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    Jmjd4 jumonji domain containing 4 [ Rattus norvegicus (Norway rat) ]

    Gene ID: 287359, updated on 9-Dec-2024

    Summary

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    Official Symbol
    Jmjd4provided by RGD
    Official Full Name
    jumonji domain containing 4provided by RGD
    Primary source
    RGD:1307186
    See related
    EnsemblRapid:ENSRNOG00000022438 AllianceGenome:RGD:1307186
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    RGD1307186
    Summary
    Predicted to enable peptidyl-lysine 4-dioxygenase activity and sequence-specific DNA binding activity. Predicted to be involved in positive regulation of translational termination and protein hydroxylation. Predicted to be active in cytoplasm and nucleus. Orthologous to human JMJD4 (jumonji domain containing 4). [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in Thymus (RPKM 40.4), Spleen (RPKM 33.7) and 9 other tissues See more
    Orthologs
    human mouse all
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    Genomic context

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    See Jmjd4 in Genome Data Viewer
    Location:
    10q22
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 10 NC_086028.1 (44734047..44742296)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 10 NC_051345.1 (44234465..44242754)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 10 NC_005109.4 (45798964..45804188)

    Chromosome 10 - NC_086028.1Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102546363 Neighboring gene synaptosome associated protein 47 Neighboring gene zinc finger protein 867 Neighboring gene ferritin light chain 1 pseudogene

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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

    Bibliography

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    Related articles in PubMed

    1. Optimal translational termination requires C4 lysyl hydroxylation of eRF1. Feng T, et al. Mol Cell, 2014 Feb 20. PMID 24486019, Free PMC Article
    2. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    General gene information

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    Homology

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables 2-oxoglutarate-dependent dioxygenase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables 2-oxoglutarate-dependent dioxygenase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables peptidyl-lysine 4-dioxygenase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables sequence-specific DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in positive regulation of translational termination IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of translational termination ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein hydroxylation ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    2-oxoglutarate and iron-dependent oxygenase JMJD4
    Names
    jmjC domain-containing protein 4
    NP_001099254.1
    XP_038941317.1

    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_001105784.3 → NP_001099254.1  2-oxoglutarate and iron-dependent oxygenase JMJD4

      See identical proteins and their annotated locations for NP_001099254.1

      Status: VALIDATED

      Source sequence(s)
      JAXUCZ010000010
      UniProtKB/TrEMBL
      A6HF11, D4A029
      Related
      ENSRNOP00000037005.2, ENSRNOT00000039012.4
      Conserved Domains (1) summary
      cl21464
      Location:49 → 288
      cupin_like; Conserved domain found in cupin and related proteins

    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_086028.1 Reference GRCr8

      Range
      44734047..44742296
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_039085389.2 → XP_038941317.1  2-oxoglutarate and iron-dependent oxygenase JMJD4 isoform X1

      Conserved Domains (1) summary
      cl40423
      Location:43 → 276
      cupin_RmlC-like; RmlC-like cupin superfamily
    Nucleotide Protein Strain
    Heading Accession and Version

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