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    Jmjd6 jumonji domain containing 6 [ Mus musculus (house mouse) ]

    Gene ID: 107817, updated on 26-Feb-2019

    Summary

    Official Symbol
    Jmjd6provided by MGI
    Official Full Name
    jumonji domain containing 6provided by MGI
    Primary source
    MGI:MGI:1858910
    See related
    Ensembl:ENSMUSG00000056962
    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
    PSR; Ptdsr; PtdSerR; mKIAA0585; D11Ertd195e; 5730436I23Rik
    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 functions in differentiation of multiple tissues during development, and in anti-inflammatory cytokine signaling. It was first identified as a putative phosphatidylserine receptor involved in phagocytosis of apoptotic cells; however, subsequent studies have indicated that this protein does not directly function in the clearance of apoptotic cells, and questioned whether it is a true phosphatidylserine receptor. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in testis adult (RPKM 19.2), CNS E11.5 (RPKM 14.3) and 28 other tissues See more
    Orthologs

    Genomic context

    See Jmjd6 in Genome Data Viewer
    Location:
    11 E2; 11 81.49 cM
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    106 current GRCm38.p4 (GCF_000001635.24) 11 NC_000077.6 (116837432..116843449, complement)
    Build 37.2 previous assembly MGSCv37 (GCF_000001635.18) 11 NC_000077.5 (116698746..116704763, complement)

    Chromosome 11 - NC_000077.6Genomic Context describing neighboring genes Neighboring gene ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 1 Neighboring gene matrix-remodelling associated 7 Neighboring gene methyltransferase like 23 Neighboring gene serine/arginine-rich splicing factor 2 Neighboring gene major facilitator superfamily domain containing 11

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Variation

    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    Pathways from BioSystems

    General gene information

    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    P-TEFb complex binding ISO
    Inferred from Sequence Orthology
    more info
     
    RNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    demethylase activity ISO
    Inferred from Sequence Orthology
    more info
     
    dioxygenase activity IEA
    Inferred from Electronic Annotation
    more info
     
    histone demethylase activity ISO
    Inferred from Sequence Orthology
    more info
     
    histone demethylase activity (H3-R2 specific) ISO
    Inferred from Sequence Orthology
    more info
     
    histone demethylase activity (H4-R3 specific) ISO
    Inferred from Sequence Orthology
    more info
     
    identical protein binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    identical protein binding ISO
    Inferred from Sequence Orthology
    more info
     
    iron ion binding ISO
    Inferred from Sequence Orthology
    more info
     
    metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    oxidative RNA demethylase activity ISO
    Inferred from Sequence Orthology
    more info
     
    oxidoreductase activity IEA
    Inferred from Electronic Annotation
    more info
     
    peptidyl-lysine 5-dioxygenase activity ISO
    Inferred from Sequence Orthology
    more info
     
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein homodimerization activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    signaling receptor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    single-stranded RNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    transcription coactivator activity ISO
    Inferred from Sequence Orthology
    more info
     
    Process Evidence Code Pubs
    RNA splicing IEA
    Inferred from Electronic Annotation
    more info
     
    T cell differentiation in thymus IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    apoptotic cell clearance IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    NOT apoptotic cell clearance IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    blood vessel development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    cell differentiation IEA
    Inferred from Electronic Annotation
    more info
     
    cell surface receptor signaling pathway IDA
    Inferred from Direct Assay
    more info
    PubMed 
    chromatin organization IEA
    Inferred from Electronic Annotation
    more info
     
    erythrocyte development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    heart development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    kidney development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    lung development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    mRNA processing IEA
    Inferred from Electronic Annotation
    more info
     
    macrophage activation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    multicellular organism development IEA
    Inferred from Electronic Annotation
    more info
     
    oxidation-reduction process IEA
    Inferred from Electronic Annotation
    more info
     
    oxidative RNA demethylation ISO
    Inferred from Sequence Orthology
    more info
     
    peptidyl-lysine hydroxylation to 5-hydroxy-L-lysine ISO
    Inferred from Sequence Orthology
    more info
     
    positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
     
    positive regulation of transcription, DNA-templated ISO
    Inferred from Sequence Orthology
    more info
     
    protein demethylation ISO
    Inferred from Sequence Orthology
    more info
     
    protein homooligomerization ISO
    Inferred from Sequence Orthology
    more info
     
    recognition of apoptotic cell IDA
    Inferred from Direct Assay
    more info
    PubMed 
    recognition of apoptotic cell IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of mRNA splicing, via spliceosome IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of mRNA splicing, via spliceosome ISO
    Inferred from Sequence Orthology
    more info
     
    retina development in camera-type eye IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    sprouting angiogenesis IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    cytoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    cytosol IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleolus ISO
    Inferred from Sequence Orthology
    more info
     
    nucleoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nucleus ISO
    Inferred from Sequence Orthology
    more info
     
    plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    ribonucleoprotein complex IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    bifunctional arginine demethylase and lysyl-hydroxylase JMJD6
    Names
    apoptotic cell clearance receptor PtdSerR
    histone arginine demethylase JMJD6
    jmjC domain-containing protein 6
    jumonji domain-containing protein 6
    lysyl-hydroxylase JMJD6
    peptide-lysine 5-dioxygenase JMJD6
    phosphatidylserine receptor
    NP_203971.2
    XP_006532023.1

    NCBI Reference Sequences (RefSeq)

    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_001363363.1NP_001350292.1  bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 isoform 1

      Status: VALIDATED

      Source sequence(s)
      AL645542, EF527405
      Conserved Domains (1) summary
      pfam02373
      Location:174288
      JmjC; JmjC domain, hydroxylase
    2. NM_033398.3NP_203971.2  bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 isoform 2

      See identical proteins and their annotated locations for NP_203971.2

      Status: VALIDATED

      Source sequence(s)
      AL645542, BP769727, CX210791
      Consensus CDS
      CCDS25678.1
      UniProtKB/Swiss-Prot
      Q9ERI5
      Related
      ENSMUSP00000047570.3, ENSMUST00000047616.9
      Conserved Domains (1) summary
      pfam02373
      Location:174288
      JmjC; JmjC domain, hydroxylase

    RNA

    1. NR_156486.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      EF527404
    2. NR_156487.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AL645542

    RefSeqs of Annotated Genomes: Mus musculus Annotation Release 106

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

    Reference GRCm38.p4 C57BL/6J

    Genomic

    1. NC_000077.6 Reference GRCm38.p4 C57BL/6J

      Range
      116837432..116843449 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006531960.3XP_006532023.1  bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 isoform X1

      UniProtKB/TrEMBL
      B2WTI2
      Conserved Domains (1) summary
      pfam02373
      Location:174288
      JmjC; JmjC domain, hydroxylase

    RNA

    1. XR_388320.1 RNA Sequence

    2. XR_388322.3 RNA Sequence

      Related
      ENSMUST00000142495.7
    3. XR_001779858.1 RNA Sequence

    4. XR_001779857.1 RNA Sequence

    5. XR_388319.3 RNA Sequence

    6. XR_879501.2 RNA Sequence

    7. XR_879502.2 RNA Sequence

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