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JMJD6 (arginine demethylase and lysine hydroxylase)

Identity

Alias_namesPTDSR
phosphatidylserine receptor
jumonji domain containing 6
Alias_symbol (synonym)PTDSR1
KIAA0585
Other aliasPSR
HGNC (Hugo) JMJD6
LocusID (NCBI) 23210
Atlas_Id 53229
Location 17q25.1  [Link to chromosome band 17q25]
Location_base_pair Starts at 76712832 and ends at 76726799 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2016)
SEPT9 (17q25.2) / JMJD6 (17q25.1)ST6GALNAC2 (17q25.1) / JMJD6 (17q25.1)SEPT9 17q25.2 / JMJD6 17q25.1
ST6GALNAC2 17q25.1 / JMJD6 17q25.1

Note

Non-annotated gene. Preliminary data : if you are an author
who wish to write a full paper/card on this gene, go to  How to contribute

DNA/RNA

 


External links

Nomenclature
HGNC (Hugo)JMJD6   19355
Cards
Entrez_Gene (NCBI)JMJD6  23210  arginine demethylase and lysine hydroxylase
AliasesPSR; PTDSR; PTDSR1
GeneCards (Weizmann)JMJD6
Ensembl hg19 (Hinxton)ENSG00000070495 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000070495 [Gene_View]  chr17:76712832-76726799 [Contig_View]  JMJD6 [Vega]
ICGC DataPortalENSG00000070495
TCGA cBioPortalJMJD6
AceView (NCBI)JMJD6
Genatlas (Paris)JMJD6
WikiGenes23210
SOURCE (Princeton)JMJD6
Genetics Home Reference (NIH)JMJD6
Genomic and cartography
GoldenPath hg38 (UCSC)JMJD6  -     chr17:76712832-76726799 -  17q25.1   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)JMJD6  -     17q25.1   [Description]    (hg19-Feb_2009)
EnsemblJMJD6 - 17q25.1 [CytoView hg19]  JMJD6 - 17q25.1 [CytoView hg38]
Mapping of homologs : NCBIJMJD6 [Mapview hg19]  JMJD6 [Mapview hg38]
OMIM604914   
Gene and transcription
Genbank (Entrez)AA226560 AA775442 AB011157 AB073711 AK021780
RefSeq transcript (Entrez)NM_001081461 NM_015167
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)JMJD6
Cluster EST : UnigeneHs.514505 [ NCBI ]
CGAP (NCI)Hs.514505
Alternative Splicing GalleryENSG00000070495
Gene ExpressionJMJD6 [ NCBI-GEO ]   JMJD6 [ EBI - ARRAY_EXPRESS ]   JMJD6 [ SEEK ]   JMJD6 [ MEM ]
Gene Expression Viewer (FireBrowse)JMJD6 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)23210
GTEX Portal (Tissue expression)JMJD6
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ6NYC1   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ6NYC1  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ6NYC1
Splice isoforms : SwissVarQ6NYC1
Catalytic activity : Enzyme1.14.11.- [ Enzyme-Expasy ]   1.14.11.-1.14.11.- [ IntEnz-EBI ]   1.14.11.- [ BRENDA ]   1.14.11.- [ KEGG ]   
PhosPhoSitePlusQ6NYC1
Domaine pattern : Prosite (Expaxy)JMJC (PS51184)   
Domains : Interpro (EBI)JmjC_dom   
Domain families : Pfam (Sanger)JmjC (PF02373)   
Domain families : Pfam (NCBI)pfam02373   
Domain families : Smart (EMBL)JmjC (SM00558)  
Conserved Domain (NCBI)JMJD6
DMDM Disease mutations23210
Blocks (Seattle)JMJD6
PDB (SRS)3K2O    3LD8    3LDB   
PDB (PDBSum)3K2O    3LD8    3LDB   
PDB (IMB)3K2O    3LD8    3LDB   
PDB (RSDB)3K2O    3LD8    3LDB   
Structural Biology KnowledgeBase3K2O    3LD8    3LDB   
SCOP (Structural Classification of Proteins)3K2O    3LD8    3LDB   
CATH (Classification of proteins structures)3K2O    3LD8    3LDB   
SuperfamilyQ6NYC1
Human Protein AtlasENSG00000070495
Peptide AtlasQ6NYC1
HPRD05371
IPIIPI00550958   IPI00375496   IPI00604598   IPI00896458   IPI01015282   
Protein Interaction databases
DIP (DOE-UCLA)Q6NYC1
IntAct (EBI)Q6NYC1
FunCoupENSG00000070495
BioGRIDJMJD6
STRING (EMBL)JMJD6
ZODIACJMJD6
Ontologies - Pathways
QuickGOQ6NYC1
Ontology : AmiGOkidney development  sprouting angiogenesis  RNA binding  single-stranded RNA binding  receptor activity  iron ion binding  protein binding  nucleus  nucleoplasm  nucleoplasm  nucleolus  cytosol  plasma membrane  transcription, DNA-templated  regulation of transcription, DNA-templated  mRNA processing  cell surface receptor signaling pathway  heart development  RNA splicing  peptidyl-lysine hydroxylation to 5-hydroxy-L-lysine  lung development  intracellular ribonucleoprotein complex  histone demethylase activity  T cell differentiation in thymus  histone demethylase activity (H3-R2 specific)  histone demethylase activity (H4-R3 specific)  macrophage activation  identical protein binding  identical protein binding  protein homodimerization activity  recognition of apoptotic cell  regulation of mRNA splicing, via spliceosome  erythrocyte development  oxidation-reduction process  retina development in camera-type eye  histone H3-R2 demethylation  histone H4-R3 demethylation  peptidyl-lysine 5-dioxygenase activity  
Ontology : EGO-EBIkidney development  sprouting angiogenesis  RNA binding  single-stranded RNA binding  receptor activity  iron ion binding  protein binding  nucleus  nucleoplasm  nucleoplasm  nucleolus  cytosol  plasma membrane  transcription, DNA-templated  regulation of transcription, DNA-templated  mRNA processing  cell surface receptor signaling pathway  heart development  RNA splicing  peptidyl-lysine hydroxylation to 5-hydroxy-L-lysine  lung development  intracellular ribonucleoprotein complex  histone demethylase activity  T cell differentiation in thymus  histone demethylase activity (H3-R2 specific)  histone demethylase activity (H4-R3 specific)  macrophage activation  identical protein binding  identical protein binding  protein homodimerization activity  recognition of apoptotic cell  regulation of mRNA splicing, via spliceosome  erythrocyte development  oxidation-reduction process  retina development in camera-type eye  histone H3-R2 demethylation  histone H4-R3 demethylation  peptidyl-lysine 5-dioxygenase activity  
NDEx NetworkJMJD6
Atlas of Cancer Signalling NetworkJMJD6
Wikipedia pathwaysJMJD6
Orthology - Evolution
OrthoDB23210
GeneTree (enSembl)ENSG00000070495
Phylogenetic Trees/Animal Genes : TreeFamJMJD6
HOVERGENQ6NYC1
HOGENOMQ6NYC1
Homologs : HomoloGeneJMJD6
Homology/Alignments : Family Browser (UCSC)JMJD6
Gene fusions - Rearrangements
Fusion : MitelmanSEPT9/JMJD6 [17q25.2/17q25.1]  [t(17;17)(q25;q25)]  
Fusion : MitelmanST6GALNAC2/JMJD6 [17q25.1/17q25.1]  [t(17;17)(q25;q25)]  
Fusion: TCGASEPT9 17q25.2 JMJD6 17q25.1 BRCA
Fusion: TCGAST6GALNAC2 17q25.1 JMJD6 17q25.1 BRCA
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerJMJD6 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)JMJD6
dbVarJMJD6
ClinVarJMJD6
1000_GenomesJMJD6 
Exome Variant ServerJMJD6
ExAC (Exome Aggregation Consortium)JMJD6 (select the gene name)
Genetic variants : HAPMAP23210
Genomic Variants (DGV)JMJD6 [DGVbeta]
DECIPHERJMJD6 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisJMJD6 
Mutations
ICGC Data PortalJMJD6 
TCGA Data PortalJMJD6 
Broad Tumor PortalJMJD6
OASIS PortalJMJD6 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICJMJD6  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDJMJD6
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch JMJD6
DgiDB (Drug Gene Interaction Database)JMJD6
DoCM (Curated mutations)JMJD6 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)JMJD6 (select a term)
intoGenJMJD6
Cancer3DJMJD6(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM604914   
Orphanet
MedgenJMJD6
Genetic Testing Registry JMJD6
NextProtQ6NYC1 [Medical]
TSGene23210
GENETestsJMJD6
Target ValidationJMJD6
Huge Navigator JMJD6 [HugePedia]
snp3D : Map Gene to Disease23210
BioCentury BCIQJMJD6
ClinGenJMJD6
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD23210
Chemical/Pharm GKB GenePA162392513
Clinical trialJMJD6
Miscellaneous
canSAR (ICR)JMJD6 (select the gene name)
Probes
Litterature
PubMed50 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineJMJD6
EVEXJMJD6
GoPubMedJMJD6
iHOPJMJD6
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Wed Jun 7 12:39:05 CEST 2017

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