferred from Sequence Orthology more info
enables chromatin insulator sequence binding	IEA Inferred from Electronic Annotation more info
enables chromatin insulator sequence binding	ISO Inferred from Sequence Orthology more info
enables chromatin loop anchoring activity	IEA Inferred from Electronic Annotation more info
enables chromatin loop anchoring activity	ISO Inferred from Sequence Orthology more info
enables cis-regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables sequence-specific double-stranded DNA binding	ISO Inferred from Sequence Orthology more info
enables transcription cis-regulatory region binding	ISO Inferred from Sequence Orthology more info
enables transcription coregulator binding	IEA Inferred from Electronic Annotation more info
enables transcription coregulator binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in DNA methylation-dependent constitutive heterochromatin formation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within DNA methylation-dependent constitutive heterochromatin formation	ISO Inferred from Sequence Orthology more info
involved_in cardiac muscle cell development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within cardiac muscle cell development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cardiac muscle cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in chromatin looping	IEA Inferred from Electronic Annotation more info
involved_in chromatin looping	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within chromatin organization	ISO Inferred from Sequence Orthology more info
involved_in chromosome segregation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within epigenetic regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in epigenetic regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in gene expression	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within gene expression	ISO Inferred from Sequence Orthology more info
involved_in genomic imprinting	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within genomic imprinting	ISO Inferred from Sequence Orthology more info
involved_in genomic imprinting	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within heart development	ISO Inferred from Sequence Orthology more info
involved_in in utero embryonic development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within in utero embryonic development	ISO Inferred from Sequence Orthology more info
involved_in mitochondrion organization	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within mitochondrion organization	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of cell population proliferation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of cell population proliferation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of cell population proliferation	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of gene expression	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of gene expression via chromosomal CpG island methylation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of gene expression via chromosomal CpG island methylation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology 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 miRNA transcription	IMP Inferred from Mutant Phenotype more info	PubMed
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 protein localization to chromosome, centromeric region	IEA Inferred from Electronic Annotation more info
involved_in protein localization to chromosome, centromeric region	ISO Inferred from Sequence Orthology more info
involved_in protein localization to chromosome, centromeric region	ISS Inferred from Sequence or Structural Similarity more info
acts_upstream_of_or_within regulation of DNA-templated transcription	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

Component	Evidence Code	Pubs
located_in chromosome, centromeric region	IEA Inferred from Electronic Annotation more info
located_in chromosome, centromeric region	ISO Inferred from Sequence Orthology more info
located_in chromosome, centromeric region	ISS Inferred from Sequence or Structural Similarity more info
located_in condensed chromosome	IEA Inferred from Electronic Annotation more info
located_in condensed chromosome	ISO Inferred from Sequence Orthology more info
located_in dense fibrillar component	IDA Inferred from Direct Assay more info	PubMed
located_in granular component	IDA Inferred from Direct Assay more info	PubMed
located_in male germ cell nucleus	IEA Inferred from Electronic Annotation more info
located_in male germ cell nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleolus	IEA Inferred from Electronic Annotation more info
located_in nucleolus	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: transcriptional repressor CTCF

Names: 11-zinc finger protein; CCCTC-binding factor (zinc finger protein); CTCFL paralog

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_031824.1 → NP_114012.1 transcriptional repressor CTCF

See identical proteins and their annotated locations for NP_114012.1

Status: PROVISIONAL

Source sequence(s)

AF133731

UniProtKB/Swiss-Prot

Q9R1D1

UniProtKB/TrEMBL

A0A8I5ZMQ8

Conserved Domains (4) summary

COG5048
Location:366 → 500

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:268 → 288

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam06750
Location:438 → 483

DiS_P_DiS; Bacterial Peptidase A24 N-terminal domain

pfam13465
Location:394 → 418

zf-H2C2_2; Zinc-finger double domain

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086037.1 Reference GRCr8

Range

50431478..50481013

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006255536.4 → XP_006255598.1 transcriptional repressor CTCF isoform X1

See identical proteins and their annotated locations for XP_006255598.1

UniProtKB/TrEMBL

A0A0H2UHP0, A0A8I5ZMQ8, A6IYR1

Related

ENSRNOP00000023851.4, ENSRNOT00000023853.7

Conserved Domains (4) summary

COG5048
Location:366 → 500

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:268 → 288

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam06750
Location:438 → 483

DiS_P_DiS; Bacterial Peptidase A24 N-terminal domain

pfam13465
Location:394 → 418

zf-H2C2_2; Zinc-finger double domain
XM_039098033.2 → XP_038953961.1 transcriptional repressor CTCF isoform X2

UniProtKB/TrEMBL

A0A8I5ZMQ8

Conserved Domains (4) summary

COG5048
Location:366 → 500

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:268 → 288

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam13465
Location:280 → 305

zf-H2C2_2; Zinc-finger double domain

pfam13909
Location:351 → 375

zf-H2C2_5; C2H2-type zinc-finger domain
XM_039098034.2 → XP_038953962.1 transcriptional repressor CTCF isoform X3

UniProtKB/TrEMBL

A0A8I5ZMQ8

Conserved Domains (4) summary

COG5048
Location:366 → 500

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:268 → 288

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam13465
Location:280 → 305

zf-H2C2_2; Zinc-finger double domain

pfam13909
Location:351 → 375

zf-H2C2_5; C2H2-type zinc-finger domain
XM_063278318.1 → XP_063134388.1 transcriptional repressor CTCF isoform X4