Chd7 chromodomain helicase DNA binding protein 7 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Chd7provided by RGD
Official Full Name: chromodomain helicase DNA binding protein 7provided by RGD
Primary source: RGD:1311921
See related: Ensembl:ENSRNOG00000006689 AllianceGenome:RGD:1311921
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable RNA polymerase II cis-regulatory region sequence-specific DNA binding activity and promoter-specific chromatin binding activity. Predicted to be involved in several processes, including animal organ development; nervous system development; and regulation of growth hormone secretion. Predicted to act upstream of or within several processes, including adult walking behavior; animal organ development; and nervous system development. Predicted to be located in nucleolus and nucleoplasm. 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]
Expression: Biased expression in Spleen (RPKM 51.6), Brain (RPKM 50.0) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 5q13

Exon count:: 39

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	5	NC_086023.1 (26609245..26792736)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	5	NC_051340.1 (21812007..21995358)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	5	NC_005104.4 (21769087..21952036)

Chromosome 5 - NC_086023.1 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: 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?

Submit: New GeneRIF Correction

General gene information

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Markers

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

AA998568 (e-PCR)
- UniSTS:248626

RH135218 (e-PCR)
- UniSTS:218495

AI231343 (e-PCR)
- UniSTS:260790

Gene Ontology Provided by RGD

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 DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology 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 promoter-specific chromatin binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in T cell differentiation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within adult heart development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within adult walking behavior	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within aorta development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within aorta morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within artery morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within atrioventricular canal development	ISO Inferred from Sequence Orthology more info
involved_in biological_process	ND No biological Data available more info
acts_upstream_of_or_within blood circulation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within blood vessel development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within blood vessel remodeling	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within camera-type eye development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cardiac septum morphogenesis	ISO Inferred from Sequence Orthology more info
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 remodeling	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within chromatin remodeling	ISO Inferred from Sequence Orthology 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	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within embryonic hindlimb morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within epithelium development	ISO Inferred from Sequence Orthology more info
involved_in face development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within female genitalia development	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
involved_in heart morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within in utero embryonic development	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info
involved_in inner ear morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within innervation	ISO Inferred from Sequence Orthology more info
involved_in limb development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within locomotory behavior	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within nose development	ISO Inferred from Sequence Orthology more info
involved_in nose development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within olfactory behavior	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within olfactory bulb development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within olfactory nerve development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of multicellular organism growth	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in regulation of gene expression	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of growth hormone secretion	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of neurogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within response to bacterium	ISO Inferred from Sequence Orthology 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	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within roof of mouth development	ISO Inferred from Sequence Orthology more info
involved_in secondary palate development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within semicircular canal morphogenesis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within sensory perception of sound	ISO Inferred from Sequence Orthology more info
involved_in skeletal system development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within tissue remodeling	ISO Inferred from Sequence Orthology more info
acts_upstream_of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within ventricular trabecula myocardium morphogenesis	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of 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	ISO Inferred from Sequence Orthology more info

General protein information

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

NP_001101376.2

EC 3.6.4.12

XP_006237910.1

EC 3.6.4.12

XP_038965692.1

EC 3.6.4.12

XP_038965693.1

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_001107906.4 → NP_001101376.2 chromodomain-helicase-DNA-binding protein 7

Status: VALIDATED

Source sequence(s)

JAXUCZ010000005

UniProtKB/TrEMBL

D3ZAP7

Related

ENSRNOP00000008901.7, ENSRNOT00000008901.8

Conserved Domains (7) summary

smart00592
Location:2630 → 2674

BRK; domain in transcription and CHROMO domain helicases

PLN03142
Location:956 → 1555

PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional

pfam09606
Location:2 → 318

Med15; ARC105 or Med15 subunit of Mediator complex non-fungal

cd18663
Location:868 → 925

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:785 → 849

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

pfam03154
Location:194 → 582

Atrophin-1; Atrophin-1 family

pfam07533
Location:2552 → 2594

BRK; BRK 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_086023.1 Reference GRCr8

Range

26609245..26792736

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006237848.5 → XP_006237910.1 chromodomain-helicase-DNA-binding protein 7 isoform X2

UniProtKB/TrEMBL

D3ZAP7

Conserved Domains (8) summary

smart00592
Location:2629 → 2673

BRK; domain in transcription and CHROMO domain helicases

cd00046
Location:976 → 1125

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.

pfam08430
Location:299 → 416

Forkhead_N; Forkhead N-terminal region

pfam09606
Location:182 → 567

Med15; ARC105 or Med15 subunit of Mediator complex non-fungal

pfam00176
Location:960 → 1247

SNF2_N; SNF2 family N-terminal domain

pfam00271
Location:1279 → 1393

Helicase_C; Helicase conserved C-terminal domain

pfam00385
Location:872 → 924

Chromo; Chromo (CHRromatin Organization MOdifier) domain

pfam07533
Location:2551 → 2591

BRK; BRK domain
XM_039109764.2 → XP_038965692.1 chromodomain-helicase-DNA-binding protein 7 isoform X1

UniProtKB/TrEMBL

D3ZAP7

Conserved Domains (7) summary

smart00592
Location:2630 → 2674

BRK; domain in transcription and CHROMO domain helicases

PLN03142
Location:956 → 1555

PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional

pfam09606
Location:2 → 318

Med15; ARC105 or Med15 subunit of Mediator complex non-fungal

cd18663
Location:868 → 925

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:785 → 849

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

pfam03154
Location:194 → 582

Atrophin-1; Atrophin-1 family

pfam07533
Location:2552 → 2594

BRK; BRK domain
XM_039109765.2 → XP_038965693.1 chromodomain-helicase-DNA-binding protein 7 isoform X3

Conserved Domains (6) summary

smart00592
Location:1836 → 1880

BRK; domain in transcription and CHROMO domain helicases

PLN03142
Location:162 → 761

PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional

cd18663
Location:74 → 131

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:1 → 55

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

pfam07533
Location:1758 → 1800

BRK; BRK domain

cl28899
Location:163 → 384

DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily