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    kdm4b lysine (K)-specific demethylase 4B [ Danio rerio (zebrafish) ]

    Gene ID: 556504, updated on 9-Dec-2024

    Summary

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    Official Symbol
    kdm4bprovided by ZNC
    Official Full Name
    lysine (K)-specific demethylase 4Bprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-060503-664
    See related
    Ensembl:ENSDARG00000099675 AllianceGenome:ZFIN:ZDB-GENE-060503-664
    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
    jmjd2b; si:ch211-124a3.4
    Summary
    Predicted to enable histone H3K9 demethylase activity. Predicted to be involved in chromatin remodeling and regulation of gene expression. Predicted to act upstream of or within chromatin organization. Predicted to be located in chromatin. Predicted to be active in nucleus. Is expressed in caudal hematopoietic tissue. Human ortholog(s) of this gene implicated in autosomal dominant intellectual developmental disorder; breast cancer; colorectal cancer; malignant peripheral nerve sheath tumor; and stomach cancer. Orthologous to human KDM4B (lysine demethylase 4B). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    all
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    Genomic context

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    See kdm4b in Genome Data Viewer
    Location:
    chromosome: 22
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 22 NC_007133.7 (4315256..4407871, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 22 NC_007133.6 (3862408..3955023, complement)

    Chromosome 22 - NC_007133.7Genomic Context describing neighboring genes Neighboring gene major histocompatibility complex class I ULA Neighboring gene uncharacterized LOC101883897 Neighboring gene uncharacterized LOC110438264 Neighboring gene ubiquitin-like with PHD and ring finger domains 1 Neighboring gene TIR domain containing adaptor molecule 1

    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 histone demethylase Jmjd3 regulates zebrafish myeloid development by promoting spi1 expression. Yu SH, et al. Biochim Biophys Acta Gene Regul Mech, 2018 Feb. PMID 29378332, Free PMC Article
    2. Zbtb46 Controls Dendritic Cell Activation by Reprogramming Epigenetic Regulation of cd80/86 and cd40 Costimulatory Signals in a Zebrafish Model. Shao T, et al. J Immunol, 2022 Jun 15. PMID 35675955
    3. The Kdm/Kmt gene families in the self-fertilizing mangrove rivulus fish, Kryptolebias marmoratus, suggest involvement of histone methylation machinery in development and reproduction. Fellous A, et al. Gene, 2019 Mar 1. PMID 30458291
    4. A network of epigenetic regulators guides developmental haematopoiesis in vivo. Huang HT, et al. Nat Cell Biol, 2013 Dec. PMID 24240475, Free PMC Article
    5. 15000 unique zebrafish EST clusters and their future use in microarray for profiling gene expression patterns during embryogenesis. Lo J, et al. Genome Res, 2003 Mar. PMID 12618376, Free PMC Article

    See all (7) 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 dioxygenase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H3K9 demethylase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables histone H3K9me2/H3K9me3 demethylase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables oxidoreductase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within chromatin organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in chromatin remodeling IBA
    Inferred from Biological aspect of Ancestor
    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
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    lysine-specific demethylase 4B
    Names
    jumonji domain containing 2B
    NP_001076274.1

    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_001082805.1 → NP_001076274.1  lysine-specific demethylase 4B

      See identical proteins and their annotated locations for NP_001076274.1

      Status: PROVISIONAL

      Source sequence(s)
      BX927276, CU074310
      UniProtKB/TrEMBL
      A0A8M9P494, B7ZVT3, Q1LUQ0
      Related
      ENSDARP00000133766.1, ENSDART00000162523.2
      Conserved Domains (7) summary
      smart00545
      Location:95 → 136
      JmjN; Small domain found in the jumonji family of transcription factors
      PRK00404
      Location:978 → 1099
      tatB; sec-independent translocase; Provisional
      smart00333
      Location:905 → 953
      TUDOR; Tudor domain
      pfam02373
      Location:256 → 372
      JmjC; JmjC domain, hydroxylase
      cd15576
      Location:676 → 774
      PHD_JMJD2B; PHD finger found in Jumonji domain-containing protein 2B (JMJD2B)
      pfam07321
      Location:408 → 512
      YscO; Type III secretion protein YscO
      cl22851
      Location:783 → 892
      PHD_SF; PHD finger superfamily

    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_007133.7 Reference GRCz11 Primary Assembly

      Range
      4315256..4407871 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein Strain
    Heading Accession and Version

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