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    JMJD4 jumonji domain containing 4 [ Homo sapiens (human) ]

    Gene ID: 65094, updated on 2-Nov-2024

    Summary

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    Official Symbol
    JMJD4provided by HGNC
    Official Full Name
    jumonji domain containing 4provided by HGNC
    Primary source
    HGNC:HGNC:25724
    See related
    Ensembl:ENSG00000081692 MIM:620928; AllianceGenome:HGNC:25724
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    Enables peptidyl-lysine 4-dioxygenase activity. Involved in positive regulation of translational termination and protein hydroxylation. Located in cytoplasm. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in testis (RPKM 7.3), adrenal (RPKM 6.8) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See JMJD4 in Genome Data Viewer
    Location:
    1q42.13
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (227731191..227735302, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (226920125..226924236, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (227918892..227923003, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene zinc finger protein 678 Neighboring gene vomeronasal 1 receptor 15 pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr1:227880161-227880375 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:227898535-227899471 Neighboring gene zinc finger protein 847, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:227915603-227916208 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2680 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1899 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1900 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:227928395-227928940 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:227928941-227929485 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:227929473-227929676 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:227937705-227938206 Neighboring gene synaptosome associated protein 47 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2682 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2681 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2683 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:227949169-227949919 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2684 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 2685 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:227952921-227953670 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:227953671-227954420 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:227961766-227962583 Neighboring gene MPRA-validated peak747 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:227965808-227966590 Neighboring gene uncharacterized LOC105373289 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1901 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1902 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:227980229-227980892 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:227981557-227982220 Neighboring gene MPRA-validated peak748 silencer Neighboring gene serine protease 38

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Correlation between high expression levels of jumonji domain-containing 4 and short survival in cases of colon adenocarcinoma. Ho YJ, et al. Biochem Biophys Res Commun, 2018 Sep 10. PMID 30029884
    2. Optimal translational termination requires C4 lysyl hydroxylation of eRF1. Feng T, et al. Mol Cell, 2014 Feb 20. PMID 24486019, Free PMC Article
    3. Jmjd4 Facilitates Pkm2 Degradation in Cardiomyocytes and Is Protective Against Dilated Cardiomyopathy. Tang Y, et al. Circulation, 2023 May 30. PMID 37066795
    4. Brd4 and JMJD6-associated anti-pause enhancers in regulation of transcriptional pause release. Liu W, et al. Cell, 2013 Dec 19. PMID 24360279, Free PMC Article
    5. A negative genetic interaction map in isogenic cancer cell lines reveals cancer cell vulnerabilities. Vizeacoumar FJ, et al. Mol Syst Biol, 2013 Oct 8. PMID 24104479, Free PMC Article

    See all (19) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Hundreds of variants clustered in genomic loci and biological pathways affect human height.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Homology

    Clone Names

    • FLJ12517, MGC129896

    Gene Ontology Provided by GOA

    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 IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables peptidyl-lysine 4-dioxygenase activity EXP
    Inferred from Experiment
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    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 IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein hydroxylation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    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
    2-oxoglutarate- and Fe(II)-dependent oxygenase
    C4 lysyl hydroxylase
    jmjC domain-containing protein 4
    jumonji domain-containing protein 4
    lysyl-hydroxylase JMJD4
    NP_001154937.2
    NP_075383.3
    XP_011542564.2
    XP_054194371.1

    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_001161465.2 → NP_001154937.2  2-oxoglutarate and iron-dependent oxygenase JMJD4 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region compared to variant 1. This results in a shorter isoform (2) compared to isoform 1.
      Source sequence(s)
      AL136378
      Consensus CDS
      CCDS59203.2
      Related
      ENSP00000387830.3, ENST00000438896.3
      Conserved Domains (1) summary
      cl40423
      Location:42 → 288
      cupin_RmlC-like; RmlC-like cupin superfamily

    2. NM_023007.3 → NP_075383.3  2-oxoglutarate and iron-dependent oxygenase JMJD4 isoform 1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AL136378
      Consensus CDS
      CCDS1561.2
      UniProtKB/Swiss-Prot
      A0A087WT84, Q5TBZ1, Q5TBZ6, Q9H970, Q9H9V9
      Related
      ENSP00000477669.1, ENST00000620518.5
      Conserved Domains (1) summary
      cl40423
      Location:42 → 288
      cupin_RmlC-like; RmlC-like cupin superfamily

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      227731191..227735302 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011544262.4 → XP_011542564.2  2-oxoglutarate and iron-dependent oxygenase JMJD4 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      226920125..226924236 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054338396.1 → XP_054194371.1  2-oxoglutarate and iron-dependent oxygenase JMJD4 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9H9V9.3 GenPept UniProtKB/Swiss-Prot:Q9H9V9

    Gene LinkOut

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

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