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

Gene ID: 71389, updated on 9-May-2024

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
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Genomic context

See Chd6 in Genome Data Viewer
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_000068.8Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC118568533 Neighboring gene elastin microfibril interfacer 3 Neighboring gene STARR-seq mESC enhancer starr_06266 Neighboring gene predicted gene, 35181 Neighboring gene STARR-seq mESC enhancer starr_06268 Neighboring gene predicted gene, 25561 Neighboring gene STARR-positive B cell enhancer ABC_E1015 Neighboring gene STARR-seq mESC enhancer starr_06271 Neighboring gene STARR-seq mESC enhancer starr_06275 Neighboring gene STARR-seq mESC enhancer starr_06276 Neighboring gene glyceraldehyde-3-phosphate dehydrogenase pseudogene Neighboring gene M phase phosphoprotein 6 pseudogene

Genomic regions, transcripts, and products

Expression

  • 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

Variation

Alleles

Alleles of this type are documented at Mouse Genome Informatics  (MGI)
  • Endonuclease-mediated (1) 
  • Targeted (2)  1 citation

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

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

Preferred Names
chromodomain-helicase-DNA-binding protein 6
Names
ATP-dependent helicase CHD6
NP_775544.2
XP_006500247.1
XP_011238078.1
XP_011238079.1
XP_017174747.1
XP_017174748.1
XP_030107940.1
XP_030107941.1
XP_036018463.1

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)

  1. NM_173368.3NP_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:101372
    PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
    PLN03142
    Location:459984
    PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
    cd18663
    Location:371429
    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:287352
    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:24022435
    BRK; BRK domain
    cl28899
    Location:460681
    DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily

RNA

  1. 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

  1. NC_000068.8 Reference GRCm39 C57BL/6J

    Range
    160788898..160951006 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011239776.4XP_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:100371
    PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
    PLN03142
    Location:458983
    PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
    cd18663
    Location:370428
    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:286351
    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:24012434
    BRK; BRK domain
    cl28899
    Location:459680
    DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily
  2. XM_036162570.1XP_036018463.1  chromodomain-helicase-DNA-binding protein 6 isoform X4

    Conserved Domains (6) summary
    PTZ00449
    Location:101372
    PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
    PLN03142
    Location:459984
    PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
    cd18663
    Location:371429
    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:287352
    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:23802413
    BRK; BRK domain
    cl28899
    Location:460681
    DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily
  3. XM_017319259.3XP_017174748.1  chromodomain-helicase-DNA-binding protein 6 isoform X5

    Conserved Domains (5) summary
    PTZ00449
    Location:101372
    PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
    PLN03142
    Location:459984
    PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
    cd18663
    Location:371429
    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:287352
    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:460681
    DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily
  4. XM_017319258.3XP_017174747.1  chromodomain-helicase-DNA-binding protein 6 isoform X1

    UniProtKB/Swiss-Prot
    A3KFM7, B9EKA7, Q3UQS6, Q80TE9
    Conserved Domains (6) summary
    PTZ00449
    Location:101372
    PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
    PLN03142
    Location:459984
    PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
    cd18663
    Location:371429
    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:287352
    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:24022435
    BRK; BRK domain
    cl28899
    Location:460681
    DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily
  5. XM_030252080.2XP_030107940.1  chromodomain-helicase-DNA-binding protein 6 isoform X3

    Conserved Domains (6) summary
    PTZ00449
    Location:79350
    PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
    PLN03142
    Location:437962
    PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
    cd18663
    Location:349407
    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:265330
    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:23802413
    BRK; BRK domain
    cl28899
    Location:438659
    DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily
  6. XM_011239777.4XP_011238079.1  chromodomain-helicase-DNA-binding protein 6 isoform X3

    Conserved Domains (6) summary
    PTZ00449
    Location:79350
    PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional
    PLN03142
    Location:437962
    PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
    cd18663
    Location:349407
    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:265330
    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:23802413
    BRK; BRK domain
    cl28899
    Location:438659
    DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily
  7. XM_006500184.4XP_006500247.1  chromodomain-helicase-DNA-binding protein 6 isoform X6

    Conserved Domains (2) summary
    PLN03142
    Location:2308
    PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional
    cl02688
    Location:17261759
    BRK; BRK domain
  8. XM_030252081.1XP_030107941.1  chromodomain-helicase-DNA-binding protein 6 isoform X7

    Conserved Domains (1) summary
    cl02688
    Location:10521085
    BRK; BRK domain

RNA

  1. XR_001783180.3 RNA Sequence

  2. XR_004940730.1 RNA Sequence

  3. XR_001783181.3 RNA Sequence