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    chd4b chromodomain helicase DNA binding protein 4b [ Danio rerio (zebrafish) ]

    Gene ID: 560622, updated on 9-Dec-2024

    Summary

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    Official Symbol
    chd4bprovided by ZNC
    Official Full Name
    chromodomain helicase DNA binding protein 4bprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-030131-4532
    See related
    Ensembl:ENSDARG00000025789 AllianceGenome:ZFIN:ZDB-GENE-030131-4532
    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
    Also known as
    wu:fb44b12; wu:fd12d03; si:ch211-57k11.10
    Summary
    Predicted to enable several functions, including ATP hydrolysis activity; ATP-dependent chromatin remodeler activity; and histone binding activity. Predicted to be involved in chromatin remodeling. Predicted to be located in chromatin. Predicted to be part of NuRD complex. Predicted to be active in nucleus. Is expressed in blastomere; central nervous system; hematopoietic multipotent progenitor cell; and telencephalon. 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 chd4b in Genome Data Viewer
    Location:
    chromosome: 16
    Exon count:
    40
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 16 NC_007127.7 (31762714..31791089, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 16 NC_007127.6 (31807126..31835649, complement)

    Chromosome 16 - NC_007127.7Genomic Context describing neighboring genes Neighboring gene retinol binding protein 1a, cellular Neighboring gene protein tyrosine phosphatase non-receptor type 6 Neighboring gene wingless-type MMTV integration site family, member 4b Neighboring gene cell division cycle 42, like

    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. Nuclear S-nitrosylation impacts tissue regeneration in zebrafish. Matrone G, et al. Nat Commun, 2021 Nov 1. PMID 34725362, Free PMC Article
    3. Specific NuRD components are required for fin regeneration in zebrafish. Pfefferli C, et al. BMC Biol, 2014 Apr 29. PMID 24779377, 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 (14) 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
    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
    		  
    Component Evidence Code Pubs
    part_of NuRD complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in 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 4
    Names
    chromodomain helicase DNA binding protein 4

    NCBI Reference Sequences (RefSeq)

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    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_007127.7 Reference GRCz11 Primary Assembly

      Range
      31762714..31791089 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_021466939.2 → XP_021322614.1  chromodomain-helicase-DNA-binding protein 4 isoform X2

      UniProtKB/TrEMBL
      A0A8M9PDP3, A0A8M9PN35
      Conserved Domains (10) summary
      smart00298
      Location:634 → 686
      CHROMO; Chromatin organization modifier domain
      cd00024
      Location:546 → 585
      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:377 → 419
      PHD1_CHD_II; PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      cd15532
      Location:459 → 501
      PHD2_CHD_II; PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      pfam06461
      Location:1393 → 1527
      DUF1086; Domain of Unknown Function (DUF1086)
      pfam06465
      Location:1308 → 1358
      DUF1087; Domain of Unknown Function (DUF1087)
      pfam08073
      Location:155 → 210
      CHDNT; CHDNT (NUC034) domain
      pfam08074
      Location:1765 → 1935
      CHDCT2; CHDCT2 (NUC038) domain
      cl26465
      Location:734 → 1274
      SNF2_N; SNF2 family N-terminal domain
      cl26511
      Location:1530 → 1734
      Neuromodulin_N; Gap junction protein N-terminal region

    2. XM_021466938.2 → XP_021322613.1  chromodomain-helicase-DNA-binding protein 4 isoform X1

      UniProtKB/TrEMBL
      A0A8M9P8D7, A0A8M9PN35, F1RBT2
      Related
      ENSDARP00000124629.1, ENSDART00000148389.2
      Conserved Domains (10) summary
      smart00298
      Location:634 → 686
      CHROMO; Chromatin organization modifier domain
      cd00024
      Location:546 → 585
      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:377 → 419
      PHD1_CHD_II; PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      cd15532
      Location:459 → 501
      PHD2_CHD_II; PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      pfam06461
      Location:1397 → 1531
      DUF1086; Domain of Unknown Function (DUF1086)
      pfam06465
      Location:1308 → 1358
      DUF1087; Domain of Unknown Function (DUF1087)
      pfam08073
      Location:155 → 210
      CHDNT; CHDNT (NUC034) domain
      pfam08074
      Location:1769 → 1939
      CHDCT2; CHDCT2 (NUC038) domain
      cl26465
      Location:734 → 1274
      SNF2_N; SNF2 family N-terminal domain
      cl26511
      Location:1534 → 1738
      Neuromodulin_N; Gap junction protein N-terminal region

    Reference GRCz11 ALT_DRER_TU_1

    Genomic

    1. NW_018394963.1 Reference GRCz11 ALT_DRER_TU_1

      Range
      27646..54301 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_021473007.2 → XP_021328682.1  chromodomain-helicase-DNA-binding protein 4 isoform X2

      UniProtKB/TrEMBL
      A0A8M9PC64, A0A8M9PN35
      Conserved Domains (10) summary
      smart00298
      Location:633 → 685
      CHROMO; Chromatin organization modifier domain
      cd00024
      Location:545 → 584
      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:376 → 418
      PHD1_CHD_II; PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      cd15532
      Location:458 → 500
      PHD2_CHD_II; PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      pfam06461
      Location:1392 → 1526
      DUF1086; Domain of Unknown Function (DUF1086)
      pfam06465
      Location:1307 → 1357
      DUF1087; Domain of Unknown Function (DUF1087)
      pfam08073
      Location:155 → 210
      CHDNT; CHDNT (NUC034) domain
      pfam08074
      Location:1764 → 1934
      CHDCT2; CHDCT2 (NUC038) domain
      cl26465
      Location:733 → 1273
      SNF2_N; SNF2 family N-terminal domain
      cl26511
      Location:1529 → 1733
      Neuromodulin_N; Gap junction protein N-terminal region

    2. XM_680607.10 → XP_685699.5  chromodomain-helicase-DNA-binding protein 4 isoform X1

      UniProtKB/TrEMBL
      A0A8M9PN35, A0A8N7T760
      Conserved Domains (10) summary
      smart00298
      Location:633 → 685
      CHROMO; Chromatin organization modifier domain
      cd00024
      Location:545 → 584
      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:376 → 418
      PHD1_CHD_II; PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      cd15532
      Location:458 → 500
      PHD2_CHD_II; PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins
      pfam06461
      Location:1396 → 1530
      DUF1086; Domain of Unknown Function (DUF1086)
      pfam06465
      Location:1307 → 1357
      DUF1087; Domain of Unknown Function (DUF1087)
      pfam08073
      Location:155 → 210
      CHDNT; CHDNT (NUC034) domain
      pfam08074
      Location:1768 → 1938
      CHDCT2; CHDCT2 (NUC038) domain
      cl26465
      Location:733 → 1273
      SNF2_N; SNF2 family N-terminal domain
      cl26511
      Location:1533 → 1737
      Neuromodulin_N; Gap junction protein N-terminal region

    3. XM_068218819.1 → XP_068074920.1  chromodomain-helicase-DNA-binding protein 4 isoform X3

      UniProtKB/TrEMBL
      A0A8M9PN35, A0A8M9PNR4
    Nucleotide Protein Strain
    Heading Accession and Version

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