Chd8 chromodomain helicase DNA binding protein 8 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Chd8provided by RGD
Official Full Name: chromodomain helicase DNA binding protein 8provided by RGD
Primary source: RGD:620696
See related: EnsemblRapid:ENSRNOG00000025011 AllianceGenome:RGD:620696
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
Also known as: CHD-8
Summary: This gene encodes a member of the chromodomain-helicase-DNA binding protein family, which is characterized by a SNF2-like domain and two chromatin organization modifier domains. The encoded protein also contains brahma and kismet domains, which is common to the subfamily of chromodomain-helicase-DNA binding proteins to which this protein belongs. In mammals, this gene has been shown to function in several processes including transcriptional regulation, epigenetic remodeling, promotion of cell proliferation, and regulation of RNA synthesis. Knockout of this gene in mice causes early embryonic lethality due to widespread apoptosis. Heterozygous loss of function mutations in mice result in autism spectrum disorder-like behaviors that include increased anxiety, repetitive behavior, and altered social behavior. [provided by RefSeq, Dec 2016]
Expression: Biased expression in Thymus (RPKM 153.8), Spleen (RPKM 135.5) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 15p14

Exon count:: 39

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	15	NC_086033.1 (27379285..27438959, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	15	NC_051350.1 (24905789..24965461, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	15	NC_005114.4 (28612932..28672574, complement)

Chromosome 15 - NC_086033.1 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 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?

Data indicate that CHD8 exhibits a dual function through inducing a cascade of chromatin reprogramming and recruiting H3K4 histone methyltransferases to establish oligodendrocyte identity.
Title: Dual Requirement of CHD8 for Chromatin Landscape Establishment and Histone Methyltransferase Recruitment to Promote CNS Myelination and Repair.
These data add Chd8 to the short list of known nuclear AKAPs, and implicate a function for Chd8 in post-natal rat cardiac development
Title: Chromodomain helicase binding protein 8 (Chd8) is a novel A-kinase anchoring protein expressed during rat cardiac development.

Submit: New GeneRIF Correction

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

BF393768 (e-PCR)
- UniSTS:244234

RH135273 (e-PCR)
- UniSTS:218550

WI-14045 (e-PCR)
- UniSTS:39614

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP binding	ISO Inferred from Sequence Orthology more info
enables ATP binding	ISS Inferred from Sequence or Structural Similarity 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	ISO Inferred from Sequence Orthology more info
enables ATP-dependent chromatin remodeler activity	ISS Inferred from Sequence or Structural Similarity more info
enables DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA binding	ISO Inferred from Sequence Orthology more info
enables DNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables DNA helicase activity	IEA Inferred from Electronic Annotation more info
enables armadillo repeat domain binding	IPI Inferred from Physical Interaction more info	PubMed
enables beta-catenin binding	IDA Inferred from Direct Assay more info	PubMed
enables beta-catenin binding	IEA Inferred from Electronic Annotation more info
enables beta-catenin binding	ISO Inferred from Sequence Orthology more info
enables chromatin binding	IBA Inferred from Biological aspect of Ancestor more info
enables chromatin binding	IEA Inferred from Electronic Annotation more info
enables chromatin binding	ISO Inferred from Sequence Orthology more info
enables histone binding	IBA Inferred from Biological aspect of Ancestor more info
enables histone binding	IEA Inferred from Electronic Annotation more info
enables histone binding	ISO Inferred from Sequence Orthology more info
enables histone binding	ISS Inferred from Sequence or Structural Similarity more info
enables hydrolase activity	IEA Inferred from Electronic Annotation more info
enables methylated histone binding	IEA Inferred from Electronic Annotation more info
enables methylated histone binding	ISO Inferred from Sequence Orthology more info
enables methylated histone binding	ISS Inferred from Sequence or Structural Similarity more info
enables p53 binding	IEA Inferred from Electronic Annotation more info
enables p53 binding	ISO Inferred from Sequence Orthology more info
enables p53 binding	ISS Inferred from Sequence or Structural Similarity more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA duplex unwinding	IEA Inferred from Electronic Annotation more info
involved_in Wnt signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in brain development	IBA Inferred from Biological aspect of Ancestor more info
involved_in brain development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within brain development	ISO Inferred from Sequence Orthology more info
involved_in brain development	ISO Inferred from Sequence Orthology more info
involved_in chromatin remodeling	IBA Inferred from Biological aspect of Ancestor more info
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	ISO Inferred from Sequence Orthology more info
involved_in chromatin remodeling	ISS Inferred from Sequence or Structural Similarity more info
involved_in digestive tract development	IBA Inferred from Biological aspect of Ancestor more info
involved_in digestive tract development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within digestive tract development	ISO Inferred from Sequence Orthology more info
involved_in digestive tract 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 mRNA processing	IEA Inferred from Electronic Annotation more info
involved_in mRNA processing	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of DNA-templated transcription	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of Wnt signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of Wnt signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of apoptotic process	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of apoptotic process	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of canonical Wnt signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of canonical Wnt signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of canonical Wnt signaling pathway	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of canonical Wnt signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of canonical Wnt signaling pathway	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of fibroblast apoptotic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within negative regulation of fibroblast apoptotic process	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation 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	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of DNA-templated transcription	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of DNA-templated transcription	ISS Inferred from Sequence or Structural Similarity more info
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 positive regulation of transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of transcription by RNA polymerase III	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of transcription by RNA polymerase III	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase III	ISS Inferred from Sequence or Structural Similarity more info
involved_in prepulse inhibition	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within prepulse inhibition	ISO Inferred from Sequence Orthology more info
involved_in social behavior	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within social behavior	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within startle response	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of MLL1 complex	IBA Inferred from Biological aspect of Ancestor more info
part_of MLL1 complex	IEA Inferred from Electronic Annotation more info
part_of MLL1 complex	ISO Inferred from Sequence Orthology more info
part_of MLL1 complex	ISS Inferred from Sequence or Structural Similarity more info
located_in chromatin	IBA Inferred from Biological aspect of Ancestor 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
part_of protein-containing complex	IDA Inferred from Direct Assay more info	PubMed
part_of protein-containing complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: chromodomain-helicase-DNA-binding protein 8

Names: ATP-dependent helicase CHD8; axis duplication inhibitor; beta-catenin binding protein; duplin

NP_001334590.1

EC 3.6.4.12

XP_006251970.1

EC 3.6.4.12

XP_006251971.1

EC 3.6.4.12

XP_006251972.1

EC 3.6.4.12

XP_006251974.1

EC 3.6.4.12

XP_038949571.1

EC 3.6.4.12

XP_063130687.1

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_001347661.1 → NP_001334590.1 chromodomain-helicase-DNA-binding protein 8

Status: VALIDATED

Source sequence(s)

AF169825, JAXUCZ010000015

UniProtKB/Swiss-Prot

Q9JIX5

UniProtKB/TrEMBL

A0A8L2QBK0

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_086033.1 Reference GRCr8

Range

27379285..27438959 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063274617.1 → XP_063130687.1 chromodomain-helicase-DNA-binding protein 8 isoform X2

UniProtKB/Swiss-Prot

Q9JIX5
XM_006251912.5 → XP_006251974.1 chromodomain-helicase-DNA-binding protein 8 isoform X3

UniProtKB/TrEMBL

A0A8L2QBK0

Related

ENSRNOP00000022593.7, ENSRNOT00000022593.8

Conserved Domains (6) summary

cd00024
Location:644 → 704

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:830 → 979

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:814 → 1101

SNF2_N; SNF2 family N-terminal domain

pfam00271
Location:1133 → 1247

Helicase_C; Helicase conserved C-terminal domain

pfam00385
Location:725 → 781

Chromo; Chromo (CHRromatin Organization MOdifier) domain

cl02688
Location:2327 → 2366

BRK; BRK domain
XM_006251908.5 → XP_006251970.1 chromodomain-helicase-DNA-binding protein 8 isoform X1

See identical proteins and their annotated locations for XP_006251970.1

UniProtKB/TrEMBL

A0A8L2QBK0, A0A8L2R557

Conserved Domains (7) summary

smart00592
Location:2318 → 2362

BRK; domain in transcription and CHROMO domain helicases

cd00024
Location:644 → 704

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:830 → 979

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:814 → 1101

SNF2_N; SNF2 family N-terminal domain

pfam00271
Location:1133 → 1247

Helicase_C; Helicase conserved C-terminal domain

pfam00385
Location:725 → 781

Chromo; Chromo (CHRromatin Organization MOdifier) domain

cl02688
Location:2387 → 2426

BRK; BRK domain
XM_006251910.5 → XP_006251972.1 chromodomain-helicase-DNA-binding protein 8 isoform X1

See identical proteins and their annotated locations for XP_006251972.1

UniProtKB/TrEMBL

A0A8L2QBK0, A0A8L2R557

Conserved Domains (7) summary

smart00592
Location:2318 → 2362

BRK; domain in transcription and CHROMO domain helicases

cd00024
Location:644 → 704

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:830 → 979

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:814 → 1101

SNF2_N; SNF2 family N-terminal domain

pfam00271
Location:1133 → 1247

Helicase_C; Helicase conserved C-terminal domain

pfam00385
Location:725 → 781

Chromo; Chromo (CHRromatin Organization MOdifier) domain

cl02688
Location:2387 → 2426

BRK; BRK domain
XM_006251909.5 → XP_006251971.1 chromodomain-helicase-DNA-binding protein 8 isoform X1

See identical proteins and their annotated locations for XP_006251971.1

UniProtKB/TrEMBL

A0A8L2QBK0, A0A8L2R557

Related

ENSRNOP00000071948.2, ENSRNOT00000087722.3

Conserved Domains (7) summary

smart00592
Location:2318 → 2362

BRK; domain in transcription and CHROMO domain helicases

cd00024
Location:644 → 704

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:830 → 979

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:814 → 1101

SNF2_N; SNF2 family N-terminal domain

pfam00271
Location:1133 → 1247

Helicase_C; Helicase conserved C-terminal domain

pfam00385
Location:725 → 781

Chromo; Chromo (CHRromatin Organization MOdifier) domain

cl02688
Location:2387 → 2426

BRK; BRK domain
XM_039093643.2 → XP_038949571.1 chromodomain-helicase-DNA-binding protein 8 isoform X4

Conserved Domains (7) summary

PTZ00121
Location:447 → 583

PTZ00121; MAEBL; Provisional

PLN03142
Location:810 → 1409

PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional

PHA03247
Location:68 → 279

PHA03247; large tegument protein UL36; Provisional

cd18663
Location:721 → 779

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:638 → 703

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

cd18060
Location:811 → 1032

DEXHc_CHD8; DEAH-box helicase domain of the chromodomain helicase DNA binding protein 8

cl41773
Location:143 → 442

SP1-4_N; N-terminal domain of transcription factor Specificity Proteins (SP) 1-4

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_022933.2: Suppressed sequence

Description

NM_022933.2: This RefSeq was removed because currently there is insufficient support for the transcript.