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    chd4a chromodomain helicase DNA binding protein 4a [ Danio rerio (zebrafish) ]

    Gene ID: 558344, updated on 9-Dec-2024

    Summary

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    Official Symbol
    chd4aprovided by ZNC
    Official Full Name
    chromodomain helicase DNA binding protein 4aprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-041111-187
    See related
    Ensembl:ENSDARG00000063535 AllianceGenome:ZFIN:ZDB-GENE-041111-187
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    im:7143343; si:ch211-51m24.3
    Summary
    Predicted to enable several functions, including ATP hydrolysis activity; ATP-dependent chromatin remodeler activity; and histone binding activity. Acts upstream of or within fin regeneration. Predicted to be located in chromatin. Predicted to be part of NuRD complex. Predicted to be active in nucleus. Is expressed in blastomere and central nervous system. Human ortholog(s) of this gene implicated in Sifrim-Hitz-Weiss syndrome; colorectal cancer (multiple); lung cancer (multiple); and lymphoma. Orthologous to human CHD4 (chromodomain helicase DNA binding protein 4). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    all
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    Genomic context

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    See chd4a in Genome Data Viewer
    Location:
    chromosome: 19
    Exon count:
    41
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 19 NC_007130.7 (5000885..5058908, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 19 NC_007130.6 (5084399..5142422, complement)

    Chromosome 19 - NC_007130.7Genomic Context describing neighboring genes Neighboring gene StAR related lipid transfer domain containing 3 Neighboring gene zgc:91968 Neighboring gene enolase 2 Neighboring gene uncharacterized LOC137488464 Neighboring gene triosephosphate isomerase 1a

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • BioProject: PRJEB1986
    • Analysis date: Fri Dec 8 19:48:10 2017

    Bibliography

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    Related articles in PubMed

    1. The chromatin remodeler chd5 is necessary for proper head development during embryogenesis of Danio rerio. Bishop B, et al. Biochim Biophys Acta, 2015 Aug. PMID 26092436, Free PMC Article
    2. Specific NuRD components are required for fin regeneration in zebrafish. Pfefferli C, et al. BMC Biol, 2014 Apr 29. PMID 24779377, Free PMC Article
    3. Rescue of neural crest-derived phenotypes in a zebrafish CHARGE model by Sox10 downregulation. Asad Z, et al. Hum Mol Genet, 2016 Aug 15. PMID 27418670, Free PMC Article
    4. Biphasic Role of Tgf-β Signaling during Müller Glia Reprogramming and Retinal Regeneration in Zebrafish. Sharma P, et al. iScience, 2020 Feb 21. PMID 32004993, Free PMC Article
    5. Expansion of transducin subunit gene families in early vertebrate tetraploidizations. Lagman D, et al. Genomics, 2012 Oct. PMID 22814267

    See all (10) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP-dependent chromatin remodeler activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables helicase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables hydrolase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables nucleotide binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within fin regeneration IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    chromodomain-helicase-DNA-binding protein 4a
    Names
    chromodomain helicase DNA binding protein 4
    NP_001038323.1
    XP_005159409.1
    XP_021323760.1

    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_001044858.1 → NP_001038323.1  chromodomain-helicase-DNA-binding protein 4a

      Status: PROVISIONAL

      Source sequence(s)
      BX004850
      UniProtKB/TrEMBL
      A0A8N7UY84, E7EZ96, Q1LYP4
      Related
      ENSDARP00000111640.2, ENSDART00000130062.3
      Conserved Domains (11) summary
      cd00024
      Location:522 → 559
      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:731 → 889
      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.
      cd15531
      Location:356 → 398
      PHD1_CHD_II; PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      cd15532
      Location:433 → 475
      PHD2_CHD_II; PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      pfam00176
      Location:714 → 1010
      SNF2_N; SNF2 family N-terminal domain
      pfam00271
      Location:1034 → 1149
      Helicase_C; Helicase conserved C-terminal domain
      pfam00385
      Location:607 → 659
      Chromo; Chromo (CHRromatin Organization MOdifier) domain
      pfam06461
      Location:1361 → 1495
      DUF1086; Domain of Unknown Function (DUF1086)
      pfam06465
      Location:1270 → 1327
      DUF1087; Domain of Unknown Function (DUF1087)
      pfam08073
      Location:153 → 205
      CHDNT; CHDNT (NUC034) domain
      pfam08074
      Location:1740 → 1915
      CHDCT2; CHDCT2 (NUC038) domain

    RefSeqs of Annotated Genomes: GCF_000002035.6-RS_2024_08

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007130.7 Reference GRCz11 Primary Assembly

      Range
      5000885..5058908 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005159352.4 → XP_005159409.1  chromodomain-helicase-DNA-binding protein 4a isoform X2

      UniProtKB/TrEMBL
      A0A8M2B5Z8
      Conserved Domains (11) summary
      cd00024
      Location:521 → 558
      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:730 → 888
      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.
      cd15531
      Location:355 → 397
      PHD1_CHD_II; PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      cd15532
      Location:432 → 474
      PHD2_CHD_II; PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      pfam00176
      Location:713 → 1009
      SNF2_N; SNF2 family N-terminal domain
      pfam00271
      Location:1033 → 1148
      Helicase_C; Helicase conserved C-terminal domain
      pfam00385
      Location:606 → 658
      Chromo; Chromo (CHRromatin Organization MOdifier) domain
      pfam06461
      Location:1367 → 1501
      DUF1086; Domain of Unknown Function (DUF1086)
      pfam06465
      Location:1279 → 1333
      DUF1087; Domain of Unknown Function (DUF1087)
      pfam08073
      Location:153 → 205
      CHDNT; CHDNT (NUC034) domain
      pfam08074
      Location:1746 → 1916
      CHDCT2; CHDCT2 (NUC038) domain

    2. XM_021468085.2 → XP_021323760.1  chromodomain-helicase-DNA-binding protein 4a isoform X1

      UniProtKB/TrEMBL
      A0A8M9PRM2
      Conserved Domains (11) summary
      cd00024
      Location:522 → 559
      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 ...
      cd15531
      Location:356 → 398
      PHD1_CHD_II; PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      cd15532
      Location:433 → 475
      PHD2_CHD_II; PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      pfam00385
      Location:607 → 659
      Chromo; Chromo (CHRromatin Organisation MOdifier) domain
      pfam06461
      Location:1368 → 1502
      DUF1086; Domain of Unknown Function (DUF1086)
      pfam06465
      Location:1280 → 1334
      DUF1087; Domain of Unknown Function (DUF1087)
      pfam08073
      Location:153 → 206
      CHDNT; CHDNT (NUC034) domain
      pfam08074
      Location:1747 → 1917
      CHDCT2; CHDCT2 (NUC038) domain
      cl25580
      Location:196 → 280
      OxoGdeHyase_C; 2-oxoglutarate dehydrogenase C-terminal
      cl26465
      Location:709 → 1250
      SNF2_N; SNF2 family N-terminal domain
      cl26511
      Location:1547 → 1713
      Neuromodulin_N; Gap junction protein N-terminal region
    Nucleotide Protein Strain
    Heading Accession and Version

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