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    kdm8 lysine (K)-specific demethylase 8 [ Danio rerio (zebrafish) ]

    Gene ID: 436936, updated on 24-Nov-2024

    Summary

    Official Symbol
    kdm8provided by ZNC
    Official Full Name
    lysine (K)-specific demethylase 8provided by ZNC
    Primary source
    ZFIN:ZDB-GENE-040718-411
    See related
    Ensembl:ENSDARG00000102512 AllianceGenome:ZFIN:ZDB-GENE-040718-411
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    jmjd5; zgc:91962; zgc:173863
    Summary
    Predicted to enable chromatin binding activity; histone H3K36 demethylase activity; and peptidyl-arginine 3-dioxygenase activity. Predicted to be involved in G2/M transition of mitotic cell cycle and regulation of gene expression. Predicted to act upstream of or within chromatin organization and rhythmic process. Predicted to be active in nucleus. Orthologous to human KDM8 (lysine demethylase 8). [provided by Alliance of Genome Resources, Nov 2024]
    Orthologs
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    Genomic context

    See kdm8 in Genome Data Viewer
    Location:
    chromosome: 3
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCz11 (GCF_000002035.6) 3 NC_007114.7 (44081620..44094278, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 3 NC_007114.6 (43380703..43393391, complement)

    Chromosome 3 - NC_007114.7Genomic Context describing neighboring genes Neighboring gene interleukin 4 receptor, tandem duplicate 1 Neighboring gene NSE1 homolog, SMC5-SMC6 complex component Neighboring gene uncharacterized LOC137490744 Neighboring gene uncharacterized LOC137490745

    Genomic regions, transcripts, and products

    Expression

    • 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

    General gene information

    Clone Names

    • MGC173863

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables chromatin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables chromatin binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    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 H3K36 demethylase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables histone H3K36me/H3K36me2 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
     
    enables peptidyl-arginine 3-dioxygenase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Process Evidence Code Pubs
    involved_in G2/M transition of mitotic cell cycle ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    acts_upstream_of_or_within chromatin organization IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in circadian regulation of gene expression ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in negative regulation of DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in positive regulation of DNA-templated transcription ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    acts_upstream_of_or_within rhythmic process IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
     
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
     

    General protein information

    Preferred Names
    lysine-specific demethylase 8
    Names
    jmjC domain-containing protein 5
    jumonji domain containing 5
    jumonji domain-containing protein 5
    NP_001103339.2
    XP_068072685.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001109869.2NP_001103339.2  lysine-specific demethylase 8

      See identical proteins and their annotated locations for NP_001103339.2

      Status: VALIDATED

      Source sequence(s)
      BX571715, CT573829
      UniProtKB/Swiss-Prot
      A8E534
      UniProtKB/TrEMBL
      A0A0R4IGD4, A0A8M1NG82
      Related
      ENSDARP00000134388.1, ENSDART00000166866.2
      Conserved Domains (1) summary
      pfam13621
      Location:180406
      Cupin_8; Cupin-like domain

    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_007114.7 Reference GRCz11 Primary Assembly

      Range
      44081620..44094278 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_068216584.1XP_068072685.1  lysine-specific demethylase 8 isoform X1

      Related
      ENSDARP00000133489.1, ENSDART00000157902.2