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PRDM6 Gene

protein-coding   GIFtS: 40
GCID: GC05P122424

PR Domain Containing 6

  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)
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Aliases
PR Domain Containing 61 2     Putative Histone-Lysine N-Methyltransferase PRDM62
PR Domain Zinc Finger Protein 62 3     EC 2.1.1.433
PR Domain-Containing Protein 62 3     PFM33
PR-Domain Zinc Finger Protein 62     

External Ids:    HGNC: 93501   Entrez Gene: 931662   Ensembl: ENSG000000614557   UniProtKB: Q9NQX03   

Export aliases for PRDM6 gene to outside databases

Previous GC identifers: GC05P122055 GC05P122751 GC05P122455 GC05P122480 GC05P122452 GC05U900559 GC05P117612


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for PRDM6 Gene:
PRDM6 (PR domain containing 6) is a protein-coding gene. Diseases associated with PRDM6 include intracranial aneurysm, and endotheliitis. GO annotations related to this gene include protein homodimerization activity and histone-lysine N-methyltransferase activity. An important paralog of this gene is PRDM12.

UniProtKB/Swiss-Prot: PRDM6_HUMAN, Q9NQX0
Function: Putative histone methyltransferase that acts as a transcriptional repressor of smooth muscle gene
expression. Promotes the transition from differentiated to proliferative smooth muscle by suppressing
differentiation and maintaining the proliferative potential of vascular smooth muscle cells. Also plays a role in
endothelial cells by inhibiting endothelial cell proliferation, survival and differentiation. It is unclear
whether it has histone methyltransferase activity in vivo. According to some authors, it does not act as a
histone methyltransferase by itself and represses transcription by recruiting EHMT2/G9a. According to others, it
possesses histone methyltransferase activity when associated with other proteins and specifically methylates
'Lys-20' of histone H4 in vitro. 'Lys-20' methylation represents a specific tag for epigenetic transcriptional
repression (By similarity)




(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:
NC_000005.10  NT_034772.7  NC_018916.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the PRDM6 gene promoter:
         SRF   Sp1   SRF (504 AA)   USF2   USF-1:USF-2   C/EBPalpha   CHOP-10   USF-1   ARP-1   Pax-4a   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for PRDM6

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat PRDM6


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

Entrez Gene cytogenetic band: 5q23.2   Ensembl cytogenetic band:  5q23.2   HGNC cytogenetic band: 5q21-q23

PRDM6 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PRDM6 gene location

GeneLoc information about chromosome 5         GeneLoc Exon Structure

GeneLoc location for GC05P122424:  view genomic region     (about GC identifiers)

Start:
122,424,816 bp from pter      End:
122,529,960 bp from pter
Size:
105,145 bases      Orientation:
plus 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, 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., 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: PRDM6_HUMAN, Q9NQX0 (See protein sequence)
Recommended Name: Putative histone-lysine N-methyltransferase PRDM6  
Size: 595 amino acids; 64452 Da
Subunit: Interacts with HDAC1, HDAC2, HDAC3, CBX1 and EP300 (By similarity)
Sequence caution: Sequence=AAF78078.1; Type=Erroneous initiation; Sequence=AAF78079.1; Type=Erroneous initiation;
Secondary accessions: B5MCJ4 Q9NQW9
Alternative splicing: 3 isoforms:  Q9NQX0-3   Q9NQX0-2   Q9NQX0-1   

Explore the universe of human proteins at neXtProt for PRDM6: NX_Q9NQX0

Explore proteomics data for PRDM6 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See PRDM6 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_001129711.1  
    ENSEMBL proteins: 
     ENSP00000384725   ENSP00000390919  

    PRDM6 Human Recombinant Protein Products:

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    ZNF: Zinc fingers, C2H2-type

    4 InterPro protein domains:
     IPR001214 SET_dom
     IPR015880 Znf_C2H2-like
     IPR013087 Znf_C2H2/integrase_DNA-bd
     IPR007087 Znf_C2H2

    Graphical View of Domain Structure for InterPro Entry Q9NQX0

    ProtoNet protein and cluster: Q9NQX0

    UniProtKB/Swiss-Prot: PRDM6_HUMAN, Q9NQX0
    Similarity: Belongs to the class V-like SAM-binding methyltransferase superfamily
    Similarity: Contains 4 C2H2-type zinc fingers
    Similarity: Contains 1 SET domain


    PRDM6 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,
    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, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: PRDM6_HUMAN, Q9NQX0
    Function: Putative histone methyltransferase that acts as a transcriptional repressor of smooth muscle gene
    expression. Promotes the transition from differentiated to proliferative smooth muscle by suppressing
    differentiation and maintaining the proliferative potential of vascular smooth muscle cells. Also plays a role in
    endothelial cells by inhibiting endothelial cell proliferation, survival and differentiation. It is unclear
    whether it has histone methyltransferase activity in vivo. According to some authors, it does not act as a
    histone methyltransferase by itself and represses transcription by recruiting EHMT2/G9a. According to others, it
    possesses histone methyltransferase activity when associated with other proteins and specifically methylates
    'Lys-20' of histone H4 in vitro. 'Lys-20' methylation represents a specific tag for epigenetic transcriptional
    repression (By similarity)
    Catalytic activity: S-adenosyl-L-methionine + L-lysine-[histone] = S-adenosyl-L-homocysteine +
    N(6)-methyl-L-lysine-[histone]

         Enzyme Number (IUBMB): EC 2.1.1.431

         Gene Ontology (GO): 5 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003676nucleic acid binding IEA--
    GO:0005515protein binding ----
    GO:0018024histone-lysine N-methyltransferase activity IEA--
    GO:0042803protein homodimerization activity IEA--
    GO:0046872metal ion binding IEA--
         
    PRDM6 for ontologies           About GeneDecksing


    Animal Models:
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    (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
    PRDM6_HUMAN, Q9NQX0: Nucleus (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus3

    Gene Ontology (GO): 1 cellular component term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IEA--

    PRDM6 for ontologies           About GeneDecksing


    (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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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for PRDM6
    Interactions:

        Search GeneGlobe Interaction Network for PRDM6

    Gene Ontology (GO): 4 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006351transcription, DNA-templated IEA--
    GO:0022008neurogenesis IEA--
    GO:0045892negative regulation of transcription, DNA-templated IEA--
    GO:0051151negative regulation of smooth muscle cell differentiation IEA--

    PRDM6 for ontologies           About GeneDecksing



    (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 PRDM6



    (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, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for PRDM6 gene: 
    NM_001136239.1  

    Unigene Cluster for PRDM6:

    PR domain containing 6
    Hs.135118  [show with all ESTs]
    Unigene Representative Sequence: NM_001136239
    4 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000407847(uc003kti.3 uc003ktj.3) ENST00000434521 ENST00000464424
    ENST00000427739
    miRNA
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    hsa-miR-502-5p hsa-miR-19b-2* hsa-miR-16-2* hsa-miR-216b hsa-miR-488 hsa-miR-3125 hsa-miR-3916 hsa-miR-4314
    Browse SwitchGear 3'UTR luciferase reporter plasmids
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      QuantiFast Probe-based Assays in human, mouse, rat PRDM6

    Additional mRNA sequence: 

    AF272898.1 AK297992.1 

    4 DOTS entries:

    DT.100743089  DT.106068  DT.70104022  DT.91738989 

    GeneLoc Exon Structure

    4 Alternative Splicing Database (ASD) splice patterns (SP) for PRDM6    About this scheme

    ExUns: 1 ^ 2 ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7a · 7b ^ 8 ^ 9
    SP1:                                                                  
    SP2:                                -     -                           
    SP3:                                      -                           
    SP4:                                                                  


    ECgene alternative splicing isoforms for PRDM6

    (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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    PRDM6 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TAAAATGTAC
    PRDM6 Expression
    About this image

    PRDM6 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    PRDM6 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.135118
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    In Situ
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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 PRDM6 gene from Selected species (see all 13)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Prdm61 , 5 PR domain containing 61, 5 87.16(n)1
    92.06(a)1
      18 (29.04 cM)5
    2255181  NM_001033281.31  NP_001028453.11 
     534650515 
    chicken
    (Gallus gallus)
    Aves PRDM61 PR domain containing 6 82.16(n)
    88.87(a)
      426800  XM_424413.4  XP_424413.3 
    lizard
    (Anolis carolinensis)
    Reptilia PRDM66
    PR domain containing 6
    81(a)
    1 ↔ 1
    GL343193.1(12347333-12473407)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.123112 Xenopus laevis transcribed sequences 83.84(n)    BJ067457.1 
    zebrafish
    (Danio rerio)
    Actinopterygii LOC1018865161 putative histone-lysine N-methyltransferase PRDM6-like 75.24(n)
    84.29(a)
      101886516  XM_005172423.1  XP_005172480.1 
    worm
    (Caenorhabditis elegans)
    Secernentea set-176
    Protein SET-17 (set-17) mRNA, complete cds
    17(a)
    1 → many
    II(8939057-8940488) WBGene00011887


    ENSEMBL Gene Tree for PRDM6 (if available)
    TreeFam Gene Tree for PRDM6 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for PRDM6 gene
    PRDM122  PRDM142  PRDM72  PRDM112  PRDM42  
    Selected SIMAP similar genes for PRDM6 using alignment to 2 protein entries:     PRDM6_HUMAN (see all proteins) (see all similar genes):
    smap-7    kr-znf3    ZNF78L1    ZNF826P    HZF16    ZFS-5
    ZNF664    ZNF    DKFZp434J0650    ZNF697    ZFP41    ZNF808
    DKFZp686M04222    DKFZp686N0199    ZFS-2    ZNF22    ZNF702P    zf30

    PRDM6 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), 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 PRDM6 (see all 2313)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 5 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1164401041,2
    F--122422912(+) CGGCAC/TGTCCA 1 -- us2k11Minor allele frequency- T:0.03WA 118
    rs1883240031,2
    C--122423034(+) TCAAAA/GTCCAG 1 -- us2k10--------
    rs8888541,2
    F,A--122423068(+) GTGAAA/GGGGTA 1 -- us2k11Minor allele frequency- G:0.00MN 184
    rs1850036061,2
    --122423074(+) GGGTAA/GGGGGG 1 -- us2k10--------
    rs42621051,2
    C,F,A--122423084(+) GAGGCA/GGGGTT 1 -- us2k16Minor allele frequency- G:0.37NA CSA WA 246
    rs8888551,2
    F--122423108(+) GTAGGT/CTCTTG 1 -- us2k11Minor allele frequency- C:0.00MN 184
    rs8888561,2
    C,F,A--122423113(+) TTCTTG/TGGGAC 1 -- us2k1 tfbs36Minor allele frequency- T:0.19MN NA CSA WA 428
    rs37497241,2
    C,F--122423196(+) GCCGCC/AGGAGT 1 -- us2k14Minor allele frequency- A:0.05EA NA 1596
    rs1158827611,2
    F--122423278(+) ACCAGG/CAGAGT 1 -- us2k11Minor allele frequency- C:0.04WA 118
    rs8888571,2
    C,F,A,H--122423281(+) AGGAGA/CGTGTG 1 -- us2k111Minor allele frequency- C:0.22NA EA MN NS 2464

    HapMap Linkage Disequilibrium report for PRDM6 (122424816 - 122529960 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 5 variations for PRDM6:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2730713CNV Deletion23290073
    esv2730710CNV Deletion23290073
    esv2730712CNV Deletion23290073
    nsv4979CNV Insertion18451855
    nsv520349CNV Loss19592680

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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    2 diseases for PRDM6:    
    About MalaCards
    intracranial aneurysm    endotheliitis


    PRDM6 for disorders           About GeneDecksing

    Genetic Association Database (GAD): PRDM6
    Human Genome Epidemiology (HuGE) Navigator: PRDM6 (1 document)

    Export disorders for PRDM6 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 PRDM6 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with PRDM6)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1, 4 Rose J.E....Uhl G.R. (Mol. Med. 2010)
    2. Hundreds of variants clustered in genomic loci and biological pathways affect human height. (PubMed id 20881960)4 Lango Allen H....Hirschhorn J.N. (Nature 2010)
    3. Genetic variants associated with cardiac structure and function: a meta-analysis and replication of genome-wide association data. (PubMed id 19584346)4 Vasan R.S....Blankenberg S. (JAMA 2009)
    4. Genome-wide association with diabetes-related traits in the Framingham Heart Study. (PubMed id 17903298)4 Meigs J.B....Dupuis J. (BMC Med. Genet. 2007)
    5. Genome-wide association with bone mass and geometry in the Framingham Heart Study. (PubMed id 17903296)4 Kiel D.P....Karasik D. (BMC Med. Genet. 2007)
    6. The DNA sequence and comparative analysis of human chromosome 5. (PubMed id 15372022)2 Schmutz J.... Rubin E.M. (Nature 2004)
    7. The yin-yang of PR-domain family genes in tumorigenesis. (PubMed id 10668202)2 Jiang G.L. and Huang S. (Histol. Histopathol. 2000)

    (in PubMed, OMIM, and NCBI Bookshelf)
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 93166 HGNC: 9350 Ensembl:ENSG00000061455 euGenes: HUgn93166 ECgene: PRDM6
    H-InvDB: PRDM6

    (According to HUGE)
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      --

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

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    NameDescription
    PharmGKB entry for PRDM6 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 PRDM6 gene:
    Search GeneIP for patents involving PRDM6

    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, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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