ctcf CCCTC-binding factor (zinc finger protein) [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: ctcfprovided by ZNC
Official Full Name: CCCTC-binding factor (zinc finger protein)provided by ZNC
Primary source: ZFIN:ZDB-GENE-040624-5
See related: Ensembl:ENSDARG00000056621 AllianceGenome:ZFIN:ZDB-GENE-040624-5
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: im:7152666
Summary: Enables chromatin binding activity. Acts upstream of or within regulation of transcription by RNA polymerase II and skeletal muscle tissue development. Is expressed in brain; digestive system; immature eye; notochord; and somite. Human ortholog(s) of this gene implicated in autosomal dominant non-syndromic intellectual disability 21. Orthologous to human CTCF (CCCTC-binding factor). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 18

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
106	current	GRCz11 (GCF_000002035.6)	18	NC_007129.7 (22286011..22293372)
105	previous assembly	GRCz10 (GCF_000002035.5)	18	NC_007129.6 (22296360..22304317)

Chromosome 18 - NC_007129.7 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: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

We propose that cohesin and CTCF have distinct functions in the regulation of runx1 during zebrafish embryogenesis.
Title: Cohesin and CTCF differentially regulate spatiotemporal runx1 expression during zebrafish development.
Data conclude that CTCF modulates MRF functional interactions in the orchestration of myogenesis.
Title: CTCF promotes muscle differentiation by modulating the activity of myogenic regulatory factors.

Submit: New GeneRIF Correction

General gene information

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Markers

fd10b10.y1 (e-PCR)
- UniSTS:195098

fc46d03.y1 (e-PCR)
- UniSTS:193925

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in regulation of DNA-templated transcription	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within regulation of gene expression	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within skeletal muscle tissue development	IMP Inferred from Mutant Phenotype more info	PubMed

General protein information

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Preferred Names: transcriptional repressor CTCF

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_001001844.1 → NP_001001844.1 transcriptional repressor CTCF

See identical proteins and their annotated locations for NP_001001844.1

Status: PROVISIONAL

Source sequence(s)

AY547282

UniProtKB/TrEMBL

B3DKQ0, E7F7B5, Q6JAA4

Related

ENSDARP00000073595.2, ENSDART00000079139.4

Conserved Domains (4) summary

COG5048
Location:406 → 540

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

sd00017
Location:308 → 328

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam06750
Location:478 → 523

DiS_P_DiS; Bacterial Peptidase A24 N-terminal domain

pfam13465
Location:434 → 458

zf-H2C2_2; Zinc-finger double domain