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

PRDM12 Gene

protein-coding   GIFtS: 43
GCID: GC09P133539

PR Domain Containing 12

  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
PR Domain Containing 121 2     PR Domain-Containing Protein 122 3
PR-Domain Containing Protein 121 2     PR Domain Zinc Finger Protein 122
PR-Domain Zinc Finger Protein 121 2     EC 2.1.1.-3
PFM92 3     

External Ids:    HGNC: 139971   Entrez Gene: 593352   Ensembl: ENSG000001307117   UniProtKB: Q9H4Q43   

Export aliases for PRDM12 gene to outside databases

Previous GC identifers: GC09P124554 GC09P125086 GC09P126893 GC09P128816 GC09P130569 GC09P132529 GC09P103027


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

GeneCards Summary for PRDM12 Gene: 
PRDM12 (PR domain containing 12) is a protein-coding gene. Diseases associated with PRDM12 include chronic myeloid leukemia, and myeloid leukemia. GO annotations related to this gene include DNA binding and zinc ion binding. An important paralog of this gene is PRDM9.

UniProtKB/Swiss-Prot: PRD12_HUMAN, Q9H4Q4
Function: May be involved in transcriptional regulation




(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_000009.11  NC_018920.2  NT_035014.4  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the PRDM12 gene promoter:
         GATA-2   GATA-1   NF-AT   MZF-1   NF-AT4   NF-AT2   NF-AT3   NF-AT1   Ik-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidPRDM12 promoter sequence
   Search SABiosciences Chromatin IP Primers for PRDM12

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat PRDM12


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

Entrez Gene cytogenetic band: 9q33-q34   Ensembl cytogenetic band:  9q34.12   HGNC cytogenetic band: 9q33-q34

PRDM12 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PRDM12 gene location

GeneLoc information about chromosome 9         GeneLoc Exon Structure

GeneLoc location for GC09P133539:  view genomic region     (about GC identifiers)

Start:
133,539,981 bp from pter      End:
133,558,384 bp from pter
Size:
18,404 bases      Orientation:
plus 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: PRD12_HUMAN, Q9H4Q4 (See protein sequence)
Recommended Name: PR domain zinc finger protein 12  
Size: 367 amino acids; 40403 Da
Subcellular location: Nucleus (Potential)
1 PDB 3D structure from and Proteopedia for PRDM12:
3EP0 (3D)    
Secondary accessions: A3KFK9

Explore the universe of human proteins at neXtProt for PRDM12: NX_Q9H4Q4

Explore proteomics data for PRDM12 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_Q9H4Q4

  • PRDM12 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    PRDM12 Protein Expression
    REFSEQ proteins: NP_067632.2  
    ENSEMBL proteins: 
     ENSP00000253008  

    Human Recombinant Protein Products for PRDM12: 
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    Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

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

    PRDM12 for ontologies           About GeneDecksing



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

    5 InterPro protein domains:
     IPR001214 SET_dom
     IPR017126 Znf_PRDM12
     IPR015880 Znf_C2H2-like
     IPR013087 Znf_C2H2/integrase_DNA-bd
     IPR007087 Znf_C2H2

    Graphical View of Domain Structure for InterPro Entry Q9H4Q4

    ProtoNet protein and cluster: Q9H4Q4

    UniProtKB/Swiss-Prot: PRD12_HUMAN, Q9H4Q4
    Similarity: Belongs to the class V-like SAM-binding methyltransferase superfamily
    Similarity: Contains 3 C2H2-type zinc fingers
    Similarity: Contains 1 SET domain


    PRDM12 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: PRD12_HUMAN, Q9H4Q4
    Function: May be involved in transcriptional regulation

         Enzyme Number (IUBMB): EC 2.1.1.-1

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding IEA--
    GO:0005515protein binding ----
    GO:0008168methyltransferase activity IEA--
    GO:0008270zinc ion binding ----
    GO:0046872metal ion binding IEA--
         
    PRDM12 for ontologies           About GeneDecksing


    Phenotypes:
         1 GenomeRNAi human phenotype for PRDM12:
     Increased cell number in G2M,  

    Animal Models:
       inGenious Targeting Laboratory - Custom generated mouse model solutions for PRDM12 
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    SwitchGear 3'UTR luciferase reporter plasmidPRDM12 3' UTR sequence
    Inhib. RNA
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PRDM12


    (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 PRDM12

    Gene Ontology (GO): 3 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006351transcription, DNA-dependent IEA--
    GO:0006355regulation of transcription, DNA-dependent IEA--
    GO:0022008neurogenesis IEA--

    PRDM12 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
    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for PRDM12 (PRD12)

    Search CenterWatch for drugs/clinical trials and news about PRDM12 / PRD12

    (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 PRDM12 gene: 
    NM_021619.2  

    Unigene Cluster for PRDM12:

    PR domain containing 12
    Hs.495311  [show with all ESTs]
    Unigene Representative Sequence: AY004252
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000253008(uc004bzt.1)
    miRNA
    Products:
         
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    8/34 QIAGEN miScript miRNA Assays for microRNAs that regulate PRDM12 (see all 34):
    hsa-miR-300 hsa-miR-4328 hsa-miR-106a hsa-let-7a-2* hsa-miR-578 hsa-miR-570 hsa-miR-93 hsa-miR-889
    SwitchGear 3'UTR luciferase reporter plasmidPRDM12 3' UTR sequence
    Inhib. RNA
    Products:
         
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    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat PRDM12
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat PRDM12
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat PRDM12

    Additional mRNA sequence: AY004252.2 

    1 DOTS entry:

    DT.86835748 

    7 AceView cDNA sequences:

    AY004252 BE294489 NM_021619 AW409624 BX114816 AA974575 AW409886 

    GeneLoc Exon Structure


    (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

    PRDM12 expression in normal human tissues (normalized intensities)      PRDM12 embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GTGCTGTGAG
    PRDM12 Expression
    About this image


    PRDM12 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/5 selected tissues (see all 5) fully expand
     
     Brain (Nervous System)    fully expand to see all 6 entries
             Thalamus
             ganglion/cranial   
     
     Peripheral Nervous System (Nervous System)    fully expand to see all 2 entries
             spinal/ganglion/dorsal root ganglion   
     
     Spinal Cord (Nervous System)    fully expand to see all 2 entries
             spinal/ganglion/dorsal root ganglion   
     
     Neural Tube (Nervous System)    fully expand to see all 2 entries
             Telencephalon
     
     Heart (Cardiovascular System)

    See PRDM12 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for PRDM12

    SOURCE GeneReport for Unigene cluster: Hs.495311
        SABiosciences Custom PCR Arrays for PRDM12
    Primer
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PRDM12

    (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 chordates.

    Orthologs for PRDM12 gene from 4/10 species (see all 10)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Prdm121 , 5 PR domain containing 121, 5 91.32(n)1
    98.63(a)1
      2 (21.85 cM)5
    3813591  NM_001123362.11  NP_001116834.11 
     316400375 
    chicken
    (Gallus gallus)
    Aves PRDM121 PR domain containing 12 87.37(n)
    92.31(a)
      417183  XM_415465.2  XP_415465.2 
    African clawed frog
    (Xenopus laevis)
    Amphibia MGC689442 hypothetical protein MGC68944 80.57(n)    BC056019.1 
    zebrafish
    (Danio rerio)
    Actinopterygii zgc:1016061 zgc:101606 77.5(n)
    85.15(a)
      492816  NM_001007457.1  NP_001007458.1 


    ENSEMBL Gene Tree for PRDM12 (if available)
    TreeFam Gene Tree for PRDM12 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for PRDM12 gene
    PRDM92  PRDM62  PRDM142  PRDM72  PRDM112  

    PRDM12 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

    10/462 SNPs in PRDM12 are shown (see all 462)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 9 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs735518301,2
    C,F--133538014(+) CTTTGC/AGTCCC 1 -- us2k11Minor allele frequency- A:0.50WA 2
    rs1825378411,2
    --133538033(+) CGGGGA/GATGCC 1 -- us2k10--------
    rs1872400511,2
    --133538206(+) AAGTCC/GTCCGC 1 -- us2k10--------
    rs1477861771,2
    --133538212(+) TCCGCA/GCTGAG 1 -- us2k10--------
    rs1412291881,2
    --133538292(+) CCAGGA/CACCTC 1 -- us2k10--------
    rs1122794501,2
    C--133538345(+) AAGTGC/TGGCAG 1 -- us2k14Minor allele frequency- T:0.04CSA WA NA EA 359
    rs1469685101,2
    --133538415(+) ACTGGA/GGAGCC 1 -- us2k10--------
    rs1382644861,2
    --133538497(+) GCTCCA/GAGGTG 1 -- us2k10--------
    rs798431261,2
    C--133538543(+) ATGATG/TGGCAG 1 -- us2k10--------
    rs735518321,2
    C,F--133538797(+) TCAATC/ACCCCT 1 -- us2k12Minor allele frequency- A:0.12WA 120

    HapMap Linkage Disequilibrium report for PRDM12 (133539981 - 133558384 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 4 variations for PRDM12:    About this table     
    Variant IDTypeSubtypePubMed ID
    nsv831735CNV Loss17160897
    nsv825122CNV Gain20364138
    nsv825124CNV Gain20364138
    nsv825123CNV Gain20364138

    SABiosciences Cancer Mutation PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
    About This Section
    3 diseases for PRDM12:    About MalaCards
    chronic myeloid leukemia    myeloid leukemia    leukemia


    PRDM12 for disorders           About GeneDecksing


    Export disorders for PRDM12 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 PRDM12 gene integrated from 9 sources:
    (articles sorted by number of sources associating them with PRDM12)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. A potential role for PRDM12 in the pathogenesis of chronic myeloid leukaemia with derivative chromosome 9 deletion. (PubMed id 14523459)1, 3 Reid A.G. and Nacheva E.P. (2004)
    2. DNA sequence and analysis of human chromosome 9. (PubMed id 15164053)2 Humphray S.J.... Dunham I. (2004)
    3. SET domains and histone methylation. (PubMed id 14675547)1 Xiao B....Gamblin S.J. (2003)
    4. The prototypical 4.1R-10-kDa domain and the 4.1g-10-kDa paralog mediate fodrin-actin complex formation. (PubMed id 11274145)1 Kontrogianni-Konstantopoulos A....Huang S.C. (2001)
    5. Hepatitis C virus core protein interacts with 14-3-3 protein and activates the kinase Raf-1. (PubMed id )2 Aoki H.... Hino O. (2000)
    6. The yin-yang of PR-domain family genes in tumorigenesis. (PubMed id 10668202)1 Jiang G.L. and Huang S. (2000)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     ANDOR
    Aliases
    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: 59335 HGNC: 13997 AceView: PRDM12 Ensembl:ENSG00000130711 euGenes: HUgn59335
    ECgene: PRDM12 H-InvDB: PRDM12

    (According to HUGE)
    About This Section
      --

    (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 PRDM12 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 PRDM12 gene:
    Search GeneIP for patents involving PRDM12

    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 Purified and Recombinant Proteins at EMD Millipore
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    GeneCards Homepage - Last full update: 23 Oct 2013 - Incrementals: 4 Nov 2013 , 7 Nov 2013 , 23 Jan 2014

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    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 


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