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

Gene ID: 266962, updated on 4-Jan-2025

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, Jan 2025]
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
RS_2024_08 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 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
  
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: GCF_000002035.6-RS_2024_08

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

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