Chd7 chromodomain helicase DNA binding protein 7 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Chd7provided by MGI
Official Full Name: chromodomain helicase DNA binding protein 7provided by MGI
Primary source: MGI:MGI:2444748
See related: Ensembl:ENSMUSG00000041235 AllianceGenome:MGI:2444748
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Dz; Mt; Cyn; Edy; Flo; Lda; Obt; Whi; Cycn; Todo; WBE1; metis; GENA 47; GENA 60; Gena 52; A730019I05Rik
Summary: This gene encodes a protein containing two chromodomains and an ATP-binding helicase domain that functions as a regulator of transcription. Mutations in this gene result in an array of development defects, including inner ear problems. Mice defective for this gene exhibit many of the clinical features of the CHARGE syndrome caused by mutations in the homologous gene in human. [provided by RefSeq, Sep 2015]
Expression: Broad expression in CNS E11.5 (RPKM 14.2), cerebellum adult (RPKM 11.8) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 4 A1; 4 3.68 cM

Exon count:: 39

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	4	NC_000070.7 (8690345..8868449)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	4	NC_000070.6 (8690402..8868449)

Chromosome 4 - NC_000070.7 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: Mouse ENCODE transcriptome data 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?

CHD7 variants associated with hearing loss and enlargement of the vestibular aqueduct.
Title: CHD7 variants associated with hearing loss and enlargement of the vestibular aqueduct.
Chromatin remodeler Chd7 regulates photoreceptor development and outer segment length.
Title: Chromatin remodeler Chd7 regulates photoreceptor development and outer segment length.
Loss of the chromatin remodeler CHD7 impacts glial cells and myelination in the mouse cochlear spiral ganglion.
Title: Loss of the chromatin remodeler CHD7 impacts glial cells and myelination in the mouse cochlear spiral ganglion.
Characterization of Two Mouse Chd7 Heterozygous Loss-of-Function Models Shows Dysgenesis of the Corpus Callosum and Previously Unreported Features of CHARGE Syndrome.
Title: Characterization of Two Mouse Chd7 Heterozygous Loss-of-Function Models Shows Dysgenesis of the Corpus Callosum and Previously Unreported Features of CHARGE Syndrome.
CHD7 regulates bone-fat balance by suppressing PPAR-gamma signaling.
Title: CHD7 regulates bone-fat balance by suppressing PPAR-γ signaling.
CHARGE syndrome-associated proteins FAM172A and CHD7 influence male sex determination and differentiation through transcriptional and alternative splicing mechanisms.
Title: CHARGE syndrome-associated proteins FAM172A and CHD7 influence male sex determination and differentiation through transcriptional and alternative splicing mechanisms.
The chromatin remodelling factor Chd7 protects auditory neurons and sensory hair cells from stress-induced degeneration.
Title: The chromatin remodelling factor Chd7 protects auditory neurons and sensory hair cells from stress-induced degeneration.
CHD7 promotes neural progenitor differentiation in embryonic stem cells via altered chromatin accessibility and nascent gene expression.
Title: CHD7 promotes neural progenitor differentiation in embryonic stem cells via altered chromatin accessibility and nascent gene expression.
CHD7 regulates cardiovascular development through ATP-dependent and -independent activities.
Title: CHD7 regulates cardiovascular development through ATP-dependent and -independent activities.
CHD7 and Runx1 interaction provides a braking mechanism for hematopoietic differentiation.
Title: CHD7 and Runx1 interaction provides a braking mechanism for hematopoietic differentiation.

Submit: New GeneRIF Correction See all GeneRIFs (40)

Phenotypes

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Associated conditions

Description	Tests
cyclone GeneReviews: Not available
dizzy GeneReviews: Not available
eddy GeneReviews: Not available
leda GeneReviews: Not available
orbitor GeneReviews: Not available
tornado GeneReviews: Not available
whirligig GeneReviews: Not available

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Chemically induced (ENU) (12) 1 citation
Endonuclease-mediated (7) 1 citation
Gene trapped (4) 1 citation
Spontaneous (1) 1 citation
Targeted (7) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Chd7 (e-PCR), detects polymorphism
- UniSTS:472878

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP hydrolysis activity	IBA Inferred from Biological aspect of Ancestor more info
enables ATP hydrolysis activity	IEA Inferred from Electronic Annotation more info
enables ATP-dependent H2AZ histone chaperone activity	IEA Inferred from Electronic Annotation more info
enables ATP-dependent H3-H4 histone complex chaperone activity	IEA Inferred from Electronic Annotation more info
enables ATP-dependent chromatin remodeler activity	IBA Inferred from Biological aspect of Ancestor more info
enables DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables DNA clamp loader activity	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables chromatin binding	IBA Inferred from Biological aspect of Ancestor more info
enables chromatin extrusion motor activity	IEA Inferred from Electronic Annotation more info
enables cohesin loader activity	IEA Inferred from Electronic Annotation more info
enables double-stranded DNA helicase activity	IEA Inferred from Electronic Annotation more info
enables forked DNA-dependent helicase activity	IEA Inferred from Electronic Annotation more info
enables four-way junction helicase activity	IEA Inferred from Electronic Annotation more info
enables histone binding	IBA Inferred from Biological aspect of Ancestor more info
enables promoter-specific chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables single-stranded 3'-5' DNA helicase activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in DNA duplex unwinding	IEA Inferred from Electronic Annotation more info
involved_in T cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in T cell differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within adult heart development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within adult walking behavior	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within aorta development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within aorta morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within artery morphogenesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within atrioventricular canal development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within blood circulation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within blood vessel development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within blood vessel remodeling	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within camera-type eye development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cardiac septum morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in central nervous system development	IBA Inferred from Biological aspect of Ancestor more info
involved_in central nervous system development	ISO Inferred from Sequence Orthology more info
involved_in chordate embryonic development	IBA Inferred from Biological aspect of Ancestor more info
involved_in chromatin looping	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within chromatin remodeling	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cognition	IEA Inferred from Electronic Annotation more info
involved_in cognition	ISO Inferred from Sequence Orthology more info
involved_in cranial nerve development	IBA Inferred from Biological aspect of Ancestor more info
involved_in cranial nerve development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within ear morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within embryonic hindlimb morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within epithelium development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in face development	IEA Inferred from Electronic Annotation more info
involved_in face development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within female genitalia development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in genitalia development	ISO Inferred from Sequence Orthology more info
involved_in heart morphogenesis	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within heart morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in heart morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within in utero embryonic development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in in utero embryonic development	ISO Inferred from Sequence Orthology more info
involved_in inner ear morphogenesis	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within inner ear morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in inner ear morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within innervation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in limb development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within locomotory behavior	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within nose development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nose development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within olfactory behavior	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within olfactory bulb development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within olfactory nerve development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of multicellular organism growth	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in rRNA processing	IEA Inferred from Electronic Annotation more info
involved_in regulation of gene expression	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of growth hormone secretion	IEA Inferred from Electronic Annotation more info
involved_in regulation of growth hormone secretion	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of neurogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within response to bacterium	IEP Inferred from Expression Pattern more info	PubMed
involved_in retina development in camera-type eye	IEA Inferred from Electronic Annotation more info
involved_in retina development in camera-type eye	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within right ventricular compact myocardium morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within roof of mouth development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in secondary palate development	IEA Inferred from Electronic Annotation more info
involved_in secondary palate development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within semicircular canal morphogenesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within sensory perception of sound	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in skeletal system development	IEA Inferred from Electronic Annotation more info
involved_in skeletal system development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within tissue remodeling	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within ventricular trabecula myocardium morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in chromatin	IBA Inferred from Biological aspect of Ancestor 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
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	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: chromodomain-helicase-DNA-binding protein 7

Names: ATP-dependent helicase CHD7

NP_001264078.1

EC 3.6.4.12

NP_001342311.1

EC 3.6.4.12

XP_006538067.1

EC 3.6.4.12

XP_006538068.1

EC 3.6.4.12

XP_006538069.1

EC 3.6.4.12

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_001277149.1 → NP_001264078.1 chromodomain-helicase-DNA-binding protein 7 isoform 1

See identical proteins and their annotated locations for NP_001264078.1

Status: REVIEWED

Source sequence(s)

AL732627, AL805903

Consensus CDS

CCDS38689.1

UniProtKB/Swiss-Prot

A2AJK6, Q3TA86, Q3TAG7, Q3TBU4, Q8C986, Q8K244

Conserved Domains (6) summary

smart00592
Location:2631 → 2675

BRK; domain in transcription and CHROMO domain helicases

PLN03142
Location:957 → 1556

PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional

cd18663
Location:869 → 926

CD2_tandem_CHD5-9_like; repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins

cd18668
Location:786 → 850

CD1_tandem_CHD5-9_like; repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins

pfam03157
Location:23 → 553

Glutenin_hmw; High molecular weight glutenin subunit

pfam07533
Location:2552 → 2593

BRK; BRK domain
NM_001355382.1 → NP_001342311.1 chromodomain-helicase-DNA-binding protein 7 isoform 2

Status: REVIEWED

Source sequence(s)

AL732627, AL805903, CD540105, CJ102897, CN717040

Conserved Domains (3) summary

smart00592
Location:1396 → 1440

BRK; domain in transcription and CHROMO domain helicases

pfam07533
Location:1318 → 1358

BRK; BRK domain

cl26465
Location:2 → 322

SNF2_N; SNF2 family N-terminal domain

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_000070.7 Reference GRCm39 C57BL/6J

Range

8690345..8868449

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006538005.5 → XP_006538068.1 chromodomain-helicase-DNA-binding protein 7 isoform X2

See identical proteins and their annotated locations for XP_006538068.1

Conserved Domains (6) summary

smart00592
Location:2630 → 2674

BRK; domain in transcription and CHROMO domain helicases

PLN03142
Location:957 → 1556

PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional

cd18663
Location:869 → 926

CD2_tandem_CHD5-9_like; repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins

cd18668
Location:786 → 850

CD1_tandem_CHD5-9_like; repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins

pfam03157
Location:23 → 553

Glutenin_hmw; High molecular weight glutenin subunit

pfam07533
Location:2551 → 2592

BRK; BRK domain
XM_006538004.5 → XP_006538067.1 chromodomain-helicase-DNA-binding protein 7 isoform X1

See identical proteins and their annotated locations for XP_006538067.1

UniProtKB/Swiss-Prot

A2AJK6, Q3TA86, Q3TAG7, Q3TBU4, Q8C986, Q8K244

Related

ENSMUSP00000059079.4, ENSMUST00000051558.10

Conserved Domains (6) summary

smart00592
Location:2631 → 2675

BRK; domain in transcription and CHROMO domain helicases

PLN03142
Location:957 → 1556

PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional

cd18663
Location:869 → 926

CD2_tandem_CHD5-9_like; repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins

cd18668
Location:786 → 850

CD1_tandem_CHD5-9_like; repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins

pfam03157
Location:23 → 553

Glutenin_hmw; High molecular weight glutenin subunit

pfam07533
Location:2552 → 2593

BRK; BRK domain
XM_006538006.3 → XP_006538069.1 chromodomain-helicase-DNA-binding protein 7 isoform X3

Conserved Domains (3) summary

smart00592
Location:1397 → 1441

BRK; domain in transcription and CHROMO domain helicases

PLN03142
Location:2 → 322

PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional

pfam07533
Location:1318 → 1359

BRK; BRK domain

RNA

XR_004941924.1 RNA Sequence
XR_004941925.1 RNA Sequence
XR_003954972.2 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_001033395.1: Suppressed sequence

Description

NM_001033395.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.
NM_001081417.1: Suppressed sequence

Description

NM_001081417.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript.