Set Analyses:
Advanced Search

Advanced Search

 
Search By
Section (entire)
for


 
or upload a file of gene symbols


Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

JMJD6 Gene

protein-coding   GIFtS: 55
GCID: GC17M074708

Jumonji Domain Containing 6

(Previous name: phosphatidylserine receptor)
(Previous symbol: PTDSR)
  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

Aliases
Jumonji Domain Containing 61 2     PSR2 5
Phosphatidylserine Receptor1 2 3     PTDSR12
PTDSR1 2 3     Bifunctional Arginine Demethylase And Lysyl-Hydroxylase JMJD62
Histone Arginine Demethylase JMJD62 3     EC 1.14.11.-3
JmjC Domain-Containing Protein 62 3     KIAA05853
Jumonji Domain-Containing Protein 62 3     Protein PTDSR3
Lysyl-Hydroxylase JMJD62 3     EC 1.14.118
Peptide-Lysine 5-Dioxygenase JMJD62 3     

External Ids:    HGNC: 193551   Entrez Gene: 232102   Ensembl: ENSG000000704957   OMIM: 6049145   UniProtKB: Q6NYC13   

Export aliases for JMJD6 gene to outside databases

Previous GC identifers: GC17M072221 GC17M070137


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for JMJD6 Gene:
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)

GeneCards Summary for JMJD6 Gene: 
JMJD6 (jumonji domain containing 6) is a protein-coding gene. Diseases associated with JMJD6 include intramuscular hemangioma, and chorioretinal scar. GO annotations related to this gene include RNA binding and receptor activity. An important paralog of this gene is JMJD4.

UniProtKB/Swiss-Prot: JMJD6_HUMAN, Q6NYC1
Function: Dioxygenase that can both act as a histone arginine demethylase and a lysyl-hydroxylase. Acts as a
lysyl-hydroxylase that catalyzes 5-hydroxylation on specific lysine residues of target proteins such as
U2AF2/U2AF65 and LUC7L2. Acts as a regulator of RNA splicing by mediating 5-hydroxylation of U2AF2/U2AF65,
affecting the pre-mRNA splicing activity of U2AF2/U2AF65. In addition to peptidyl-lysine 5-dioxygenase activity,
may act as a RNA hydroxylase, as suggested by its ability to bind single strand RNA. Also acts as an arginine
demethylase which demethylates histone H3 at 'Arg-2' (H3R2me) and histone H4 at 'Arg-3' (H4R3me), thereby playing
a role in histone code. However, histone arginine demethylation may not constitute the primary activity in vivo.
Has no histone lysine demethylase activity. Required for differentiation of multiple organs during embryogenesis.
Acts as a key regulator of hematopoietic differentiation: required for angiogenic sprouting by regulating the
pre-mRNA splicing activity of U2AF2/U2AF65. Seems to be necessary for the regulation of macrophage cytokine
responses

Gene Wiki entry for JMJD6 Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000017.10  NT_010783.15  NC_018928.2  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the JMJD6 gene promoter:
         Max1   Max   AML1a   MyoD   c-Myc   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidJMJD6 promoter sequence
   Search SABiosciences Chromatin IP Primers for JMJD6

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat JMJD6


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 17q25   Ensembl cytogenetic band:  17q25.1   HGNC cytogenetic band: 17q25

JMJD6 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
JMJD6 gene location

GeneLoc information about chromosome 17         GeneLoc Exon Structure

GeneLoc location for GC17M074708:  view genomic region     (about GC identifiers)

Start:
74,708,914 bp from pter      End:
74,722,881 bp from pter
Size:
13,968 bases      Orientation:
minus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: JMJD6_HUMAN, Q6NYC1 (See protein sequence)
Recommended Name: Bifunctional arginine demethylase and lysyl-hydroxylase JMJD6  
Size: 403 amino acids; 46462 Da
Cofactor: Binds 1 Fe(2+) ion per subunit
Subunit: Interacts with LUC7L2, LUC7L3 and U2AF2/U2AF65. Interacts with BRD4
Subcellular location: Nucleus, nucleoplasm. Nucleus, nucleolus. Note=Mainly found throughout the nucleoplasm
outside of regions containing heterochromatic DNA, with some localization in nucleolus. During mitosis, excluded
from the nucleus and reappears in the telophase of the cell cycle
Caution: Was initially thought to constitute the phosphatidylserine receptor, a receptor that mediates recognition
of phosphatidylserine, a specific marker only present at the surface of apoptotic cells. Phosphatidylserine
receptor probably participates in apoptotic cell phagocytosis. This protein was identified using phage display
expressing mAb 217, an antibody that specifically recognizes phosphatidylserine receptor. However, its nuclear
localization and the fact that mAb 217 antibody still recognizes the phosphatidylserine receptor in mice lacking
JMJD6, strongly suggest that it does not constitute the receptor for phosphatidylserine and is not involved in
apoptotic cell removal
Sequence caution: Sequence=AAH47003.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;
Sequence=BAA25511.1; Type=Erroneous initiation; Note=Translation N-terminally shortened;
3 PDB 3D structures from and Proteopedia for JMJD6:
3K2O (3D)        3LD8 (3D)        3LDB (3D)    
Secondary accessions: B3KMN8 B4DGX1 Q86VY0 Q8IUM5 Q9Y4E2
Alternative splicing: 3 isoforms:  Q6NYC1-1   Q6NYC1-2   Q6NYC1-3   

Explore the universe of human proteins at neXtProt for JMJD6: NX_Q6NYC1

Explore proteomics data for JMJD6 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q6NYC1

  • 4/20 DME Specific Peptides for JMJD6 (Q6NYC1) (see all 20)
     GSEGDGT  DEAITWF  RWFVMGP  YPRTQLP 

    JMJD6 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    JMJD6 Protein Expression
    REFSEQ proteins (2 alternative transcripts): 
    NP_001074930.1  NP_055982.2  

    ENSEMBL proteins: 
     ENSP00000394085   ENSP00000442362   ENSP00000302916   ENSP00000380750   ENSP00000465330  

    Human Recombinant Protein Products for JMJD6: 
    Browse Purified and Recombinant Proteins at EMD Millipore
    Browse R&D Systems for human recombinant proteins
    Browse recombinant and purified proteins available from Enzo Life Sciences
    OriGene Purified Proteins for JMJD6
    OriGene Protein Over-expression Lysate for JMJD6
    OriGene MassSpec for JMJD6 
    OriGene Custom Protein Services for JMJD6
    GenScript Custom Purified and Recombinant Proteins Services for JMJD6
    Novus Biologicals JMJD6 Proteins
    Novus Biologicals JMJD6 Lysates
    Browse Sino Biological Recombinant Proteins
    Browse Sino Biological Cell Lysates 
    Browse ProSpec Recombinant Proteins
    Browse Proteins at Cloud-Clone Corp. 

    Gene Ontology (GO): 4 cellular component terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA14729065
    GO:0005654nucleoplasm IDA--
    GO:0005730nucleolus IDA--
    GO:0005886plasma membrane IEA--

    JMJD6 for ontologies           About GeneDecksing



    JMJD6 Antibody Products: 
    EMD Millipore Mono- and Polyclonal Antibodies for the study of JMJD6
    R&D Systems Antibodies for JMJD6 (JMJD6/PSR)
    OriGene Antibodies for JMJD6
    OriGene Custom Antibody Services for JMJD6
    GenScript Custom Superior Antibodies Services for JMJD6
    Novus Biologicals JMJD6 Antibodies
    Abcam antibodies for JMJD6
    Browse Antibodies at Cloud-Clone Corp. 
    ThermoFisher Antibody for JMJD6
    LSBio Antibodies in human, mouse, rat for JMJD6 

    Assay Products for JMJD6: 
    Browse Kits and Assays available from EMD Millipore
    OriGene Custom Assay Services for JMJD6
    Browse R&D Systems for biochemical assays
    GenScript Custom Assay Services for JMJD6
    Browse Enzo Life Sciences for kits & assays
    Browse ELISAs at Cloud-Clone Corp. 
    Browse CLIAs at Cloud-Clone Corp.


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    1 InterPro protein domain:
     IPR003347 JmjC_dom

    Graphical View of Domain Structure for InterPro Entry Q6NYC1

    ProtoNet protein and cluster: Q6NYC1

    UniProtKB/Swiss-Prot: JMJD6_HUMAN, Q6NYC1
    Domain: The nuclear localization signal motifs are necessary and sufficient to target it into the nucleus
    Similarity: Belongs to the JMJD6 family
    Similarity: Contains 1 JmjC domain


    JMJD6 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
    About This Section

    Molecular Function:

         UniProtKB/Swiss-Prot Summary: JMJD6_HUMAN, Q6NYC1
    Function: Dioxygenase that can both act as a histone arginine demethylase and a lysyl-hydroxylase. Acts as a
    lysyl-hydroxylase that catalyzes 5-hydroxylation on specific lysine residues of target proteins such as
    U2AF2/U2AF65 and LUC7L2. Acts as a regulator of RNA splicing by mediating 5-hydroxylation of U2AF2/U2AF65,
    affecting the pre-mRNA splicing activity of U2AF2/U2AF65. In addition to peptidyl-lysine 5-dioxygenase activity,
    may act as a RNA hydroxylase, as suggested by its ability to bind single strand RNA. Also acts as an arginine
    demethylase which demethylates histone H3 at 'Arg-2' (H3R2me) and histone H4 at 'Arg-3' (H4R3me), thereby playing
    a role in histone code. However, histone arginine demethylation may not constitute the primary activity in vivo.
    Has no histone lysine demethylase activity. Required for differentiation of multiple organs during embryogenesis.
    Acts as a key regulator of hematopoietic differentiation: required for angiogenic sprouting by regulating the
    pre-mRNA splicing activity of U2AF2/U2AF65. Seems to be necessary for the regulation of macrophage cytokine
    responses
    Biophysicochemical properties: Kinetic parameters: KM=39 uM for 2-oxoglutarate;
    Induction: Up-regulated upon cytokine treatment, but not upon TNF treatment

         Enzyme Numbers (IUBMB): EC 1.14.11.-1 EC 1.14.112

         Gene Ontology (GO): 5/10 molecular function terms (GO ID links to tree view) (see all 10):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003723RNA binding TAS--
    GO:0003727single-stranded RNA binding IDA--
    GO:0004872receptor activity IEA--
    GO:0005506iron ion binding IDA--
    GO:0005515protein binding IPI19574390
         
    JMJD6 for ontologies           About GeneDecksing


    Phenotypes:
         3 GenomeRNAi human phenotypes for JMJD6:
     Cells with protrusions  Increased cell number in G2M,   Increased gamma-H2AX phosphory 

         15/17 MGI mutant phenotypes (inferred from 5 alleles(MGI details for Jmjd6) (see all 17):
     cardiovascular system  cellular  craniofacial  digestive/alimentary  growth/size 
     hematopoietic system  homeostasis/metabolism  immune system  integument  liver/biliary system 
     mortality/aging  muscle  nervous system  no phenotypic analysis  renal/urinary system 

    JMJD6 for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-outs for JMJD6: Jmjd6tm1Ysfk Jmjd6tm1Gbf Jmjd6tm1Flv Jmjd6tm1.1Gbf

       inGenious Targeting Laboratory - Custom generated mouse model solutions for JMJD6 
       inGenious Targeting Laboratory - Custom generated inducible mouse model solutions for JMJD6

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for JMJD6 
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for JMJD6 

    miRNA
    Products:
        
    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat JMJD6
    8/9 QIAGEN miScript miRNA Assays for microRNAs that regulate JMJD6 (see all 9):
    hsa-miR-3910 hsa-miR-1271 hsa-miR-1205 hsa-miR-124 hsa-miR-298 hsa-miR-3662 hsa-miR-506 hsa-miR-96
    SwitchGear 3'UTR luciferase reporter plasmidJMJD6 3' UTR sequence
    Inhib. RNA
    Products:
        
    Browse for Gene Knock-down Tools from EMD Millipore
    OriGene RNAi products in human, mouse, rat for JMJD6
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat JMJD6

    Gene Editing
    Products:
    DNA2.0 Custom Protein Engineering Service for JMJD6
    Sirion Biotech Customized adenovirus for overexpression of JMJD6

    Clone
    Products:
         
    Browse Clones for the Expression of Recombinant Proteins Available from EMD Millipore
    OriGene clones in human, mouse for JMJD6 (see all 14)
    OriGene ORF clones in mouse, rat for JMJD6
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 2): JMJD6 (NM_015167)
    Sino Biological Human cDNA Clone for JMJD6
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for JMJD6
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat JMJD6
    Sirion Biotech Customized lentivirus for stable overexpression of JMJD6 
                         Customized lentivirus expression plasmids for stable overexpression of JMJD6 

    Cell Line
    Products:
         
    GenScript Custom overexpressing Cell Line Services for JMJD6
    Search LifeMap BioReagents cell lines for JMJD6
    In Situ Assay
    Products:
       

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for JMJD6


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene).
    About This Section




    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for JMJD6

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    5/51 Interacting proteins for JMJD6 (Q6NYC13 ENSP000003940854) via UniProtKB, MINT, STRING, and/or I2D (see all 51)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    WASP427683, ENSP000003658914I2D: score=1 STRING: ENSP00000365891
    AK2P548193I2D: score=5 
    KCTD2Q146813I2D: score=5 
    KCTD5Q9NXV23I2D: score=5 
    WEE1P302913I2D: score=5 
    About this table

    Gene Ontology (GO): 5/21 biological process terms (GO ID links to tree view) (see all 21):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001568blood vessel development ----
    GO:0001822kidney development IEA--
    GO:0002040sprouting angiogenesis ISS--
    GO:0006351transcription, DNA-dependent IEA--
    GO:0006355regulation of transcription, DNA-dependent IEA--

    JMJD6 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
    About This Section

    JMJD6 for compounds           About GeneDecksing

    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for JMJD6

    10/124 HMDB Compounds for JMJD6 (see all 124)    About this table
    CompoundSynonyms CAS #PubMed Ids
    PS(14:0/14:0)Phosphatidylserine(14:0/14:0) (see all 7)----
    PS(14:0/14:1(9Z))Phosphatidylserine(14:0/14:1n5) (see all 13)----
    PS(14:0/16:0)1-myristoyl-2-palmitoyl-sn-glycero-3-phosphoserine (see all 7)----
    PS(14:0/16:1(9Z))PS(14:0/16:1n7) (see all 13)----
    PS(14:0/18:0)Phosphatidylserine(32:0) (see all 7)----
    PS(14:0/18:1(9Z))PSer(14:0/18:1n9) (see all 13)----
    PS(14:0/18:2(9Z,12Z))PS(14:0/18:2) (see all 13)----
    PS(14:0/18:3(9Z,12Z,15Z))Phosphatidylserine(14:0/18:3) (see all 14)----
    PS(14:0/20:3(8Z,11Z,14Z))PSer(14:0/20:3) (see all 14)----
    PS(14:0/20:4(5Z,8Z,11Z,14Z))PS(34:4) (see all 13)----

    4 Novoseek inferred chemical compound relationships for JMJD6 gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    phosphatidylserine 89.7 83 11877474 (5), 11742274 (3), 15622002 (3), 17534843 (2) (see all 44)
    phosphoserine 58.3 2 10936187 (1), 7583670 (1)
    phospholipid 26.7 2 9915844 (1), 7583670 (1)
    lipid 3.1 1 10936187 (1)

    Search CenterWatch for drugs/clinical trials and news about JMJD6

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    RNAi Products from EMD Millipore,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
    Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for JMJD6 gene (2 alternative transcripts): 
    NM_001081461.1  NM_015167.2  

    Unigene Cluster for JMJD6:

    Jumonji domain containing 6
    Hs.514505  [show with all ESTs]
    Unigene Representative Sequence: NM_001081461
    7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000445478(uc002jsn.1) ENST00000542934 ENST00000303996(uc002jso.3)
    ENST00000591460 ENST00000397625 ENST00000585429 ENST00000589982
    miRNA
    Products:
         
    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat JMJD6
    8/9 QIAGEN miScript miRNA Assays for microRNAs that regulate JMJD6 (see all 9):
    hsa-miR-3910 hsa-miR-1271 hsa-miR-1205 hsa-miR-124 hsa-miR-298 hsa-miR-3662 hsa-miR-506 hsa-miR-96
    SwitchGear 3'UTR luciferase reporter plasmidJMJD6 3' UTR sequence
    Inhib. RNA
    Products:
         
    Browse for Gene Knock-down Tools from EMD Millipore
    OriGene RNAi products in human, mouse, rat for JMJD6
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat JMJD6
    Clone
    Products:
         
    OriGene clones in human, mouse for JMJD6 (see all 14)
    OriGene ORF clones in mouse, rat for JMJD6
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 2): JMJD6 (NM_015167)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for JMJD6
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat JMJD6
    Sirion Biotech Customized lentivirus for stable overexpression of JMJD6 
                         Customized lentivirus expression plasmids for stable overexpression of JMJD6 
    Primer
    Products:
        
    OriGene qPCR primer pairs and template standards for JMJD6
    OriGene qSTAR qPCR primer pairs in human, mouse for JMJD6
    SABiosciences RT2 qPCR Primer Assay in human, mouse, rat JMJD6
      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat JMJD6
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat JMJD6

    Additional mRNA sequence: 

    AB011157.1 AB073711.1 AK021780.1 AK294816.1 AK314541.1 BC016837.1 BC047003.1 BC066654.1 

    15 DOTS entries:

    DT.100701748  DT.95298523  DT.100812905  DT.316217  DT.100812903  DT.120924927  DT.91824600  DT.203158 
    DT.95298519  DT.100812912  DT.100812901  DT.100812900  DT.100812909  DT.120925009  DT.95298521 

    24/263 AceView cDNA sequences (see all 263):

    BC047003 AW613617 BX417653 AW079645 CR602714 BF940715 BI910055 CD673337 
    BX345922 BU633979 BQ668503 BQ005106 CN480788 AI361495 CR594304 BQ669329 
    CK904897 BI759425 BX090664 BM916892 AI253789 CD364672 BM423427 CA436956 

    GeneLoc Exon Structure

    2 Alternative Splicing Database (ASD) splice patterns (SP) for JMJD6    About this scheme

    ExUns: 1 ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6a · 6b ^ 7
    SP1:                                -                     
    SP2:                                                      


    ECgene alternative splicing isoforms for JMJD6

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

    JMJD6 expression in normal human tissues (normalized intensities)      JMJD6 embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GTGGGAAACG
    JMJD6 Expression
    About this image


    JMJD6 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/36 selected tissues (see all 36) fully expand
     
     Blood (Hematopoietic System)    fully expand to see all 6 entries
             Hematopoietic Stem Cells Hematopoietic Bone Marrow
             lung ; macrophages   
             cd8+ t cell   
     
     Brain (Nervous System)    fully expand to see all 5 entries
             Cerebral Cortex
             cerebellum   
     
     Epithelium
             vagina ; squamous epithelial cells   
     
     Testis (Reproductive System)    fully expand to see all 4 entries
             Leydig Cells Testis Interstitium
             seminal vesicle ; glandular cells   
     
     Colon (Gastrointestinal Tract)    fully expand to see all 4 entries
             colon ; peripheral nerve/ganglion   

    See JMJD6 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for JMJD6

    SOURCE GeneReport for Unigene cluster: Hs.514505

    UniProtKB/Swiss-Prot: JMJD6_HUMAN, Q6NYC1
    Tissue specificity: Highly expressed in the heart, skeletal muscle and kidney. Expressed at moderate or low level
    in brain, placenta, lung, liver, pancreas, spleen, thymus, prostate, testis and ovary. Up-regulated in many
    patients with chronic pancreatitis. Expressed in nursing thymic epithelial cells

        SABiosciences Expression via Pathway-Focused PCR Arrays including JMJD6: 
              Epigenetic Chromatin Modification Enzymes in human mouse rat
              Hypoxia Signaling Pathway in human mouse rat

    Primer
    Products:
    OriGene qPCR primer pairs and template standards for JMJD6
    OriGene qSTAR qPCR primer pairs in human, mouse for JMJD6
    SABiosciences RT2 qPCR Primer Assay in human, mouse, rat JMJD6
    QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat JMJD6
    QIAGEN QuantiFast Probe-based Assays in human, mouse, rat JMJD6
    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for JMJD6

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
    About This Section

    This gene was present in the common ancestor of animals.

    Orthologs for JMJD6 gene from 7/17 species (see all 17)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Jmjd61 , 5 jumonji domain containing 61, 5 89.99(n)1
    97.77(a)1
      11 (81.49 cM)5
    1078171  NM_033398.21  NP_203971.21 
     1168374325 
    chicken
    (Gallus gallus)
    Aves JMJD61 jumonji domain containing 6 82.69(n)
    94.2(a)
      417355  NM_001030703.1  NP_001025874.1 
    lizard
    (Anolis carolinensis)
    Reptilia JMJD66
    Uncharacterized protein
    91(a)
    1 ↔ 1
    2(111674359-111693362)
    African clawed frog
    (Xenopus laevis)
    Amphibia cg5383-prov2 phosphatidylserine receptor 78.97(n)    BC045252.1 
    zebrafish
    (Danio rerio)
    Actinopterygii LOC2669622 phosphatidylserine receptor 73.22(n)   266962  AF401484.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta PSR1 phosphatidylserine receptor 64.46(n)
    70.63(a)
      42616  NM_142769.3  NP_651026.1 
    worm
    (Caenorhabditis elegans)
    Secernentea psr-11 Protein PSR-1 56.13(n)
    55.04(a)
      177229  NM_001047475.2  NP_001040940.1 


    ENSEMBL Gene Tree for JMJD6 (if available)
    TreeFam Gene Tree for JMJD6 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for JMJD6 gene
    JMJD42  

    JMJD6 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
    About This Section

    10/268 SNPs in JMJD6 are shown (see all 268)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 17 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1452767921,2
    C--74709062(+) GTGTTC/GTGACA 1 -- ut310--------
    rs1472204351,2
    C--74709107(+) CAGTTA/CTTCTG 1 -- ut310--------
    rs1818838511,2
    --74709343(+) CCTGGC/TTAATT 1 -- ut310--------
    rs1395689771,2
    C--74709424(+) ATCCAC/GCTGCC 1 -- ut310--------
    rs1869609251,2
    --74709469(+) GCTACA/GGCGCC 1 -- ut310--------
    rs1893376881,2
    --74709483(+) CCGAAA/GTTTCT 1 -- ut310--------
    rs1817537571,2
    --74709551(+) CTGCAG/TAGGAT 1 -- ut310--------
    rs1177111051,2
    C,F--74709609(+) CCAGAC/GTCCAC 1 -- ut311Minor allele frequency- G:0.03EA 120
    rs1851478741,2
    --74709688(+) CTAAAC/GAACCT 1 -- ut310--------
    rs571483181,2
    C,F--74709703(+) CTGGGG/CCATCC 1 -- ut313Minor allele frequency- C:0.11WA CSA 122

    HapMap Linkage Disequilibrium report for JMJD6 (74708914 - 74722881 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 3 variations for JMJD6:    About this table     
    Variant IDTypeSubtypePubMed ID
    nsv833550CNV Loss17160897
    nsv908833CNV Loss21882294
    esv28006CNV Gain19812545

    SABiosciences Cancer Mutation PCR Assays
    SeqTarget long-range PCR primers for resequencing JMJD6
    DNA2.0 Custom Variant and Variant Library Synthesis for JMJD6

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    OMIM gene information: 604914    OMIM disorders: --

    19 diseases for JMJD6:    About MalaCards
    intramuscular hemangioma    chorioretinal scar    retinal perforation    trigeminal neuralgia
    congenital heart block    chorioretinitis    bronchiectasis    retinal detachment
    wiskott-aldrich syndrome    periodontal disease    hemangioma    periodontitis
    retinitis    cystic fibrosis    endotheliitis    hypoxia
    pancreatitis    neuronitis    prostatitis

    4 diseases from the University of Copenhagen DISEASES database for JMJD6:
    Trigeminal neuralgia     Periodontal disease     Intramuscular hemangioma     Chorioretinal scar

    JMJD6 for disorders           About GeneDecksing

    1 Novoseek inferred disease relationship for JMJD6 gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    inflammation 37 2 11877474 (2)


    Export disorders for JMJD6 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
    About This Section

    PubMed articles for JMJD6 gene, integrated from 9 sources (see all 81):
    (articles sorted by number of sources associating them with JMJD6)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Phosphatidylserine receptor in chronic pancreatitis: evidence for a macrophage independent role. (PubMed id 15622002)1, 2, 9 Koeninger J.... Friess H. (2005)
    2. Phosphatidylserine receptor cooperates with high-density lipoprotein receptor in recognition of apoptotic cells by thymic nurse cells. (PubMed id 15072554)1, 2, 9 Cao W.M.... Ishida T. (2004)
    3. Elastase-mediated phosphatidylserine receptor cleavage impairs apoptotic cell clearance in cystic fibrosis and bronchiectasis. (PubMed id 11877474)1, 3, 9 Vandivier R.W....Henson P.M. (2002)
    4. The Brd4 extraterminal domain confers transcription a ctivation independent of pTEFb by recruiting multiple proteins, including NSD3. (PubMed id 21555454)1, 2 Rahman S....Howley P.M. (2011)
    5. Crystal structure of the 2-oxoglutarate- and Fe(II)-d ependent lysyl hydroxylase JMJD6. (PubMed id 20684070)1, 2 Mantri M....Schofield C.J. (2010)
    6. Interaction of JMJD6 with single-stranded RNA. (PubMed id 20679243)1, 2 Hong X....Zhang G. (2010)
    7. Jmjd6 catalyses lysyl-hydroxylation of U2AF65, a protein associated with RNA splicing. (PubMed id 19574390)1, 2 Webby C.J....Boettger A. (2009)
    8. JMJD6 is a histone arginine demethylase. (PubMed id 17947579)1, 2 Chang B.... Bruick R.K. (2007)
    9. Nuclear localization of the phosphatidylserine receptor protein via multiple nuclear localization signals. (PubMed id 14729065)1, 2 Cui P.... Pei D. (2004)
    10. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 23210 HGNC: 19355 AceView: PTDSR Ensembl:ENSG00000070495 euGenes: HUgn23210
    ECgene: JMJD6 H-InvDB: JMJD6

    (According to HUGE)
    About This Section
    HUGE: KIAA0585

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
    Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
    About This Section
    NameDescription
    PharmGKB entry for JMJD6 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    Patent Information for JMJD6 gene:
    Search GeneIP for patents involving JMJD6

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0 and Sirion Biotech, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Sirion Biotech, Cell lines from GenScript, and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
    About This Section

     Browse Kits and Assays available from EMD Millipore
     EMD Millipore Mono- and Polyclonal Antibodies for the study of JMJD6
     Browse Clones for the Expression of Recombinant Proteins Available from EMD Millipore
     Browse for Gene Knock-down Tools from EMD Millipore
     Browse Small Molecules at EMD Millipore
     Browse Purified and Recombinant Proteins at EMD Millipore
     
     EMD Millipore Custom Antibody & Bulk Services
     EMD Millipore Preclinical / Clinical Development Services
     EMD Millipore Immunoassay Services
     EMD Millipore Target Screening & Profiling Services

      
     Antibodies for JMJD6 (JMJD6/PSR)   Browse Cell Culture Products  
     Browse ELISAs   Browse Flow Cytometry Kits  
     Browse Primer Pairs   Browse Kinase Activity Assays/Reagents  
     Browse ELISpot Kits/Development Modules   Browse TFB/Immunoprecipitation Assays  
     Browse Apoptosis Detection Kits/Reagents   Browse Ubiquitin Proteasome Pathway (UPP) Assay Kits/Reagents  
     Browse DNA Damage/Repair Kits/Reagents   Browse Multiplex/Array Assay Kits/Reagents  
     Browse Cell Selection/Detection Kits/Reagents   Browse Secondary Antibodies/Controls/Staining Reagents  
     Browse Protease Activity Assays and Reagents   Browse Recombinant/Natural Proteins  
     Browse Stem Cell Products   Browse Tocris Biochemicals & Compounds  
     Browse cDNA Clones   Browse Proteome Profiler Antibody Arrays  
     OriGene Antibodies for JMJD6   OriGene RNAi products in human, mouse, rat for JMJD6  
     OriGene qPCR primer pairs and template standards for JMJD6   OriGene Protein Over-expression Lysate for JMJD6  
     OriGene MassSpec something-or-other for JMJD6   OriGene clones in human, mouse for JMJD6  
     OriGene qSTAR qPCR primer pairs in human, mouse for JMJD6   OriGene Purified Protein for JMJD6  
     OriGene ORF clones in mouse, rat for JMJD6   OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling  
     OriGene Custom Antibody Services for JMJD6   OriGene Custom Protein Services for JMJD6  

     
     
     QIAGEN Custom miScript Target Protector blocks miRNA-binding site of in human, mouse, rat JMJD6
     QIAGEN SeqTarget long-range PCR primers for resequencing JMJD6
     QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat JMJD6
     QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat JMJD6
     QIAGEN QuantiFast Probe-based Assays in human, mouse, rat JMJD6
     QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat JMJD6
     GenScript Custom Purified and Recombinant Proteins Services for JMJD6 GenScript cDNA clones with any tag delivered in your preferred vector for JMJD6
     GenScript Custom Assay Services for JMJD6 GenScript Custom Superior Antibodies Services for JMJD6
     GenScript Custom overexpressing Cell Line Services for JMJD6 CloneReady with Over 120,000 Genes
     Gene Synthesis: Any Gene in Any Vector Vector-based siRNA and miRNA, Ready for Transfection
     Gene Mutant Library, Variants up to 10^11 Plasmid Preparation
     Custom Peptide Services
     Search for Antibodies & Assays

     Regulatory tfbs in JMJD6 promoter
     Search Chromatin IP Primers for JMJD6
     RT2 qPCR Primer Assay in human, mouse, rat JMJD6
     Search GNC Networks for JMJD6
     SABiosciences PCR Arrays including human, mouse, rat JMJD6
     Search Tocris compounds for JMJD6
     Browse Sino Biological Proteins and Antibodies
     Browse Sino Biological Cell Lysates
     cDNA Clones for JMJD6
     4000+ Proteins
     Search Sino Biological for antibodies, proteins & pathways
     Protein Production Services
     Transfection Reagents
     Protein A/G/L resins
     Isotyping reagents
     Search www.enzolifesciences.com for proteins, assays, substrates, inhibitors & antibodies
     Novus Tissue Slides
     JMJD6 antibodies
     JMJD6 proteins
     JMJD6 lysates
     Antibodies for JMJD6
     See all of Abcam's Antibodies, Kits and Proteins for JMJD6
     Custom Antibody / Protein Production Service
     Bulk Purchasing
     Advantages of Rabbit Monoclonal antibodies
     Abcam protocols and scientific support
     Browse ProSpec Recombinant Proteins




     Browse Proteins at Cloud-Clone Corp.
     Browse Antibodies at Cloud-Clone Corp.
     Browse ELISAs at Cloud-Clone Corp.
     Browse CLIAs at Cloud-Clone Corp.
     Search LifeMap BioReagents cell lines for JMJD6
     Gene Synthesis
     Protein Engineering
     Variant Library Synthesis
     Codon Optimization
     Protein Production and Purification
     Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for JMJD6
     SwitchGear 3'UTR luciferase reporter plasmids for JMJD6
     SwitchGear Promoter luciferase reporter plasmids for JMJD6
     ThermoFisher Antibody for JMJD6
     Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat JMJD6
     inGenious Targeting Laboratory - Custom generated mouse model solutions for JMJD6
     inGenious Targeting Laboratory - Custom generated inducible mouse model solutions for JMJD6
    Customized:
     lentivirus for stable overexpression of JMJD6
     lentivirus expression plasmids for stable overexpression of JMJD6
     adenovirus for overexpression of JMJD6
     LSBio Antibodies in human, mouse, rat for JMJD6
    Customized transgenic rodents for:
     Humanization
     Biomarker expression
     Off-target effect monitoring
     Translational medicine
     Tissue-specific gene expresssion
     Time-controlled gene expresssion
           
    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

    View Random Gene

    Category
    (GIFtS: 73)
    transforming growth factor, beta 1
    GIFtS Group
    The GeneCards human gene database gene index: 1 3 5 6 A B C D E F G H I J K L M N O P Q R S T U V W X Y Z 


    Developed at the Crown Human Genome Center, Department of Molecular Genetics, the Weizmann Institute of Science

    Hot genes      Disease genes      JMJD6 gene at Home site.
    hostname: 356980-web2.xennexinc.com index build: 106 solr: 1.4