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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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