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

Gene ID: 194952, updated on 5-Mar-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
NP_001191997.1
NP_848774.1
XP_006532663.1

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_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

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