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

Gene ID: 71389, updated on 8-May-2016
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 Vega:OTTMUSG00000001051
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Mus musculus
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Sciurognathi; 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]
Orthologs
Location:
2; 2 H2
Exon count:
40
Annotation release Status Assembly Chr Location
105 current GRCm38.p3 (GCF_000001635.23) 2 NC_000068.7 (160946978..161109102, complement)
Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 2 NC_000068.6 (160772714..160934792, complement)

Chromosome 2 - NC_000068.7Genomic Context describing neighboring genes Neighboring gene elastin microfibril interfacer 3 Neighboring gene predicted gene, 35181 Neighboring gene predicted gene, 39976 Neighboring gene glyceraldehyde-3-phosphate dehydrogenase pseudogene

Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
ATP binding IEA
Inferred from Electronic Annotation
more info
 
ATP-dependent helicase activity IEA
Inferred from Electronic Annotation
more info
 
DNA binding IEA
Inferred from Electronic Annotation
more info
 
DNA-dependent ATPase activity ISO
Inferred from Sequence Orthology
more info
 
helicase activity IEA
Inferred from Electronic Annotation
more info
 
hydrolase activity IEA
Inferred from Electronic Annotation
more info
 
nucleic acid binding IEA
Inferred from Electronic Annotation
more info
 
nucleotide binding IEA
Inferred from Electronic Annotation
more info
 
transcription cofactor binding ISO
Inferred from Sequence Orthology
more info
 
Process Evidence Code Pubs
chromatin modification IEA
Inferred from Electronic Annotation
more info
 
positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress ISO
Inferred from Sequence Orthology
more info
 
regulation of transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
colocalizes_with DNA-directed RNA polymerase II, core complex ISO
Inferred from Sequence Orthology
more info
 
nucleoplasm ISO
Inferred from Sequence Orthology
more info
 
nucleus IEA
Inferred from Electronic Annotation
more info
 
Preferred Names
chromodomain-helicase-DNA-binding protein 6
Names
ATP-dependent helicase CHD6
NP_775544.2

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
    UniProtKB/TrEMBL
    Q8BJ75
    Related
    ENSMUSP00000042291, OTTMUSP00000017124, ENSMUST00000039782, OTTMUST00000038183
    Conserved Domains (6) summary
    cd00024
    Location:375426
    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:479628
    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.
    cd00079
    Location:782904
    HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...
    pfam00176
    Location:463750
    SNF2_N; SNF2 family N-terminal domain
    pfam07533
    Location:23992436
    BRK; BRK domain
    pfam08208
    Location:101170
    RNA_polI_A34; DNA-directed RNA polymerase I subunit RPA34.5

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: Mus musculus Annotation Release 105 details...

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

Reference GRCm38.p3 C57BL/6J

Genomic

  1. NC_000068.7 Reference GRCm38.p3 C57BL/6J

    Range
    160946978..161109102 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006500181.2XP_006500244.1  

    See identical proteins and their annotated locations for XP_006500244.1

    UniProtKB/Swiss-Prot
    A3KFM7
    Conserved Domains (6) summary
    cd00024
    Location:374425
    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:478627
    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.
    cd00079
    Location:781903
    HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...
    pfam00176
    Location:462749
    SNF2_N; SNF2 family N-terminal domain
    pfam07533
    Location:23982435
    BRK; BRK domain
    pfam08208
    Location:101170
    RNA_polI_A34; DNA-directed RNA polymerase I subunit RPA34.5
  2. XM_011239778.1XP_011238080.1  

    Conserved Domains (5) summary
    cd00024
    Location:375426
    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:479628
    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.
    cd00079
    Location:782904
    HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...
    pfam00176
    Location:463750
    SNF2_N; SNF2 family N-terminal domain
    pfam08208
    Location:101170
    RNA_polI_A34; DNA-directed RNA polymerase I subunit RPA34.5
  3. XM_011239776.1XP_011238078.1  

    See identical proteins and their annotated locations for XP_011238078.1

    UniProtKB/Swiss-Prot
    A3KFM7
    Conserved Domains (6) summary
    cd00024
    Location:374425
    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:478627
    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.
    cd00079
    Location:781903
    HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...
    pfam00176
    Location:462749
    SNF2_N; SNF2 family N-terminal domain
    pfam07533
    Location:23982435
    BRK; BRK domain
    pfam08208
    Location:101170
    RNA_polI_A34; DNA-directed RNA polymerase I subunit RPA34.5
  4. XM_011239777.1XP_011238079.1  

    Conserved Domains (6) summary
    cd00024
    Location:353404
    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:457606
    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.
    cd00079
    Location:760882
    HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...
    pfam00176
    Location:441728
    SNF2_N; SNF2 family N-terminal domain
    pfam07533
    Location:23772414
    BRK; BRK domain
    pfam08208
    Location:79148
    RNA_polI_A34; DNA-directed RNA polymerase I subunit RPA34.5
  5. XM_006500184.2XP_006500247.1  

    Conserved Domains (2) summary
    cd00079
    Location:106228
    HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...
    pfam07533
    Location:17231760
    BRK; BRK domain
  6. XM_011239779.1XP_011238081.1  

    Conserved Domains (1) summary
    pfam07533
    Location:10491086
    BRK; BRK domain

RNA

  1. XR_374526.2 RNA Sequence

  2. XR_866342.1 RNA Sequence

    Related
    ENSMUST00000134178, OTTMUST00000002093
  3. XR_866341.1 RNA Sequence

Alternate Mm_Celera

Genomic

  1. AC_000024.1 Alternate Mm_Celera

    Range
    166877653..167040039 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)