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

    Gene ID: 71389, updated on 2-Oct-2018

    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 Vega:OTTMUSG00000001051
    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

    Genomic context

    See Chd6 in Genome Data Viewer
    Location:
    2; 2 H2
    Exon count:
    40
    Annotation release Status Assembly Chr Location
    106 current GRCm38.p4 (GCF_000001635.24) 2 NC_000068.7 (160946978..161109086, 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 14228 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)

    General gene information

    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    ATP binding 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
     
    hydrolase activity, acting on acid anhydrides 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 organization 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
     
    Component Evidence Code Pubs
    colocalizes_with 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
     

    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

    NCBI Reference Sequences (RefSeq)

    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
      ENSMUSP00000042291.7, OTTMUSP00000017124, ENSMUST00000039782.13, OTTMUST00000038183
      Conserved Domains (6) summary
      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.
      pfam00176
      Location:463750
      SNF2_N; SNF2 family N-terminal domain
      pfam00271
      Location:782896
      Helicase_C; Helicase conserved C-terminal domain
      pfam00385
      Location:375428
      Chromo; Chromo (CHRromatin Organization MOdifier) domain
      pfam08208
      Location:100170
      RNA_polI_A34; DNA-directed RNA polymerase I subunit RPA34.5
      cl02688
      Location:24022435
      BRK; BRK domain

    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 106

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

    Reference GRCm38.p4 C57BL/6J

    Genomic

    1. NC_000068.7 Reference GRCm38.p4 C57BL/6J

      Range
      160946978..161109086 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017319259.1XP_017174748.1  chromodomain-helicase-DNA-binding protein 6 isoform X4

      Conserved Domains (5) summary
      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.
      pfam00176
      Location:463750
      SNF2_N; SNF2 family N-terminal domain
      pfam00271
      Location:782896
      Helicase_C; Helicase conserved C-terminal domain
      pfam00385
      Location:375428
      Chromo; Chromo (CHRromatin Organization MOdifier) domain
      pfam08208
      Location:100170
      RNA_polI_A34; DNA-directed RNA polymerase I subunit RPA34.5
    2. XM_017319258.1XP_017174747.1  chromodomain-helicase-DNA-binding protein 6 isoform X1

      UniProtKB/Swiss-Prot
      A3KFM7
      Conserved Domains (6) summary
      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.
      pfam00176
      Location:463750
      SNF2_N; SNF2 family N-terminal domain
      pfam00271
      Location:782896
      Helicase_C; Helicase conserved C-terminal domain
      pfam00385
      Location:375428
      Chromo; Chromo (CHRromatin Organization MOdifier) domain
      pfam08208
      Location:100170
      RNA_polI_A34; DNA-directed RNA polymerase I subunit RPA34.5
      cl02688
      Location:24022435
      BRK; BRK domain
    3. XM_011239776.2XP_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
      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.
      pfam00176
      Location:462749
      SNF2_N; SNF2 family N-terminal domain
      pfam00271
      Location:781895
      Helicase_C; Helicase conserved C-terminal domain
      pfam00385
      Location:374427
      Chromo; Chromo (CHRromatin Organization MOdifier) domain
      pfam08208
      Location:100170
      RNA_polI_A34; DNA-directed RNA polymerase I subunit RPA34.5
      cl02688
      Location:24012434
      BRK; BRK domain
    4. XM_011239777.2XP_011238079.1  chromodomain-helicase-DNA-binding protein 6 isoform X3

      Conserved Domains (6) summary
      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.
      pfam00176
      Location:441728
      SNF2_N; SNF2 family N-terminal domain
      pfam00271
      Location:760874
      Helicase_C; Helicase conserved C-terminal domain
      pfam00385
      Location:353406
      Chromo; Chromo (CHRromatin Organization MOdifier) domain
      pfam08208
      Location:78148
      RNA_polI_A34; DNA-directed RNA polymerase I subunit RPA34.5
      cl02688
      Location:23802413
      BRK; BRK domain
    5. XM_006500184.3XP_006500247.1  chromodomain-helicase-DNA-binding protein 6 isoform X5

      Conserved Domains (2) summary
      pfam00271
      Location:106220
      Helicase_C; Helicase conserved C-terminal domain
      cl02688
      Location:17261759
      BRK; BRK domain

    RNA

    1. XR_001783180.1 RNA Sequence

    2. XR_001783182.1 RNA Sequence

    3. XR_001783181.1 RNA Sequence

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