chd7 chromodomain helicase DNA binding protein 7 [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: chd7provided by ZNC
Official Full Name: chromodomain helicase DNA binding protein 7provided by ZNC
Primary source: ZFIN:ZDB-GENE-070912-179
See related: Ensembl:ENSDARG00000075211 AllianceGenome:ZFIN:ZDB-GENE-070912-179
Gene type: protein coding
RefSeq status: MODEL
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: wu:fb37f10; wu:fb39h04; wu:fd19h06; wu:cegs2051; si:ch211-197o6.2
Summary: Predicted to enable several functions, including ATP binding activity; DNA binding activity; and DNA helicase activity. Involved in myelination and neuron development. Acts upstream of or within several processes, including animal organ development; nervous system development; and rRNA transcription. Predicted to be located in nucleus. Is expressed in several structures, including central nervous system; digestive system; gonad; musculature system; and somite. Used to study CHARGE syndrome. Human ortholog(s) of this gene implicated in CHARGE syndrome and hypogonadotropic hypogonadism 5 with or without anosmia. Orthologous to human CHD7 (chromodomain helicase DNA binding protein 7). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs: human mouse all
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Genomic context

Location:: chromosome: 2

Exon count:: 38

Annotation release	Status	Assembly	Chr	Location
106	current	GRCz11 (GCF_000002035.6)	2	NC_007113.7 (21765670..21820692, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	2	NC_007113.6 (22107608..22162635, complement)

Chromosome 2 - NC_007113.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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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?

CHD7 regulates craniofacial cartilage development via controlling HTR2B expression.
Title: CHD7 regulates craniofacial cartilage development via controlling HTR2B expression.
Deletion of the chd7 Hinders Oligodendrocyte Progenitor Cell Development and Myelination in Zebrafish.
Title: Deletion of the chd7 Hinders Oligodendrocyte Progenitor Cell Development and Myelination in Zebrafish.
Chromatin remodeler Chd7 regulates photoreceptor development and outer segment length.
Title: Chromatin remodeler Chd7 regulates photoreceptor development and outer segment length.
chd7 may control the expression of sema3E to regulate cranial neural crest cell migration
Title: Sema3E is required for migration of cranial neural crest cells in zebrafish: Implications for the pathogenesis of CHARGE syndrome.
chd7 was critical for thymic development and T-lymphopenia in CHARGE syndrome may be mainly attributed to the defects of thymic organogenesis.
Title: Chd7 Is Critical for Early T-Cell Development and Thymus Organogenesis in Zebrafish.
The conserved genetics and transparency of the zebrafish have provided new insights into the consequences of chd7 gene dysfunction on the GI system and cranial nerve patterning. These findings highlight the opportunity of the zebrafish to serve as a preclinical model for studying compounds that may improve GI motility in individuals with CHARGE syndrome.
Title: Etiology and functional validation of gastrointestinal motility dysfunction in a zebrafish model of CHARGE syndrome.
Our zebrafish CHARGE model thus reveals important regulatory roles for Chd7 at multiple points of neural crest development viz., migration, fate choice and differentiation and we suggest that sox10 deregulation is an important driver of the neural crest-derived aspects of Chd7 dependent CHARGE syndrome.
Title: Rescue of neural crest-derived phenotypes in a zebrafish CHARGE model by Sox10 downregulation.
knockdown of the jumonji domain-containing histone demethylase fbxl10/kdm2bb, a repressor of ribosomal RNA genes, rescues cell proliferation and cartilage defects in chd7 morphant embryos and can lead to complete rescue of the CHARGE syndrome phenotype.
Title: Knockdown of fbxl10/kdm2bb rescues chd7 morphant phenotype in a zebrafish model of CHARGE syndrome.
Chd7 is required for the organization of the neural retina in zebrafish.
Title: Role of Chd7 in zebrafish: a model for CHARGE syndrome.
Data show that Chd7 deficiency leads to asymmetric segmentation of the presomitic mesoderm (PSM), and results in the loss of asymmetric expression of spaw in the lateral plate mesoderm, which is consistent with more general laterality defects.
Title: Chd7 plays a critical role in controlling left-right symmetry during zebrafish somitogenesis.

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General gene information

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Markers

fb57e06.x1 (e-PCR)
- UniSTS:190778

fd11c06.x1 (e-PCR)
- UniSTS:204108

fb57e06 (e-PCR)
- UniSTS:187232

fb37f10.x1 (e-PCR)
- UniSTS:203158

fi32d07.x1 (e-PCR)
- UniSTS:197283

fi64b06.x1 (e-PCR)
- UniSTS:197805

AI722567 (e-PCR)
- UniSTS:206002

fc87d04.x1 (e-PCR)
- UniSTS:188351

AI444487 (e-PCR)
- UniSTS:206561

fd19h06.x1 (e-PCR)
- UniSTS:204261

Homology

NCBI Orthologs

Orthologs from OrthoDB

Clone Names

KIAA0308

Gene Ontology Provided by ZFIN

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-dependent chromatin remodeler activity	IBA Inferred from Biological aspect of Ancestor more info
enables ATP-dependent chromatin remodeler activity	IEA Inferred from Electronic Annotation more info
enables ATP-dependent chromatin remodeler activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables chromatin binding	IBA Inferred from Biological aspect of Ancestor more info
enables histone binding	IBA Inferred from Biological aspect of Ancestor more info
enables hydrolase activity	IEA Inferred from Electronic Annotation more info
enables nucleotide binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within T cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within auditory behavior	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within bone mineralization	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cartilage development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cartilage development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in central nervous system development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within central nervous system myelination	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in chordate embryonic development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within chordate embryonic development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in chromatin remodeling	IBA Inferred from Biological aspect of Ancestor more info
involved_in cranial nerve development	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within cranial nerve morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cranial skeletal system development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within cranial skeletal system development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within determination of left/right symmetry	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within digestive tract morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within embryonic cranial skeleton morphogenesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within embryonic cranial skeleton morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within heart development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within heart looping	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in heart morphogenesis	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within hematopoietic progenitor cell differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
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
acts_upstream_of_or_within intestinal motility	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in myelination	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within myelination in peripheral nervous system	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within myelination in peripheral nervous system	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neural crest cell migration	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neural crest formation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neuron development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neuron projection morphogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within otolith development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within peripheral nervous system neuron development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within_negative_effect photoreceptor cell outer segment organization	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within_positive_effect photoreceptor cell outer segment organization	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within pigmentation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within positive regulation of oligodendrocyte differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within primitive erythrocyte differentiation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within rRNA transcription	IGI Inferred from Genetic Interaction more info	PubMed
involved_in regulation of gene expression	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within retina development in camera-type eye	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within retinal cone cell development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within somitogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within swim bladder inflation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within thymus development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within visual behavior	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of chromatin	IBA Inferred from Biological aspect of Ancestor more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
is_active_in nucleus	IC Inferred by Curator more info	PubMed
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: chromodomain-helicase-DNA-binding protein 7

XP_697956.4

EC 3.6.4.12

NCBI Reference Sequences (RefSeq)

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RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...

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

Reference GRCz11 Primary Assembly

Genomic

NC_007113.7 Reference GRCz11 Primary Assembly

Range

21765670..21820692 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_692864.8 → XP_697956.4 chromodomain-helicase-DNA-binding protein 7

UniProtKB/TrEMBL

A0A8N7UVB1, F1QGL1

Related

ENSDARP00000114372.1, ENSDART00000135230.2

Conserved Domains (7) summary

smart00592
Location:2742 → 2786

BRK; domain in transcription and CHROMO domain helicases

cd00024
Location:845 → 906

CHROMO; Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence ...

cd00046
Location:1031 → 1180

DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

pfam00176
Location:1015 → 1310

SNF2_N; SNF2 family N-terminal domain

pfam00271
Location:1342 → 1456

Helicase_C; Helicase conserved C-terminal domain

pfam00385
Location:927 → 978

Chromo; Chromo (CHRromatin Organization MOdifier) domain

pfam15240
Location:322 → 491

Pro-rich; Proline-rich