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    Jmjd4 jumonji domain containing 4 [ Mus musculus (house mouse) ]

    Gene ID: 194952, updated on 30-Apr-2024

    Summary

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    Official Symbol
    Jmjd4provided by MGI
    Official Full Name
    jumonji domain containing 4provided by MGI
    Primary source
    MGI:MGI:2144404
    See related
    Ensembl:ENSMUSG00000036819 AllianceGenome:MGI:2144404
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    6430559I23
    Summary
    Predicted to enable histone H3-methyl-arginine-3 demethylase activity and sequence-specific DNA binding activity. Predicted to be involved in cellular protein modification process and regulation of gene expression. Predicted to be active in cytoplasm and nucleus. Is expressed in early conceptus; inner cell mass; and oocyte. Orthologous to human JMJD4 (jumonji domain containing 4). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in thymus adult (RPKM 5.3), whole brain E14.5 (RPKM 5.0) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    Location:
    11 B1.3; 11 37.71 cM
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 11 NC_000077.7 (59340871..59353797)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 11 NC_000077.6 (59450032..59462971)

    Chromosome 11 - NC_000077.7Genomic Context describing neighboring genes Neighboring gene STARR-seq mESC enhancer starr_29623 Neighboring gene serine protease 38 Neighboring gene CapStarr-seq enhancer MGSCv37_chr11:59198075-59198323 Neighboring gene predicted gene 15755 Neighboring gene synaptosomal-associated protein, 47 Neighboring gene CapStarr-seq enhancer MGSCv37_chr11:59263537-59263646 Neighboring gene STARR-seq mESC enhancer starr_29624 Neighboring gene zinc finger protein 867 Neighboring gene ariadne homolog 2 pseudogene Neighboring gene zinc finger with KRAB and SCAN domains 17 Neighboring gene RIKEN cDNA 4933439C10 gene

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. JMJD4-demethylated RIG-I prevents hepatic steatosis and carcinogenesis. Li Z, et al. J Hematol Oncol, 2022 Nov 4. PMID 36333807, Free PMC Article
    2. Mouse JMJD4 is dispensable for embryogenesis. Yoo H, et al. Mol Reprod Dev, 2016 Jul. PMID 27147518
    3. Identification of Jmjd3 as an Essential Epigenetic Regulator of Hox Gene Temporal Collinear Activation for Body Axial Patterning in Mice. Zhang F, et al. Front Cell Dev Biol, 2021. PMID 34368113, Free PMC Article
    4. Resolution of cell fate decisions revealed by single-cell gene expression analysis from zygote to blastocyst. Guo G, et al. Dev Cell, 2010 Apr 20. PMID 20412781
    5. Mouse brain organization revealed through direct genome-scale TF expression analysis. Gray PA, et al. Science, 2004 Dec 24. PMID 15618518

    See all (23) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Targeted (3)  1 citation
    • Endonuclease-mediated (1) 

    General gene information

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    Homology

    Gene Ontology Provided by MGI

    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 dioxygenase 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-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 IBA
    Inferred from Biological aspect of Ancestor
    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
    jumonji domain-containing protein 4
    lysyl-hydroxylase JMJD4

    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_001205068.1 → NP_001191997.1  2-oxoglutarate and iron-dependent oxygenase JMJD4 isoform 2

      See identical proteins and their annotated locations for NP_001191997.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the coding region, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
      Source sequence(s)
      AK047586, AK052144, AL592522
      Consensus CDS
      CCDS56777.1
      UniProtKB/Swiss-Prot
      Q8BFT6
      Related
      ENSMUSP00000043473.7, ENSMUST00000045279.13
      Conserved Domains (1) summary
      cl21464
      Location:38 → 277
      cupin_like; Conserved domain found in cupin and related proteins

    2. NM_178659.6 → NP_848774.1  2-oxoglutarate and iron-dependent oxygenase JMJD4 isoform 1

      See identical proteins and their annotated locations for NP_848774.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longer isoform (1).
      Source sequence(s)
      AK047586, AL592522, BC116707
      Consensus CDS
      CCDS24768.1
      UniProtKB/Swiss-Prot
      Q4QQM9, Q80ZI5, Q8BFT6, Q8BPV8
      Related
      ENSMUSP00000104407.4, ENSMUST00000108777.10
      Conserved Domains (1) summary
      cl21464
      Location:38 → 289
      cupin_like; Conserved domain found in cupin and related proteins

    RNA

    1. NR_037992.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) uses an alternate splice site in an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AK047586, AL592522
      Related
      ENSMUST00000147163.8

    RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000077.7 Reference GRCm39 C57BL/6J

      Range
      59340871..59353797
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006532600.4 → XP_006532663.1  2-oxoglutarate and iron-dependent oxygenase JMJD4 isoform X1

      Conserved Domains (1) summary
      cl21464
      Location:32 → 116
      cupin_like; Conserved domain found in cupin and related proteins
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8BFT6.1 GenPept UniProtKB/Swiss-Prot:Q8BFT6

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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