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JMJD6 Gene

protein-coding   GIFtS: 56
GCID: GC17M074708

Jumonji Domain Containing 6

(Previous name: phosphatidylserine receptor)
(Previous symbol: PTDSR)
  See JMJD6-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)
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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, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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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 chorioretinal scar, and intramuscular hemangioma. 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 an 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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000017.10  NC_018928.2  NT_010783.16  
Regulatory elements:
   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 Chromatin IP Primers for JMJD6

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing 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 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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, Cloud-Clone Corp., and/or eBioscience,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., and/or eBioscience, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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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
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: 

  • Ubiquitination2 at Lys167, Lys204
  • Modification sites at PhosphoSitePlus
  • Selected DME Specific Peptides for JMJD6 (Q6NYC1) (see all 20)
     GSEGDGT  DEAITWF  RWFVMGP  YPRTQLP 


    See JMJD6 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

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

    ENSEMBL proteins: 
     ENSP00000394085   ENSP00000442362   ENSP00000302916   ENSP00000380750   ENSP00000465330  

    JMJD6 Human Recombinant Protein Products:

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    OriGene Protein Over-expression Lysate for JMJD6
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    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.

     
    Search eBioscience for Proteins for JMJD6 

    JMJD6 Antibody Products:

    EMD Millipore Mono- and Polyclonal Antibodies for the study of JMJD6
    R&D Systems Antibodies for JMJD6 (JMJD6/PSR)
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    Abcam antibodies for JMJD6
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    Browse ELISAs at Cloud-Clone Corp.
    Browse CLIAs at Cloud-Clone Corp.
    Search eBioscience for ELISAs for JMJD6 


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    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


    Find genes that share domains with JMJD6           About GenesLikeMe


    (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,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    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 an 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): Selected molecular function terms (see all 9):    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
         
    Find genes that share ontologies with JMJD6           About GenesLikeMe


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

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

    Find genes that share phenotypes with JMJD6           About GenesLikeMe

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

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for JMJD6
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       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:
        
    miRTarBase miRNAs that target JMJD6:
    hsa-mir-484 (MIRT041794), hsa-mir-1260b (MIRT052729), hsa-mir-92a-3p (MIRT049750)

    Block miRNA regulation of human, mouse, rat JMJD6 using miScript Target Protectors
    Selected qRT-PCR 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:
        
    OriGene RNAi products in human, mouse, rat for JMJD6
    Predesigned siRNA for gene silencing in human, mouse, rat JMJD6

    Gene Editing
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    Clone
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    OriGene clones in human, mouse for JMJD6 (see all 13)
    OriGene ORF clones in mouse, rat for JMJD6
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    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
    Addgene plasmids for JMJD6 

    Cell Line
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    Browse ESI BIO Cell Lines and PureStem Progenitors for JMJD6 
    In Situ Assay
    Products:
       

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for JMJD6


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    JMJD6_HUMAN, Q6NYC1: 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
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    extracellular2
    plasma membrane2

    Gene Ontology (GO): 4 cellular component terms:    About this table

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

    Find genes that share ontologies with JMJD6           About GenesLikeMe


    (SuperPaths according to PathCards, Pathways according to 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 QIAGEN, 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 Apr 2014 via Entrez Gene).
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        Pathway & Disease-focused RT2 Profiler PCR Arrays including JMJD6: 
              Epigenetic Chromatin Modification Enzymes in human mouse rat
              Hypoxia Signaling Pathway in human mouse rat

    Interactions:

        Search GeneGlobe Interaction Network for JMJD6

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

    Selected Interacting proteins for JMJD6 (Q6NYC11, 3 ENSP000003940854) via UniProtKB, MINT, STRING, and/or I2D (see all 70)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    WASP427683, ENSP000003658914I2D: score=1 STRING: ENSP00000365891
    PRPF38AQ8NAV11, ENSP000002571814EBI-8464037,EBI-715374 STRING: ENSP00000257181
    AK2P548193I2D: score=5 
    KCTD2Q146813I2D: score=5 
    KCTD5Q9NXV23I2D: score=5 
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 22):    About this table

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

    Find genes that share ontologies with JMJD6           About GenesLikeMe



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for JMJD6

    Selected 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)



    Find genes that share compounds with JMJD6           About GenesLikeMe



    (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,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    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
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    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
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    Addgene plasmids for JMJD6 
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      QuantiTect SYBR Green Assays in human, mouse, rat JMJD6
      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 

    Selected AceView cDNA sequences (see all 263):

    BC066654 BM557353 CD365078 CR602714 BQ223112 BM687017 AI253789 BM788992 
    BU192654 CB529456 AA262167 CR598927 BE275732 BX417653 CA866177 BF940715 
    AI951386 BU070317 CK904897 BE466065 CA309200 BQ639908 BM700095 CN480788 

    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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    JMJD6 expression in normal human tissues (normalized intensities)
    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
     selected tissues (see all 6) fully expand
     
     Brain (Nervous System)    fully expand to see all 3 entries
             Cerebral Cortex
     
     Ovary (Reproductive System)    fully expand to see all 2 entries
             Ovarian Mesenchymal Stroma Cells Ovary Interstitium
             Oviduct
     
     Trophoblast (Extraembryonic Tissues)
             Trophoblast Cells Trophoblast
     
     Pancreas (Endocrine System)
             Islets of Langerhans
     
     Testis (Reproductive System)
             Leydig Cells Testis Interstitium
    JMJD6 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    JMJD6 Protein Expression

    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

        Pathway & Disease-focused RT2 Profiler PCR Arrays including JMJD6: 
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    (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)
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    This gene was present in the common ancestor of animals.

    Orthologs for JMJD6 gene from Selected 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
    jumonji domain containing 6
    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 62.63(n)
    68.43(a)
      42616  NM_001275903.1  NP_001262832.1 
    worm
    (Caenorhabditis elegans)
    Secernentea psr-11 psr-1 58.21(n)
    56.19(a)
      177229  NM_001047475.3  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)
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    Paralogs for JMJD6 gene
    JMJD42  

    Find genes that share paralogs with JMJD6           About GenesLikeMe



    (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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for JMJD6 (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

    Site Specific Mutation Identification with 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, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 604914    OMIM disorders: --

    3 diseases for JMJD6:    
    About MalaCards
    chorioretinal scar    intramuscular hemangioma    trigeminal neuralgia

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

    Find genes that share disorders with JMJD6           About GenesLikeMe

    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)
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    PubMed articles for JMJD6 gene, integrated from 10 sources (see all 83):
    (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. (Ann. Surg. 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. (J. Mol. Endocrinol. 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. (J. Clin. Invest. 2002)
    4. Crystal structure of the 2-oxoglutarate- and Fe(II)-dependent lysyl hydroxylase JMJD6. (PubMed id 20684070)1, 2 Mantri M.... Schofield C.J. (J. Mol. Biol. 2010)
    5. Interaction of JMJD6 with single-stranded RNA. (PubMed id 20679243)1, 2 Hong X.... Zhang G. (Proc. Natl. Acad. Sci. U.S.A. 2010)
    6. Jmjd6 catalyses lysyl-hydroxylation of U2AF65, a protein associated with RNA splicing. (PubMed id 19574390)1, 2 Webby C.J....Boettger A. (Science 2009)
    7. JMJD6 is a histone arginine demethylase. (PubMed id 17947579)1, 2 Chang B.... Bruick R.K. (Science 2007)
    8. Nuclear localization of the phosphatidylserine receptor protein via multiple nuclear localization signals. (PubMed id 14729065)1, 2 Cui P.... Pei D. (Exp. Cell Res. 2004)
    9. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    10. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     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)
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    Entrez Gene: 23210 HGNC: 19355 AceView: PTDSR Ensembl:ENSG00000070495 euGenes: HUgn23210
    ECgene: JMJD6 H-InvDB: JMJD6

    (According to HUGE)
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    HUGE: KIAA0585

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    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.)
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    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



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