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

Gene ID: 23210, updated on 6-Oct-2019

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
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

Genomic context

See JMJD6 in Genome Data Viewer
Location:
17q25.1
Exon count:
8
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 17 NC_000017.11 (76712830..76726799, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (74708914..74722881, complement)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105274304 Neighboring gene matrix remodeling associated 7 Neighboring gene RNY4 pseudogene 36 Neighboring gene methyltransferase like 23 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 BioSystems

  • Chromatin modifying enzymes, organism-specific biosystem (from REACTOME)
    Chromatin modifying enzymes, organism-specific biosystemEukaryotic DNA is associated with histone proteins and organized into a complex nucleoprotein structure called chromatin. This structure decreases the accessibility of DNA but also helps to protect i...
  • Chromatin organization, organism-specific biosystem (from REACTOME)
    Chromatin organization, organism-specific biosystemChromatin organization refers to the composition and conformation of complexes between DNA, protein and RNA. It is determined by processes that result in the specification, formation or maintenance o...
  • HDMs demethylate histones, organism-specific biosystem (from REACTOME)
    HDMs demethylate histones, organism-specific biosystemHistone lysine demethylases (KDMs) are able to reverse N-methylations of histones and probably other proteins. To date KDMs have been demonstrated to catalyse demethylation of N-epsilon methylated ly...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA0585

Gene Ontology Provided by GOA

Function Evidence Code Pubs
P-TEFb complex binding IDA
Inferred from Direct Assay
more info
PubMed 
RNA binding TAS
Traceable Author Statement
more info
PubMed 
demethylase activity IDA
Inferred from Direct Assay
more info
PubMed 
histone demethylase activity IDA
Inferred from Direct Assay
more info
PubMed 
histone demethylase activity TAS
Traceable Author Statement
more info
 
histone demethylase activity (H3-R2 specific) IDA
Inferred from Direct Assay
more info
PubMed 
histone demethylase activity (H4-R3 specific) IDA
Inferred from Direct Assay
more info
PubMed 
identical protein binding IDA
Inferred from Direct Assay
more info
PubMed 
identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
iron ion binding IDA
Inferred from Direct Assay
more info
PubMed 
oxidative RNA demethylase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
peptidyl-lysine 5-dioxygenase activity IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein homodimerization activity IEA
Inferred from Electronic Annotation
more info
 
signaling receptor activity IEA
Inferred from Electronic Annotation
more info
 
single-stranded RNA binding IDA
Inferred from Direct Assay
more info
PubMed 
transcription coactivator activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
Process Evidence Code Pubs
RNA splicing IEA
Inferred from Electronic Annotation
more info
 
T cell differentiation in thymus IEA
Inferred from Electronic Annotation
more info
 
cell surface receptor signaling pathway IEA
Inferred from Electronic Annotation
more info
 
erythrocyte development IEA
Inferred from Electronic Annotation
more info
 
heart development IEA
Inferred from Electronic Annotation
more info
 
histone H3-R2 demethylation IDA
Inferred from Direct Assay
more info
PubMed 
NOT histone H3-R2 demethylation IDA
Inferred from Direct Assay
more info
PubMed 
histone H4-R3 demethylation IDA
Inferred from Direct Assay
more info
PubMed 
NOT histone H4-R3 demethylation IDA
Inferred from Direct Assay
more info
PubMed 
kidney development IEA
Inferred from Electronic Annotation
more info
 
lung development IEA
Inferred from Electronic Annotation
more info
 
mRNA processing IEA
Inferred from Electronic Annotation
more info
 
macrophage activation IEA
Inferred from Electronic Annotation
more info
 
oxidative RNA demethylation IDA
Inferred from Direct Assay
more info
PubMed 
peptidyl-lysine hydroxylation to 5-hydroxy-L-lysine IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of transcription, DNA-templated IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein demethylation IDA
Inferred from Direct Assay
more info
PubMed 
protein homooligomerization IDA
Inferred from Direct Assay
more info
PubMed 
recognition of apoptotic cell IEA
Inferred from Electronic Annotation
more info
 
regulation of mRNA splicing, via spliceosome IMP
Inferred from Mutant Phenotype
more info
PubMed 
retina development in camera-type eye IEA
Inferred from Electronic Annotation
more info
 
sprouting angiogenesis ISS
Inferred from Sequence or Structural Similarity
more info
 
Component Evidence Code Pubs
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytosol IEA
Inferred from Electronic Annotation
more info
 
nucleolus IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
nucleus IMP
Inferred from Mutant Phenotype
more info
PubMed 
plasma membrane IEA
Inferred from Electronic Annotation
more info
 
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 6
jumonji domain-containing protein 6
lysyl-hydroxylase JMJD6
peptide-lysine 5-dioxygenase JMJD6
phosphatidylserine receptor
NP_001074930.1
NP_055982.2

NCBI Reference Sequences (RefSeq)

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/Swiss-Prot
    Q6NYC1
    Related
    ENSP00000394085.2, ENST00000445478.6
    Conserved Domains (1) summary
    pfam02373
    Location:174288
    JmjC; JmjC domain, hydroxylase
  2. NM_015167.2NP_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
    Q6NYC1
    Related
    ENSP00000380750.4, ENST00000397625.8
    Conserved Domains (1) summary
    pfam02373
    Location:174288
    JmjC; JmjC domain, hydroxylase

RefSeqs of Annotated Genomes: Homo sapiens 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 GRCh38.p13 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p13 Primary Assembly

    Range
    76712830..76726799 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

RNA

  1. XR_001752457.2 RNA Sequence

  2. XR_001752456.2 RNA Sequence

    Related
    ENST00000617192.4
  3. XR_002957986.1 RNA Sequence

  4. XR_934429.3 RNA Sequence

    Related
    ENST00000303996.10
  5. XR_934428.3 RNA Sequence

    Related
    ENST00000542934.5
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