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    Kdm8 lysine demethylase 8 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 308976, updated on 3-Dec-2024

    Summary

    Official Symbol
    Kdm8provided by RGD
    Official Full Name
    lysine demethylase 8provided by RGD
    Primary source
    RGD:1304823
    See related
    EnsemblRapid:ENSRNOG00000015180 AllianceGenome:RGD:1304823
    Gene type
    protein coding
    RefSeq status
    PROVISIONAL
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Jmjd5; RGD1304823
    Summary
    Predicted to enable several functions, including 2-oxoglutarate-dependent dioxygenase activity; p53 binding activity; and peptidase activity. Predicted to be involved in G2/M transition of mitotic cell cycle; protein destabilization; and regulation of gene expression. Predicted to act upstream of or within several processes, including fibroblast proliferation; regulation of DNA-binding transcription factor activity; and regulation of signal transduction by p53 class mediator. Predicted to be located in cytosol and nucleoplasm. Predicted to be active in nucleus. Orthologous to human KDM8 (lysine demethylase 8). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Heart (RPKM 96.3), Muscle (RPKM 89.6) and 9 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See Kdm8 in Genome Data Viewer
    Location:
    1q36
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 1 NC_086019.1 (189444527..189459507)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 1 NC_051336.1 (180013969..180028829)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 1 NC_005100.4 (196838460..196854192)

    Chromosome 1 - NC_086019.1Genomic Context describing neighboring genes Neighboring gene similar to human chromosome 16 open reading frame 82 Neighboring gene uncharacterized LOC120097358 Neighboring gene NSE1 homolog, SMC5-SMC6 complex component Neighboring gene uncharacterized LOC103691233 Neighboring gene interleukin 4 receptor

    Genomic regions, transcripts, and products

    Expression

    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    General gene information

    Markers

    Clone Names

    • MGC124735

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables aminopeptidase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables aminopeptidase activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables chromatin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables chromatin binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables chromatin binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables chromatin binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables endopeptidase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables endopeptidase activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables histone H3K36 demethylase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables histone H3K36 demethylase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables histone H3K36 demethylase activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables histone H3K36 demethylase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables methylated histone binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables methylated histone binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables p53 binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables p53 binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables peptidyl-arginine 3-dioxygenase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables peptidyl-arginine 3-dioxygenase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables peptidyl-arginine 3-dioxygenase activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables peptidyl-arginine 3-dioxygenase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    Process Evidence Code Pubs
    involved_in G2/M transition of mitotic cell cycle IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in G2/M transition of mitotic cell cycle ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in G2/M transition of mitotic cell cycle ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in biological_process ND
    No biological Data available
    more info
     
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in circadian regulation of gene expression IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in circadian regulation of gene expression ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in circadian regulation of gene expression ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in fibroblast proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within fibroblast proliferation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in in utero embryonic development IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within in utero embryonic development ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of DNA-templated transcription IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in negative regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of DNA-templated transcription ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of DNA-templated transcription IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of DNA-templated transcription ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in protein destabilization IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in protein destabilization ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in protein destabilization ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in proteolysis IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within regulation of DNA-binding transcription factor activity ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in regulation of signal transduction by p53 class mediator IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within regulation of signal transduction by p53 class mediator ISO
    Inferred from Sequence Orthology
    more info
     
    Component Evidence Code Pubs
    located_in chromosome IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
     
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
     
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
     

    General protein information

    Preferred Names
    bifunctional peptidase and arginyl-hydroxylase JMJD5
    Names
    L-arginine (3R)-hydroxylase KDM8
    arginyl C3-hydroxylase KDM8
    jmjC domain-containing protein 5
    jumonji C domain-containing protein 5
    jumonji domain containing 5
    jumonji domain-containing protein 5
    lysine (K)-specific demethylase 8
    lysine-specific demethylase 8
    NP_001032273.1
    XP_063119293.1
    XP_063119297.1
    XP_063119299.1
    XP_063119307.1
    XP_063119308.1
    XP_063119309.1

    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_001037196.1NP_001032273.1  bifunctional peptidase and arginyl-hydroxylase JMJD5

      See identical proteins and their annotated locations for NP_001032273.1

      Status: PROVISIONAL

      Source sequence(s)
      BC100627
      UniProtKB/Swiss-Prot
      Q497B8
      Related
      ENSRNOP00000020388.4, ENSRNOT00000020388.7
      Conserved Domains (1) summary
      pfam13621
      Location:189414
      Cupin_8; Cupin-like domain

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCr8

    Genomic

    1. NC_086019.1 Reference GRCr8

      Range
      189444527..189459507
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_063263229.1XP_063119299.1  bifunctional peptidase and arginyl-hydroxylase JMJD5 isoform X2

    2. XM_063263223.1XP_063119293.1  bifunctional peptidase and arginyl-hydroxylase JMJD5 isoform X1

      UniProtKB/TrEMBL
      A6I912, G3V7X6
    3. XM_063263227.1XP_063119297.1  bifunctional peptidase and arginyl-hydroxylase JMJD5 isoform X2

      Related
      ENSRNOP00000112314.1, ENSRNOT00000140863.1
    4. XM_063263237.1XP_063119307.1  bifunctional peptidase and arginyl-hydroxylase JMJD5 isoform X3

      UniProtKB/TrEMBL
      A6I911
    5. XM_063263238.1XP_063119308.1  bifunctional peptidase and arginyl-hydroxylase JMJD5 isoform X4

    6. XM_063263239.1XP_063119309.1  bifunctional peptidase and arginyl-hydroxylase JMJD5 isoform X4