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    JMJD6 arginine demethylase and lysine hydroxylase [ Homo sapiens (human) ]

    Gene ID: 23210, updated on 25-Aug-2016
    Official Symbol
    JMJD6provided by HGNC
    Official Full Name
    arginine demethylase and lysine hydroxylaseprovided by HGNC
    Primary source
    HGNC:HGNC:19355
    See related
    Ensembl:ENSG00000070495 HPRD:05371; MIM:604914; Vega:OTTHUMG00000169267
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    PSR; PTDSR; PTDSR1
    Summary
    This gene encodes a nuclear protein with a JmjC domain. JmjC domain-containing proteins are predicted to function as protein hydroxylases or histone demethylases. This protein was first identified as a putative phosphatidylserine receptor involved in phagocytosis of apoptotic cells; however, subsequent studies have indicated that it does not directly function in the clearance of apoptotic cells, and questioned whether it is a true phosphatidylserine receptor. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
    Orthologs
    Location:
    17q25
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 17 NC_000017.11 (76712830..76726799, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (74708914..74722881, complement)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105274304 Neighboring gene matrix remodeling associated 7 Neighboring gene RNA, Ro-associated Y4 pseudogene 36 Neighboring gene methyltransferase like 23 Neighboring gene serine and arginine rich splicing factor 2 Neighboring gene microRNA 636 Neighboring gene major facilitator superfamily domain containing 11 Neighboring gene RNA, U6 small nuclear 97, pseudogene

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    NHGRI GWAS Catalog

    Description
    Genetic loci for retinal arteriolar microcirculation.
    NHGRI GWA Catalog
    • Chromatin modifying enzymes, organism-specific biosystem (from REACTOME)
      Chromatin modifying enzymes, organism-specific biosystemEukaryotic DNA is associated with histone proteins and organized into a complex nucleoprotein structure called chromatin. This structure decreases the accessibility of DNA but also helps to protect i...
    • Chromatin organization, organism-specific biosystem (from REACTOME)
      Chromatin organization, organism-specific biosystemChromatin organization refers to the composition and conformation of complexes between DNA, protein and RNA. It is determined by processes that result in the specification, formation or maintenance o...
    • HDMs demethylate histones, organism-specific biosystem (from REACTOME)
      HDMs demethylate histones, organism-specific biosystemHistone lysine demethylases (KDMs) are able to reverse N-methylations of histones and probably other proteins. To date KDMs have been demonstrated to catalyse demethylation of N-epsilon methylated ly...
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Clone Names

    • KIAA0585

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    RNA binding TAS
    Traceable Author Statement
    more info
    PubMed 
    histone demethylase activity TAS
    Traceable Author Statement
    more info
     
    histone demethylase activity (H3-R2 specific) IDA
    Inferred from Direct Assay
    more info
    PubMed 
    histone demethylase activity (H4-R3 specific) IDA
    Inferred from Direct Assay
    more info
    PubMed 
    identical protein binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    iron ion binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    peptidyl-lysine 5-dioxygenase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein homodimerization activity IEA
    Inferred from Electronic Annotation
    more info
     
    receptor activity IEA
    Inferred from Electronic Annotation
    more info
     
    single-stranded RNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    RNA splicing IEA
    Inferred from Electronic Annotation
    more info
     
    T cell differentiation in thymus IEA
    Inferred from Electronic Annotation
    more info
     
    cell surface receptor signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    erythrocyte development IEA
    Inferred from Electronic Annotation
    more info
     
    heart development IEA
    Inferred from Electronic Annotation
    more info
     
    histone H3-R2 demethylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    histone H4-R3 demethylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    kidney development IEA
    Inferred from Electronic Annotation
    more info
     
    lung development IEA
    Inferred from Electronic Annotation
    more info
     
    mRNA processing IEA
    Inferred from Electronic Annotation
    more info
     
    macrophage activation IEA
    Inferred from Electronic Annotation
    more info
     
    oxidation-reduction process IEA
    Inferred from Electronic Annotation
    more info
     
    peptidyl-lysine hydroxylation to 5-hydroxy-L-lysine IDA
    Inferred from Direct Assay
    more info
    PubMed 
    recognition of apoptotic cell IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of mRNA splicing, via spliceosome IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of transcription, DNA-templated IEA
    Inferred from Electronic Annotation
    more info
     
    retina development in camera-type eye IEA
    Inferred from Electronic Annotation
    more info
     
    sprouting angiogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    transcription, DNA-templated IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    cytosol IEA
    Inferred from Electronic Annotation
    more info
     
    intracellular ribonucleoprotein complex IEA
    Inferred from Electronic Annotation
    more info
     
    nucleolus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleoplasm TAS
    Traceable Author Statement
    more info
     
    nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    plasma membrane IEA
    Inferred from Electronic Annotation
    more info
     
    Preferred Names
    bifunctional arginine demethylase and lysyl-hydroxylase JMJD6
    Names
    histone arginine demethylase JMJD6
    jmjC domain-containing protein 6
    jumonji domain containing 6
    jumonji domain-containing protein 6
    lysyl-hydroxylase JMJD6
    peptide-lysine 5-dioxygenase JMJD6
    phosphatidylserine receptor
    NP_001074930.1
    NP_055982.2

    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_001081461.1NP_001074930.1  bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 isoform 1

      See identical proteins and their annotated locations for NP_001074930.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AA775442, AB011157, AC005837, DB451815
      Consensus CDS
      CCDS42383.1
      UniProtKB/Swiss-Prot
      Q6NYC1
      Related
      ENSP00000394085, OTTHUMP00000240609, ENST00000445478, OTTHUMT00000403208
      Conserved Domains (1) summary
      pfam02373
      Location:174288
      JmjC; JmjC domain, hydroxylase
    2. NM_015167.2NP_055982.2  bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 isoform 2

      See identical proteins and their annotated locations for NP_055982.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate splice site in the 3' coding region and an alternate polyadenylation site, compared to variant 1. The resulting protein (isoform 2) has a shorter C-terminus, compared to isoform 1.
      Source sequence(s)
      AA226560, BC066654, DB451815
      Consensus CDS
      CCDS42384.1
      UniProtKB/Swiss-Prot
      Q6NYC1
      Related
      ENSP00000380750, OTTHUMP00000240612, ENST00000397625, OTTHUMT00000403211
      Conserved Domains (1) summary
      pfam02373
      Location:174288
      JmjC; JmjC domain, hydroxylase

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108 details...

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000017.11 Reference GRCh38.p7 Primary Assembly

      Range
      76712830..76726799 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    RNA

    1. XR_001752457.1 RNA Sequence

    2. XR_001752456.1 RNA Sequence

      Related
      ENST00000617192
    3. XR_934429.2 RNA Sequence

      Related
      ENST00000303996, OTTHUMT00000403210
    4. XR_934428.2 RNA Sequence

      Related
      ENST00000542934, OTTHUMT00000403209

    Alternate CHM1_1.1

    Genomic

    1. NC_018928.2 Alternate CHM1_1.1

      Range
      74773704..74787689 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)