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    JMJD6 jumonji domain containing 6, arginine demethylase and lysine hydroxylase [ Homo sapiens (human) ]

    Gene ID: 23210, updated on 17-Jun-2024

    Summary

    Official Symbol
    JMJD6provided by HGNC
    Official Full Name
    jumonji domain containing 6, arginine demethylase and lysine hydroxylaseprovided by HGNC
    Primary source
    HGNC:HGNC:19355
    See related
    Ensembl:ENSG00000070495 MIM:604914; AllianceGenome:HGNC:19355
    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]
    Expression
    Ubiquitous expression in bone marrow (RPKM 17.6), heart (RPKM 4.9) and 24 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See JMJD6 in Genome Data Viewer
    Location:
    17q25.1
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (76712836..76726606, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (77609799..77623589, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (74708918..74722688, complement)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105274304 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:74678511-74679057 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:74680151-74680695 Neighboring gene matrix remodeling associated 7 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:74682678-74683473 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:74693235-74693788 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:74693789-74694342 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:74694343-74694895 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:74696218-74696722 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:74696723-74697227 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:74697733-74698236 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9024 Neighboring gene RNY4 pseudogene 36 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:74722561-74723190 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:74723821-74724449 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:74725107-74725737 Neighboring gene methyltransferase 23, arginine Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:74732487-74733112 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12814 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:74736456-74736653 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

    Genomic regions, transcripts, and products

    Expression

    • Project title: 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • KIAA0585

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables P-TEFb complex binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables P-TEFb complex binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables RNA binding TAS
    Traceable Author Statement
    more info
    PubMed 
    enables histone H3R2 demethylase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables histone H4R3 demethylase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables histone H4R3 demethylase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables histone demethylase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables histone demethylase activity TAS
    Traceable Author Statement
    more info
     
    enables identical protein binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables iron ion binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables oxidative RNA demethylase activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    enables peptidyl-lysine 5-dioxygenase activity EXP
    Inferred from Experiment
    more info
    PubMed 
    enables peptidyl-lysine 5-dioxygenase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein demethylase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables signaling receptor activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables single-stranded RNA binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables transcription regulator activator activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in RNA splicing IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in T cell differentiation in thymus IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cell surface receptor signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in chromatin remodeling IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in erythrocyte development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in heart development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in kidney development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in lung development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in mRNA processing IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in macrophage activation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of protein homooligomerization ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in non-membrane-bounded organelle assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    involved_in oxidative RNA demethylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in peptidyl-lysine hydroxylation to 5-hydroxy-L-lysine IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in phagocytosis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in positive regulation of DNA-templated transcription IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in protein homooligomerization IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in recognition of apoptotic cell IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of mRNA splicing, via spliceosome IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in retina development in camera-type eye IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in sprouting angiogenesis ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    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 IEA
    Inferred from Electronic Annotation
    more info
     
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleus IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    is_active_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
     
    part_of ribonucleoprotein complex IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    bifunctional arginine demethylase and lysyl-hydroxylase JMJD6
    Names
    arginine demethylase and lysine hydroxylase
    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_001074930.1
    NP_055982.2
    XP_047291644.1
    XP_047291645.1
    XP_054171569.1
    XP_054171570.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_001081461.2NP_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/TrEMBL
      A0A0S2PZM4
      Related
      ENSP00000394085.2, ENST00000445478.6
      Conserved Domains (1) summary
      pfam02373
      Location:174288
      JmjC; JmjC domain, hydroxylase
    2. NM_015167.3NP_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
      B3KMN8, B4DGX1, Q6NYC1, Q86VY0, Q8IUM5, Q9Y4E2
      UniProtKB/TrEMBL
      A0A0S2PZM4
      Related
      ENSP00000380750.4, ENST00000397625.9
      Conserved Domains (1) summary
      pfam02373
      Location:174288
      JmjC; JmjC domain, hydroxylase

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      76712836..76726606 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047435688.1XP_047291644.1  bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 isoform X1

      UniProtKB/TrEMBL
      B2WTI4, K7EJU9
      Related
      ENSP00000442362.1, ENST00000542934.5
    2. XM_047435689.1XP_047291645.1  bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 isoform X2

      UniProtKB/TrEMBL
      B2WTI3, K7EJU9
      Related
      ENSP00000302916.6, ENST00000303996.10

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      77609799..77623589 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054315594.1XP_054171569.1  bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 isoform X1

      UniProtKB/TrEMBL
      B2WTI4, K7EJU9
    2. XM_054315595.1XP_054171570.1  bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 isoform X2

      UniProtKB/TrEMBL
      B2WTI3, K7EJU9