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    Jmjd6 jumonji domain containing 6, arginine demethylase and lysine hydroxylase [ Rattus norvegicus (Norway rat) ]

    Gene ID: 360665, updated on 3-Dec-2024

    Summary

    Official Symbol
    Jmjd6provided by RGD
    Official Full Name
    jumonji domain containing 6, arginine demethylase and lysine hydroxylaseprovided by RGD
    Primary source
    RGD:1305395
    See related
    EnsemblRapid:ENSRNOG00000000250 AllianceGenome:RGD:1305395
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Rattus norvegicus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
    Also known as
    Ptdsr
    Summary
    Predicted to enable several functions, including 2-oxoglutarate-dependent dioxygenase activity; P-TEFb complex binding activity; and transcription regulator activator activity. Predicted to be involved in several processes, including oxidative RNA demethylation; peptidyl-lysine hydroxylation to 5-hydroxy-L-lysine; and regulation of RNA metabolic process. Predicted to act upstream of or within several processes, including circulatory system development; hemopoiesis; and recognition of apoptotic cell. Predicted to be located in cytosol; nuclear lumen; and plasma membrane. Predicted to be part of ribonucleoprotein complex. Predicted to be active in cytoplasm and nucleus. Orthologous to human JMJD6 (jumonji domain containing 6, arginine demethylase and lysine hydroxylase). [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in Thymus (RPKM 77.8), Heart (RPKM 75.5) and 9 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See Jmjd6 in Genome Data Viewer
    Location:
    10q32.2
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCr8 (GCF_036323735.1) 10 NC_086028.1 (102539935..102545986, complement)
    RS_2023_06 previous assembly mRatBN7.2 (GCF_015227675.2) 10 NC_051345.1 (102041131..102047182, complement)
    106 previous assembly Rnor_6.0 (GCF_000001895.5) 10 NC_005109.4 (105781752..105787803, complement)

    Chromosome 10 - NC_086028.1Genomic Context describing neighboring genes Neighboring gene ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 1 Neighboring gene matrix remodeling associated 7 Neighboring gene methyltransferase 23, arginine Neighboring gene serine and arginine rich splicing factor 2

    Genomic regions, transcripts, and products

    Expression

    • Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
    • Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
    • BioProject: PRJNA238328
    • Publication: PMID 24510058
    • Analysis date: Mon Jun 6 17:44:12 2016

    Pathways from PubChem

    General gene information

    Markers

    Gene Ontology Provided by RGD

    Function Evidence Code Pubs
    enables P-TEFb complex binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables P-TEFb complex binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables P-TEFb complex binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables RNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables dioxygenase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables histone H3R2 demethylase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables histone H3R2 demethylase activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables histone H3R2 demethylase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables histone H4R3 demethylase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables histone H4R3 demethylase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables histone H4R3 demethylase activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables histone H4R3 demethylase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables histone demethylase activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables histone demethylase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables identical protein binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables identical protein binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables iron ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables iron ion binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables oxidative RNA demethylase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables oxidative RNA demethylase activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables oxidative RNA demethylase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables peptidyl-lysine 5-dioxygenase activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables peptidyl-lysine 5-dioxygenase activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables peptidyl-lysine 5-dioxygenase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables protein demethylase activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables signaling receptor activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables signaling receptor activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables single-stranded RNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables single-stranded RNA binding ISO
    Inferred from Sequence Orthology
    more info
     
    enables single-stranded RNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    enables transcription regulator activator activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables transcription regulator activator activity ISO
    Inferred from Sequence Orthology
    more info
     
    enables transcription regulator activator activity ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    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
     
    acts_upstream_of_or_within T cell differentiation in thymus ISO
    Inferred from Sequence Orthology
    more info
     
    NOT acts_upstream_of_or_within apoptotic cell clearance ISO
    Inferred from Sequence Orthology
    more info
     
    acts_upstream_of_or_within apoptotic cell clearance ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in biological_process ND
    No biological Data available
    more info
     
    acts_upstream_of_or_within blood vessel development ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in cell surface receptor signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within cell surface receptor signaling pathway ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in chromatin organization IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in chromatin remodeling ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in erythrocyte development IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within erythrocyte development ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in heart development IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within heart development ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in kidney development IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within kidney development ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in lung development IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within lung development ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in mRNA processing IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in macrophage activation IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within macrophage activation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in membraneless organelle assembly IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in membraneless organelle assembly ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in negative regulation of protein homooligomerization IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of protein homooligomerization ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in oxidative RNA demethylation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in oxidative RNA demethylation ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in oxidative RNA demethylation ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in peptidyl-lysine hydroxylation to 5-hydroxy-L-lysine ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in peptidyl-lysine hydroxylation to 5-hydroxy-L-lysine ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in phagocytosis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in positive regulation of DNA-templated transcription ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of DNA-templated transcription ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in positive regulation of transcription by RNA polymerase II IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in positive regulation of transcription by RNA polymerase II ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in positive regulation of transcription by RNA polymerase II ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in protein homooligomerization IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in protein homooligomerization ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in protein homooligomerization ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in recognition of apoptotic cell IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within recognition of apoptotic cell ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in regulation of mRNA splicing, via spliceosome IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of mRNA splicing, via spliceosome ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in regulation of mRNA splicing, via spliceosome ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in retina development in camera-type eye IEA
    Inferred from Electronic Annotation
    more info
     
    acts_upstream_of_or_within retina development in camera-type eye ISO
    Inferred from Sequence Orthology
    more info
     
    involved_in sprouting angiogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in sprouting angiogenesis ISO
    Inferred from Sequence Orthology
    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 ISO
    Inferred from Sequence Orthology
    more info
     
    located_in cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
     
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
     
    located_in nucleolus IEA
    Inferred from Electronic Annotation
    more info
     
    located_in nucleolus ISO
    Inferred from Sequence Orthology
    more info
     
    located_in nucleolus ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in nucleoplasm IEA
    Inferred from Electronic Annotation
    more info
     
    located_in nucleoplasm ISO
    Inferred from Sequence Orthology
    more info
     
    located_in nucleoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in nucleus ISO
    Inferred from Sequence Orthology
    more info
     
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
     
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in plasma membrane ISO
    Inferred from Sequence Orthology
    more info
     
    part_of ribonucleoprotein complex IEA
    Inferred from Electronic Annotation
    more info
     
    part_of ribonucleoprotein complex ISO
    Inferred from Sequence Orthology
    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_001012143.2
    XP_006247868.1
    XP_063125543.1
    XP_063125544.1
    XP_063125545.1
    XP_063125546.1
    XP_063125547.1

    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_001012143.2NP_001012143.2  bifunctional arginine demethylase and lysyl-hydroxylase JMJD6

      See identical proteins and their annotated locations for NP_001012143.2

      Status: VALIDATED

      Source sequence(s)
      BC079012, BM391923, CB789826
      UniProtKB/Swiss-Prot
      Q6AYK2
      UniProtKB/TrEMBL
      A0A8I6AJV5, A6HKZ3
      Conserved Domains (1) summary
      pfam02373
      Location:174288
      JmjC; JmjC domain, hydroxylase

    RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

    Reference GRCr8

    Genomic

    1. NC_086028.1 Reference GRCr8

      Range
      102539935..102545986 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006247806.2XP_006247868.1  bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 isoform X1

      See identical proteins and their annotated locations for XP_006247868.1

      UniProtKB/TrEMBL
      A0A8I6AJV5, A6HKZ2
      Conserved Domains (1) summary
      pfam02373
      Location:174288
      JmjC; JmjC domain, hydroxylase
    2. XM_063269475.1XP_063125545.1  bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 isoform X4

    3. XM_063269473.1XP_063125543.1  bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 isoform X2

      UniProtKB/TrEMBL
      A0A8I6AJV5
      Related
      ENSRNOP00000062806.4, ENSRNOT00000064671.4
    4. XM_063269474.1XP_063125544.1  bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 isoform X3

      UniProtKB/TrEMBL
      A0A8I5Y5A5, A0A8I6AJV5
      Related
      ENSRNOP00000077039.1, ENSRNOT00000116096.2
    5. XM_063269477.1XP_063125547.1  bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 isoform X6

      UniProtKB/TrEMBL
      A6HKZ4
    6. XM_063269476.1XP_063125546.1  bifunctional arginine demethylase and lysyl-hydroxylase JMJD6 isoform X5

      UniProtKB/TrEMBL
      A0A8L2QWD0, A6HKZ4

    RNA

    1. XR_010055213.1 RNA Sequence

    2. XR_010055212.1 RNA Sequence