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    kdm4ab lysine (K)-specific demethylase 4A, genome duplicate b [ Danio rerio (zebrafish) ]

    Gene ID: 334347, updated on 9-Dec-2024

    Summary

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    Official Symbol
    kdm4abprovided by ZNC
    Official Full Name
    lysine (K)-specific demethylase 4A, genome duplicate bprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-030131-6279
    See related
    Ensembl:ENSDARG00000019103 AllianceGenome:ZFIN:ZDB-GENE-030131-6279
    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
    Jmjd2a; jmjd2al; wu:fi42b08; si:ch211-262l3.1
    Summary
    Predicted to enable histone H3K36 demethylase activity and histone H3K9 demethylase activity. Acts upstream of or within blood vessel morphogenesis. Predicted to be located in chromatin. Predicted to be active in nucleus. Orthologous to human KDM4A (lysine demethylase 4A). [provided by Alliance of Genome Resources, Dec 2024]
    Orthologs
    all
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    Genomic context

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    See kdm4ab in Genome Data Viewer
    Location:
    chromosome: 2
    Exon count:
    22
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 2 NC_007113.7 (17450227..17492067, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 2 NC_007113.6 (17779058..17820920, complement)

    Chromosome 2 - NC_007113.7Genomic Context describing neighboring genes Neighboring gene artemin Neighboring gene ST3 beta-galactoside alpha-2,3-sialyltransferase 3b Neighboring gene uncharacterized LOC137487458 Neighboring gene Pim proto-oncogene, serine/threonine kinase, related 199

    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. Histone Demethylases KDM4A and KDM4C Regulate Differentiation of Embryonic Stem Cells to Endothelial Cells. Wu L, et al. Stem Cell Reports, 2015 Jul 14. PMID 26120059, Free PMC Article
    2. Hypoxia drives transient site-specific copy gain and drug-resistant gene expression. Black JC, et al. Genes Dev, 2015 May 15. PMID 25995187, Free PMC Article
    3. Revealing sex-specific molecular changes in hypoxia-ischemia induced neural damage and subsequent recovery using zebrafish model. Das T, et al. Neurosci Lett, 2019 Nov 1. PMID 31518677
    4. Variation of DNA Methylome of Zebrafish Cells under Cold Pressure. Han B, et al. PLoS One, 2016. PMID 27494266, Free PMC Article
    5. Whole exome sequencing coupled with unbiased functional analysis reveals new Hirschsprung disease genes. Gui H, et al. Genome Biol, 2017 Mar 8. PMID 28274275, 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 dioxygenase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone H3K36 demethylase activity IBA
    Inferred from Biological aspect of Ancestor
    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 blood vessel morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    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 4A
    Names
    jumonji domain containing 2A, like
    XP_001339664.2

    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_007113.7 Reference GRCz11 Primary Assembly

      Range
      17450227..17492067 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_001339628.9 → XP_001339664.2  lysine-specific demethylase 4A

      UniProtKB/TrEMBL
      A0A8M1PZC5, F1QNG0
      Related
      ENSDARP00000009763.7, ENSDART00000024302.8
      Conserved Domains (5) summary
      smart00545
      Location:10 → 52
      JmjN; Small domain found in the jumonji family of transcription factors
      smart00333
      Location:879 → 932
      TUDOR; Tudor domain
      pfam02373
      Location:172 → 288
      JmjC; JmjC domain, hydroxylase
      cd15713
      Location:755 → 864
      ePHD_JMJD2A; Extended PHD finger (ePHD) found in Jumonji domain-containing protein 2A (JMJD2A)
      cl22851
      Location:654 → 746
      PHD_SF; PHD finger superfamily
    Nucleotide Protein Strain
    Heading Accession and Version

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