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    jmjd6 jumonji domain containing 6, arginine demethylase and lysine hydroxylase [ Danio rerio (zebrafish) ]

    Gene ID: 266962, updated on 27-Mar-2024

    Summary

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    Official Symbol
    jmjd6provided by ZNC
    Official Full Name
    jumonji domain containing 6, arginine demethylase and lysine hydroxylaseprovided by ZNC
    Primary source
    ZFIN:ZDB-GENE-040426-17
    See related
    Ensembl:ENSDARG00000102896 AllianceGenome:ZFIN:ZDB-GENE-040426-17
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Danio rerio
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
    Also known as
    psr; ptdsr; zfpsr; jmjd6a; zgc:66264
    Summary
    Predicted to enable 2-oxoglutarate-dependent dioxygenase activity; P-TEFb complex binding activity; and single-stranded RNA binding activity. Acts upstream of or within phagocytosis. Predicted to be located in nucleolus and nucleoplasm. Predicted to be active in cytoplasm and nucleus. Is expressed in brain; hatching gland; heart; pronephros; and somite. Orthologous to human JMJD6 (jumonji domain containing 6, arginine demethylase and lysine hydroxylase). [provided by Alliance of Genome Resources, Apr 2022]
    Orthologs
    human mouse all
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    Genomic context

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    See jmjd6 in Genome Data Viewer
    Location:
    chromosome: 3
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    106 current GRCz11 (GCF_000002035.6) 3 NC_007114.7 (60577513..60589538, complement)
    105 previous assembly GRCz10 (GCF_000002035.5) 3 NC_007114.6 (60497709..60509734, complement)

    Chromosome 3 - NC_007114.7Genomic Context describing neighboring genes Neighboring gene si:ch211-214b16.3 Neighboring gene uncharacterized LOC103910353 Neighboring gene si:ch73-366l1.5 Neighboring gene methyltransferase 23, arginine Neighboring gene serine and arginine rich splicing factor 2b Neighboring gene major facilitator superfamily domain containing 11

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
    • BioProject: PRJEB1986
    • Analysis date: Fri Dec 8 19:48:10 2017

    Bibliography

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    Related articles in PubMed

    1. Phosphatidylserine receptor is required for the engulfment of dead apoptotic cells and for normal embryonic development in zebrafish. Hong JR, et al. Development, 2004 Nov. PMID 15469976
    2. Knockdown of zebrafish YY1a can downregulate the phosphatidylserine (PS) receptor expression, leading to induce the abnormal brain and heart development. Shiu WL, et al. J Biomed Sci, 2016 Feb 29. PMID 26924789, Free PMC Article
    3. Ras-Induced miR-146a and 193a Target Jmjd6 to Regulate Melanoma Progression. Anelli V, et al. Front Genet, 2018. PMID 30619488, Free PMC Article
    4. Revealing sex-specific molecular changes in hypoxia-ischemia induced neural damage and subsequent recovery using zebrafish model. Das T, et al. Neurosci Lett, 2019 Nov 1. PMID 31518677
    5. Microarray Expression Profiling and Raman Spectroscopy Reveal Anti-Fatty Liver Action of Berberine in a Diet-Induced Larval Zebrafish Model. Chen B, et al. Front Pharmacol, 2019. PMID 31969822, Free PMC Article

    See all (13) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. results suggest that YY1a regulates PS receptor expression that linked to function of PSR-phagocyte mediated apoptotic cell engulfment during development
      Title: Knockdown of zebrafish YY1a can downregulate the phosphatidylserine (PS) receptor expression, leading to induce the abnormal brain and heart development.
    2. PSR-dependent system in zebrafish embryos that engulfs apoptotic cells mediated by PSR-phagocytes during development, with the system assuming an important role in the normal development of tissues such as the brain, heart, notochord and somite
      Title: Phosphatidylserine receptor is required for the engulfment of dead apoptotic cells and for normal embryonic development in zebrafish.
    Submit: New GeneRIF Correction

    Pathways from PubChem

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    General gene information

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    Homology

    Gene Ontology Provided by ZFIN

    Function Evidence Code Pubs
    enables 2-oxoglutarate-dependent dioxygenase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables P-TEFb complex binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables RNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables dioxygenase activity IEA
    Inferred from Electronic Annotation
    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 ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables histone demethylase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables oxidoreductase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables peptidyl-lysine 5-dioxygenase activity ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables single-stranded RNA binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within RNA splicing IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within cell differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within chromatin organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    acts_upstream_of_or_within mRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in phagocytosis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within phagocytosis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in protein homooligomerization ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of mRNA splicing, via spliceosome ISS
    Inferred from Sequence or Structural Similarity
    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 IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in nucleolus ISS
    Inferred from Sequence or Structural Similarity
    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
    		  
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    bifunctional arginine demethylase and lysyl-hydroxylase JMJD6
    Names
    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_739567.3

    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_170761.3 → NP_739567.3  bifunctional arginine demethylase and lysyl-hydroxylase JMJD6

      Status: VALIDATED

      Source sequence(s)
      CU463857
      UniProtKB/Swiss-Prot
      Q6PFM0, Q8JI07, Q8JI08
      Related
      ENSDARP00000139813.1, ENSDART00000157822.2
      Conserved Domains (1) summary
      pfam02373
      Location:174 → 288
      JmjC; JmjC domain, hydroxylase

    RefSeqs of Annotated Genomes: Danio rerio Annotation Release 106 details...Open this link in a new tab

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

    Reference GRCz11 Primary Assembly

    Genomic

    1. NC_007114.7 Reference GRCz11 Primary Assembly

      Range
      60577513..60589538 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q6PFM0.2 GenPept UniProtKB/Swiss-Prot:Q6PFM0

    Gene LinkOut

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

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