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

Gene ID: 107817, updated on 13-Oct-2022

Summary

Official Symbol
Jmjd6provided by MGI
Official Full Name
jumonji domain containing 6provided by MGI
Primary source
MGI:MGI:1858910
See related
Ensembl:ENSMUSG00000056962 AllianceGenome:MGI:1858910
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
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Genomic context

See Jmjd6 in Genome Data Viewer
Location:
11 E2; 11 81.49 cM
Exon count:
7
Annotation release Status Assembly Chr Location
109 current GRCm39 (GCF_000001635.27) 11 NC_000077.7 (116728258..116734593, complement)
108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 11 NC_000077.6 (116837432..116843767, complement)

Chromosome 11 - NC_000077.7Genomic 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 major facilitator superfamily domain containing 11 Neighboring gene serine and arginine-rich splicing factor 2 Neighboring gene mannoside acetylglucosaminyltransferase 5, isoenzyme B Neighboring gene predicted gene, 33829

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 Functions

What's a GeneRIF?

Variation

Alleles

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by MGI

Function Evidence Code Pubs
enables P-TEFb complex binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables P-TEFb complex binding ISO
Inferred from Sequence Orthology
more info
 
enables RNA binding IDA
Inferred from Direct Assay
more info
PubMed 
enables dioxygenase activity IEA
Inferred from Electronic Annotation
more info
 
enables histone H3R2 demethylase activity ISO
Inferred from Sequence Orthology
more info
 
enables histone H3R3 demethylase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
enables histone H3R3 demethylase activity ISO
Inferred from Sequence Orthology
more info
 
enables histone demethylase activity ISO
Inferred from Sequence Orthology
more info
 
enables identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables identical protein binding ISO
Inferred from Sequence Orthology
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 ISO
Inferred from Sequence Orthology
more info
 
enables oxidoreductase activity IEA
Inferred from Electronic Annotation
more info
 
enables peptidyl-lysine 5-dioxygenase activity ISO
Inferred from Sequence Orthology
more info
 
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein demethylase activity ISO
Inferred from Sequence Orthology
more info
 
enables signaling receptor activity IDA
Inferred from Direct Assay
more info
PubMed 
enables single-stranded RNA binding ISO
Inferred from Sequence Orthology
more info
 
enables transcription regulator activator activity ISO
Inferred from Sequence Orthology
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 T cell differentiation in thymus IMP
Inferred from Mutant Phenotype
more info
PubMed 
NOT acts_upstream_of_or_within apoptotic cell clearance IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within apoptotic cell clearance IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within blood vessel development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within cell differentiation IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within cell surface receptor signaling pathway IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within chromatin organization IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within erythrocyte development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within heart development IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in histone H3-R2 demethylation ISO
Inferred from Sequence Orthology
more info
 
involved_in histone H4-R3 demethylation ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within kidney development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within lung development IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within mRNA processing IEA
Inferred from Electronic Annotation
more info
 
acts_upstream_of_or_within macrophage activation IMP
Inferred from Mutant Phenotype
more info
PubMed 
acts_upstream_of_or_within multicellular organism development IEA
Inferred from Electronic Annotation
more info
 
involved_in oxidative RNA demethylation ISO
Inferred from Sequence Orthology
more info
 
involved_in peptidyl-lysine hydroxylation to 5-hydroxy-L-lysine ISO
Inferred from Sequence Orthology
more info
 
involved_in phagocytosis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in positive regulation of DNA-templated transcription ISO
Inferred from Sequence Orthology
more info
 
involved_in positive regulation of transcription by RNA polymerase II ISO
Inferred from Sequence Orthology
more info
 
involved_in protein homooligomerization ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within recognition of apoptotic cell IDA
Inferred from Direct Assay
more info
PubMed 
acts_upstream_of_or_within recognition of apoptotic cell IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of mRNA splicing, via spliceosome IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in regulation of mRNA splicing, via spliceosome ISO
Inferred from Sequence Orthology
more info
 
acts_upstream_of_or_within retina development in camera-type eye IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in sprouting angiogenesis IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in cytoplasm ISO
Inferred from Sequence Orthology
more info
 
located_in cytosol IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleolus IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleolus ISO
Inferred from Sequence Orthology
more info
 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleoplasm ISO
Inferred from Sequence Orthology
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in nucleus IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleus ISO
Inferred from Sequence Orthology
more info
 
located_in plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
part_of 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_001350292.1
NP_203971.2

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

    Status: VALIDATED

    Source sequence(s)
    AL645542, EF527405
    UniProtKB/TrEMBL
    B2WTI2
    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
    Q80TX1, Q9ERI5
    UniProtKB/TrEMBL
    A0A8C6I480
    Related
    ENSMUSP00000047570.4, ENSMUST00000047616.10
    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
    Related
    ENSMUST00000142495.8

RefSeqs of Annotated Genomes: Mus musculus Annotation Release 109 details...Open this link in a new tab

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

Reference GRCm39 C57BL/6J

Genomic

  1. NC_000077.7 Reference GRCm39 C57BL/6J

    Range
    116728258..116734593 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RNA

  1. XR_388322.4 RNA Sequence

  2. XR_001779858.2 RNA Sequence

  3. XR_388319.4 RNA Sequence

  4. XR_004936682.1 RNA Sequence

  5. XR_879501.4 RNA Sequence