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    kdm3b lysine (K)-specific demethylase 3B [ Danio rerio (zebrafish) ]

    Gene ID: 326643, updated on 4-Jan-2025

    Summary

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    Official Symbol
    kdm3bprovided by ZNC
    Official Full Name
    lysine (K)-specific demethylase 3Bprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-101007-4
    See related
    Ensembl:ENSDARG00000062267 AllianceGenome:ZFIN:ZDB-GENE-101007-4
    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
    Also known as
    jmjd1b; im:7163548; wu:fa12c09; wu:fe01c10
    Summary
    Predicted to enable histone H3K9me/H3K9me2 demethylase activity and metal ion binding activity. Predicted to be involved in demethylation. Predicted to be located in nucleus. Is expressed in female organism. Orthologous to human KDM3B (lysine demethylase 3B). [provided by Alliance of Genome Resources, Jan 2025]
    Orthologs
    human mouse all
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    Genomic context

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    See kdm3b in Genome Data Viewer
    Location:
    chromosome: 14
    Exon count:
    26
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 14 NC_007125.7 (21622876..21660569, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 14 NC_007125.6 (21325633..21363353, complement)

    Chromosome 14 - NC_007125.7Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC137487582 Neighboring gene receptor accessory protein 2 Neighboring gene uncharacterized LOC103908747 Neighboring gene NADH:ubiquinone oxidoreductase core subunit S8b

    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. 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
    3. Brain transcriptome analysis of a familial Alzheimer's disease-like mutation in the zebrafish presenilin 1 gene implies effects on energy production. Newman M, et al. Mol Brain, 2019 May 3. PMID 31053140, Free PMC Article
    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. RFX transcription factors are essential for hearing in mice. Elkon R, et al. Nat Commun, 2015 Oct 15. PMID 26469318, 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 histone H3K9 demethylase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H3K9me/H3K9me2 demethylase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in demethylation IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    lysine-specific demethylase 3B
    XP_005173195.1
    XP_005173196.1
    XP_005173197.1
    XP_005173198.1
    XP_005173199.1
    XP_021328444.1
    XP_021328445.1
    XP_021328446.1
    XP_068069431.1
    XP_068069432.1
    XP_068069433.1
    XP_068074854.1

    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_007125.7 Reference GRCz11 Primary Assembly

      Range
      21622876..21660569 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_068213332.1 → XP_068069433.1  lysine-specific demethylase 3B isoform X8

    2. XM_005173142.5 → XP_005173199.1  lysine-specific demethylase 3B isoform X6

      UniProtKB/TrEMBL
      A0A8M2BKF8
      Conserved Domains (2) summary
      smart00558
      Location:1511 → 1581
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      cl21464
      Location:1627 → 1719
      cupin_like; Conserved domain found in cupin and related proteins

    3. XM_068213331.1 → XP_068069432.1  lysine-specific demethylase 3B isoform X7

      Related
      ENSDARP00000084278.5, ENSDART00000089845.6

    4. XM_005173141.5 → XP_005173198.1  lysine-specific demethylase 3B isoform X5

      UniProtKB/TrEMBL
      A0A0R4ISI0, A0A8M2BKF5
      Related
      ENSDARP00000138150.3, ENSDART00000172442.3
      Conserved Domains (2) summary
      smart00558
      Location:1512 → 1582
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      cl21464
      Location:1628 → 1720
      cupin_like; Conserved domain found in cupin and related proteins

    5. XM_068213330.1 → XP_068069431.1  lysine-specific demethylase 3B isoform X4

    6. XM_005173139.5 → XP_005173196.1  lysine-specific demethylase 3B isoform X2

      UniProtKB/TrEMBL
      A0A0R4IDZ5, A0A8M2BKG5
      Related
      ENSDARP00000133582.1, ENSDART00000161713.2
      Conserved Domains (2) summary
      smart00558
      Location:1558 → 1628
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      cl21464
      Location:1674 → 1766
      cupin_like; Conserved domain found in cupin and related proteins

    7. XM_005173140.5 → XP_005173197.1  lysine-specific demethylase 3B isoform X3

      UniProtKB/TrEMBL
      A0A8M2BKG3
      Conserved Domains (2) summary
      smart00558
      Location:1559 → 1629
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      cl21464
      Location:1667 → 1759
      cupin_like; Conserved domain found in cupin and related proteins

    8. XM_005173138.5 → XP_005173195.1  lysine-specific demethylase 3B isoform X1

      UniProtKB/TrEMBL
      A0A8M2BKX2
      Conserved Domains (2) summary
      smart00558
      Location:1559 → 1629
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      cl21464
      Location:1675 → 1767
      cupin_like; Conserved domain found in cupin and related proteins

    Reference GRCz11 ALT_DRER_TU_1

    Genomic

    1. NW_018394903.1 Reference GRCz11 ALT_DRER_TU_1

      Range
      442392..465837 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_068218753.1 → XP_068074854.1  lysine-specific demethylase 3B isoform X12

    2. XM_021472770.1 → XP_021328445.1  lysine-specific demethylase 3B isoform X10

      UniProtKB/TrEMBL
      A0A8M9Q560
      Conserved Domains (2) summary
      smart00558
      Location:407 → 477
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      cl21464
      Location:523 → 615
      cupin_like; Conserved domain found in cupin and related proteins

    3. XM_021472771.1 → XP_021328446.1  lysine-specific demethylase 3B isoform X11

      UniProtKB/TrEMBL
      A0A8M9Q1E0
      Conserved Domains (2) summary
      smart00558
      Location:408 → 478
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      cl21464
      Location:516 → 608
      cupin_like; Conserved domain found in cupin and related proteins

    4. XM_021472769.1 → XP_021328444.1  lysine-specific demethylase 3B isoform X9

      UniProtKB/TrEMBL
      A0A8M9PUA8
      Conserved Domains (2) summary
      smart00558
      Location:408 → 478
      JmjC; A domain family that is part of the cupin metalloenzyme superfamily
      cl21464
      Location:524 → 616
      cupin_like; Conserved domain found in cupin and related proteins
    Nucleotide Protein Strain
    Heading Accession and Version

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