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

    Gene ID: 71389, updated on 27-Nov-2024

    Summary

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    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
    VALIDATED
    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

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    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

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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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    Related articles in PubMed

    1. Deletion of the Chd6 exon 12 affects motor coordination. Lathrop MJ, et al. Mamm Genome, 2010 Apr. PMID 20111866, Free PMC Article
    2. CHD chromatin remodelling enzymes and the DNA damage response. Stanley FK, et al. Mutat Res, 2013 Oct. PMID 23954449
    3. CHD6, a cellular repressor of influenza virus replication, is degraded in human alveolar epithelial cells and mice lungs during infection. Alfonso R, et al. J Virol, 2013 Apr. PMID 23408615, Free PMC Article
    4. CHD6 is a DNA-dependent ATPase and localizes at nuclear sites of mRNA synthesis. Lutz T, et al. FEBS Lett, 2006 Oct 30. PMID 17027977
    5. TWIST1 and chromatin regulatory proteins interact to guide neural crest cell differentiation. Fan X, et al. Elife, 2021 Feb 8. PMID 33554859, Free PMC Article

    See all (28) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Variation

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    Alleles

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

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    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 hydrolysis activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP-dependent H2AZ histone chaperone activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP-dependent H3-H4 histone complex chaperone activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP-dependent activity, acting on DNA ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables ATP-dependent activity, acting on DNA ISS
    Inferred from Sequence or Structural Similarity
    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 DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA clamp loader activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables chromatin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables chromatin extrusion motor activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables cohesin loader activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables double-stranded DNA helicase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables forked DNA-dependent helicase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables four-way junction helicase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables single-stranded 3'-5' DNA helicase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables transcription coregulator 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 DNA duplex unwinding IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cell redox homeostasis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cell redox homeostasis ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in chromatin looping IEA
    Inferred from Electronic Annotation
    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 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 regulation of gene expression IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in chromatin IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleoplasm ISS
    Inferred from Sequence or Structural Similarity
    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
    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_173368.4 → NP_775544.2  chromodomain-helicase-DNA-binding protein 6

      See identical proteins and their annotated locations for NP_775544.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript. This variant encodes the protein.
      Source sequence(s)
      AL590430, AL591763
      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

    1. NR_126509.2 RNA Sequence

      Status: VALIDATED

      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)
      AL590430, AL591763

    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_011239776.4 → 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

    2. 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

    3. 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

    4. 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

    5. 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

    6. 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

    7. 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

    8. 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

    RNA

    1. XR_001783180.3 RNA Sequence

    2. XR_004940730.1 RNA Sequence

    3. XR_001783181.3 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    A3KFM7.1 GenPept UniProtKB/Swiss-Prot:A3KFM7

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