Chd6 chromodomain helicase DNA binding protein 6 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Chd6provided by MGI
Official Full Name: chromodomain helicase DNA binding protein 6provided by MGI
Primary source: MGI:MGI:1918639
See related: Ensembl:ENSMUSG00000057133 AllianceGenome:MGI:1918639
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: CHD-6; 5430439G14Rik; 6330406J24Rik
Summary: This gene encodes a member of the chromodomain/helicase/DNA-binding domain family of chromatin remodeling enzymes. This protein has been found to be specifically involved in transcription initiation and elongation. Homozygous knockout mice exhibit impaired motor coordination. A pseudogene has been identified on chromosome 8. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Nov 2014]
Expression: Ubiquitous expression in CNS E14 (RPKM 9.4), CNS E11.5 (RPKM 9.2) and 28 other tissues See more
Orthologs: human all
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Genomic context

Location:: 2 H2; 2 80.98 cM

Exon count:: 40

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	2	NC_000068.8 (160788898..160951006, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	2	NC_000068.7 (160946978..161109086, complement)

Chromosome 2 - NC_000068.8 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
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?

The genomic location, expression pattern, and ataxic phenotype of Chd6 Exon 12 -/- mice indicate that mutations within CHD6 may be responsible for ataxias.
Title: Deletion of the Chd6 exon 12 affects motor coordination.
CHD6 colocalizes with both hypo- and hyper-phosphorlylated forms of RNA polymerase II. CHD6 was found to be present at sites of mRNA synthesis and to be part of a high molecular weight complex.
Title: CHD6 is a DNA-dependent ATPase and localizes at nuclear sites of mRNA synthesis.

Submit: New GeneRIF Correction

Variation

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Alleles

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

Targeted (2) 1 citation
Endonuclease-mediated (1)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

NoName (e-PCR)
- UniSTS:234564

NoName (e-PCR)
- UniSTS:234568

14.MMHAP4FLE2.seq (e-PCR)
- UniSTS:123213

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-dependent activity, acting on DNA	ISO Inferred from Sequence Orthology 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 chromatin binding	IBA Inferred from Biological aspect of Ancestor more info
enables helicase activity	IEA Inferred from Electronic Annotation 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
enables transcription coregulator binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in cell redox homeostasis	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within chromatin organization	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	IBA Inferred from Biological aspect of Ancestor more info
involved_in 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

Component	Evidence Code	Pubs
part_of 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

General protein information

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Preferred Names: chromodomain-helicase-DNA-binding protein 6

Names: ATP-dependent helicase CHD6

NP_775544.2

EC 3.6.4.12

XP_006500247.1

EC 3.6.4.12

XP_011238078.1

EC 3.6.4.12

XP_011238079.1

EC 3.6.4.12

XP_017174747.1

EC 3.6.4.12

XP_017174748.1

EC 3.6.4.12

XP_030107940.1

EC 3.6.4.12

XP_030107941.1

EC 3.6.4.12

XP_036018463.1

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_173368.3 → NP_775544.2 chromodomain-helicase-DNA-binding protein 6

See identical proteins and their annotated locations for NP_775544.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript. This variant encodes the protein.

Source sequence(s)

AK018129, AK040495, AK080892, AK142177, AL590430, BU708927, CJ075254, CN526286, CN664107, CN664285, CO433513, CV559963

Consensus CDS

CCDS17000.1

UniProtKB/Swiss-Prot

A3KFM7, B9EKA7, Q3UQS6, Q80TE9

Related

ENSMUSP00000042291.8, ENSMUST00000039782.14

Conserved Domains (6) summary

PTZ00449
Location:101 → 372

PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional

PLN03142
Location:459 → 984

PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional

cd18663
Location:371 → 429

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:287 → 352

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

cl02688
Location:2402 → 2435

BRK; BRK domain

cl28899
Location:460 → 681

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

RNA

NR_126509.1 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses alternate splice sites at two internal exons and lacks an alternate internal exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AK018129, AK040495, AK080892, AK142177, AL590430, BU708927, CJ075254, CN664107, CO433513, CV559963

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_000068.8 Reference GRCm39 C57BL/6J

Range

160788898..160951006 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011239776.4 → XP_011238078.1 chromodomain-helicase-DNA-binding protein 6 isoform X2

See identical proteins and their annotated locations for XP_011238078.1

UniProtKB/Swiss-Prot

A3KFM7

Conserved Domains (6) summary

PTZ00449
Location:100 → 371

PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional

PLN03142
Location:458 → 983

PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional

cd18663
Location:370 → 428

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:286 → 351

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

cl02688
Location:2401 → 2434

BRK; BRK domain

cl28899
Location:459 → 680

DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily
XM_036162570.1 → XP_036018463.1 chromodomain-helicase-DNA-binding protein 6 isoform X4

Conserved Domains (6) summary

PTZ00449
Location:101 → 372

PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional

PLN03142
Location:459 → 984

PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional

cd18663
Location:371 → 429

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:287 → 352

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

cl02688
Location:2380 → 2413

BRK; BRK domain

cl28899
Location:460 → 681

DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily
XM_017319259.3 → XP_017174748.1 chromodomain-helicase-DNA-binding protein 6 isoform X5

Conserved Domains (5) summary

PTZ00449
Location:101 → 372

PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional

PLN03142
Location:459 → 984

PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional

cd18663
Location:371 → 429

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:287 → 352

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

cl28899
Location:460 → 681

DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily
XM_017319258.3 → XP_017174747.1 chromodomain-helicase-DNA-binding protein 6 isoform X1

UniProtKB/Swiss-Prot

A3KFM7, B9EKA7, Q3UQS6, Q80TE9

Conserved Domains (6) summary

PTZ00449
Location:101 → 372

PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional

PLN03142
Location:459 → 984

PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional

cd18663
Location:371 → 429

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:287 → 352

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

cl02688
Location:2402 → 2435

BRK; BRK domain

cl28899
Location:460 → 681

DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily
XM_030252080.2 → XP_030107940.1 chromodomain-helicase-DNA-binding protein 6 isoform X3

Conserved Domains (6) summary

PTZ00449
Location:79 → 350

PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional

PLN03142
Location:437 → 962

PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional

cd18663
Location:349 → 407

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:265 → 330

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

cl02688
Location:2380 → 2413

BRK; BRK domain

cl28899
Location:438 → 659

DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily
XM_011239777.4 → XP_011238079.1 chromodomain-helicase-DNA-binding protein 6 isoform X3

Conserved Domains (6) summary

PTZ00449
Location:79 → 350

PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional

PLN03142
Location:437 → 962

PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional

cd18663
Location:349 → 407

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:265 → 330

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

cl02688
Location:2380 → 2413

BRK; BRK domain

cl28899
Location:438 → 659

DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily
XM_006500184.4 → XP_006500247.1 chromodomain-helicase-DNA-binding protein 6 isoform X6

Conserved Domains (2) summary

PLN03142
Location:2 → 308

PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional

cl02688
Location:1726 → 1759

BRK; BRK domain
XM_030252081.1 → XP_030107941.1 chromodomain-helicase-DNA-binding protein 6 isoform X7

Conserved Domains (1) summary

cl02688
Location:1052 → 1085

BRK; BRK domain