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    chd3 chromodomain helicase DNA binding protein 3 [ Danio rerio (zebrafish) ]

    Gene ID: 568230, updated on 25-Apr-2024

    Summary

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    Official Symbol
    chd3provided by ZNC
    Official Full Name
    chromodomain helicase DNA binding protein 3provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-121031-4
    See related
    Ensembl:ENSDARG00000021405 AllianceGenome:ZFIN:ZDB-GENE-121031-4
    Gene type
    protein coding
    RefSeq status
    MODEL
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Summary
    Predicted to enable several functions, including ATP binding activity; DNA helicase activity; and metal ion binding activity. Acts upstream of or within central nervous system development and developmental growth. Is expressed in blastomere and central nervous system. Orthologous to human CHD3 (chromodomain helicase DNA binding protein 3). [provided by Alliance of Genome Resources, Apr 2022]
    Orthologs
    human mouse all
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    Genomic context

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    See chd3 in Genome Data Viewer
    Location:
    chromosome: 7
    Exon count:
    41
    Annotation release Status Assembly Chr Location
    106 current GRCz11 (GCF_000002035.6) 7 NC_007118.7 (20671611..20768805, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 7 NC_007118.6 (20418916..20518963, complement)

    Chromosome 7 - NC_007118.7Genomic Context describing neighboring genes Neighboring gene spermidine/spermine N1-acetyltransferase family member 2a, tandem duplicate 2 Neighboring gene TNF superfamily member 12 Neighboring gene cytochrome b5 domain containing 1 Neighboring gene DnaJ (Hsp40) homolog, subfamily C, member 3b

    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. Large-scale discovery of novel genetic causes of developmental disorders. Deciphering Developmental Disorders Study. Nature, 2015 Mar 12. PMID 25533962, Free PMC Article
    4. 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
    5. 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

    See all (13) citations in PubMed

    GeneRIFs: Gene References Into Functions

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by ZFIN

    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 chromatin remodeler activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables ATP-dependent chromatin remodeler activity IEA
    Inferred from Electronic Annotation
    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 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 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 central nervous system development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in chromatin remodeling IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within developmental growth IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    part_of NuRD complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of chromatin IBA
    Inferred from Biological aspect of Ancestor
    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 3
    XP_005172292.1
    XP_009301392.1
    XP_009301393.1
    XP_021327560.1
    XP_021327561.1
    XP_021327562.1

    NCBI Reference Sequences (RefSeq)

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    RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...Open this link in a new tab

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007118.7 Reference GRCz11 Primary Assembly

      Range
      20671611..20768805 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005172235.4 → XP_005172292.1  chromodomain-helicase-DNA-binding protein 3 isoform X3

      UniProtKB/TrEMBL
      A0A8M2BK27
      Related
      ENSDARP00000127601.2, ENSDART00000156717.2
      Conserved Domains (10) summary
      cd00046
      Location:767 → 925
      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:385 → 427
      PHD1_CHD_II; PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      cd15532
      Location:470 → 512
      PHD2_CHD_II; PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      pfam00176
      Location:750 → 1046
      SNF2_N; SNF2 family N-terminal domain
      pfam00271
      Location:1070 → 1185
      Helicase_C; Helicase conserved C-terminal domain
      pfam00385
      Location:647 → 681
      Chromo; Chromo (CHRromatin Organization MOdifier) domain
      pfam06461
      Location:1397 → 1536
      DUF1086; Domain of Unknown Function (DUF1086)
      pfam06465
      Location:1324 → 1368
      DUF1087; Domain of Unknown Function (DUF1087)
      pfam08073
      Location:181 → 233
      CHDNT; CHDNT (NUC034) domain
      pfam08074
      Location:1809 → 1980
      CHDCT2; CHDCT2 (NUC038) domain

    2. XM_009303118.3 → XP_009301393.1  chromodomain-helicase-DNA-binding protein 3 isoform X2

      UniProtKB/TrEMBL
      A0A8M3AU49
      Related
      ENSDARP00000147575.1, ENSDART00000182629.1
      Conserved Domains (10) summary
      cd00046
      Location:767 → 925
      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:385 → 427
      PHD1_CHD_II; PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      cd15532
      Location:470 → 512
      PHD2_CHD_II; PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      pfam00176
      Location:750 → 1046
      SNF2_N; SNF2 family N-terminal domain
      pfam00271
      Location:1070 → 1185
      Helicase_C; Helicase conserved C-terminal domain
      pfam00385
      Location:647 → 681
      Chromo; Chromo (CHRromatin Organization MOdifier) domain
      pfam06461
      Location:1396 → 1535
      DUF1086; Domain of Unknown Function (DUF1086)
      pfam06465
      Location:1323 → 1367
      DUF1087; Domain of Unknown Function (DUF1087)
      pfam08073
      Location:181 → 233
      CHDNT; CHDNT (NUC034) domain
      pfam08074
      Location:1808 → 1979
      CHDCT2; CHDCT2 (NUC038) domain

    3. XM_009303117.3 → XP_009301392.1  chromodomain-helicase-DNA-binding protein 3 isoform X1

      UniProtKB/TrEMBL
      A0A8M3B137
      Conserved Domains (10) summary
      cd00046
      Location:767 → 925
      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:385 → 427
      PHD1_CHD_II; PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      cd15532
      Location:470 → 512
      PHD2_CHD_II; PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      pfam00176
      Location:750 → 1046
      SNF2_N; SNF2 family N-terminal domain
      pfam00271
      Location:1070 → 1185
      Helicase_C; Helicase conserved C-terminal domain
      pfam00385
      Location:647 → 681
      Chromo; Chromo (CHRromatin Organization MOdifier) domain
      pfam06461
      Location:1397 → 1536
      DUF1086; Domain of Unknown Function (DUF1086)
      pfam06465
      Location:1324 → 1368
      DUF1087; Domain of Unknown Function (DUF1087)
      pfam08073
      Location:181 → 233
      CHDNT; CHDNT (NUC034) domain
      pfam08074
      Location:1809 → 1980
      CHDCT2; CHDCT2 (NUC038) domain

    Reference GRCz11 ALT_DRER_TU_1

    Genomic

    1. NW_018394685.1 Reference GRCz11 ALT_DRER_TU_1

      Range
      282349..346684 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_021471887.1 → XP_021327562.1  chromodomain-helicase-DNA-binding protein 3 isoform X6

      UniProtKB/TrEMBL
      A0A8M9P9H4
      Conserved Domains (3) summary
      pfam06461
      Location:271 → 410
      DUF1086; Domain of Unknown Function (DUF1086)
      pfam08074
      Location:683 → 854
      CHDCT2; CHDCT2 (NUC038) domain
      cl26465
      Location:9 → 352
      SNF2_N; SNF2 family N-terminal domain

    2. XM_021471886.1 → XP_021327561.1  chromodomain-helicase-DNA-binding protein 3 isoform X5

      UniProtKB/TrEMBL
      A0A8M9PYZ0
      Conserved Domains (3) summary
      pfam06461
      Location:270 → 409
      DUF1086; Domain of Unknown Function (DUF1086)
      pfam08074
      Location:682 → 853
      CHDCT2; CHDCT2 (NUC038) domain
      cl26465
      Location:9 → 351
      SNF2_N; SNF2 family N-terminal domain

    3. XM_021471885.1 → XP_021327560.1  chromodomain-helicase-DNA-binding protein 3 isoform X4

      UniProtKB/TrEMBL
      A0A8M9Q2B2
      Conserved Domains (3) summary
      pfam06461
      Location:271 → 410
      DUF1086; Domain of Unknown Function (DUF1086)
      pfam08074
      Location:683 → 854
      CHDCT2; CHDCT2 (NUC038) domain
      cl26465
      Location:9 → 352
      SNF2_N; SNF2 family N-terminal domain
    Nucleotide Protein Strain
    Heading Accession and Version

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