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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)
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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, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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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 methyltransferase activity. An important paralog of this gene is PRDM6.

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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000009.12  NC_018920.2  NT_008470.20  
Regulatory elements:
   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 Chromatin IP Primers for PRDM12

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing 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 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: PRD12_HUMAN, Q9H4Q4 (See protein sequence)
Recommended Name: PR domain zinc finger protein 12  
Size: 367 amino acids; 40403 Da
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: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See PRDM12 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_067632.2  
    ENSEMBL proteins: 
     ENSP00000253008  

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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

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

         Enzyme Number (IUBMB): EC 2.1.1.-1

         Gene Ontology (GO): 4 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003677DNA binding IEA--
    GO:0005515protein binding ----
    GO:0008168methyltransferase activity IEA--
    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: Let us create your new Knockout/Knockin mouse model for PRDM12
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    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
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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
    PRD12_HUMAN, Q9H4Q4: Nucleus (Potential)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus3
    cytosol2

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

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

    PRDM12 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 PRDM12
    Interactions:

        Search GeneGlobe Interaction Network for PRDM12

    Gene Ontology (GO): 3 biological process terms:    About this table

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

    PRDM12 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 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,
    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 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
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    Selected qRT-PCR 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
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      QuantiTect SYBR Green Assays in human, mouse, rat PRDM12
      QuantiFast Probe-based Assays in human, mouse, rat PRDM12

    Additional mRNA sequence: AY004252.2 

    1 DOTS entry:

    DT.86835748 

    7 AceView cDNA sequences:

    BE294489 AY004252 NM_021619 BX114816 AW409624 AW409886 AA974575 

    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™, 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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    PRDM12 expression in normal human tissues (normalized intensities)
    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
     selected tissues (see all 4) fully expand
     
     Neural Tube (Nervous System)    fully expand to see all 2 entries
             Telencephalon
     
     Brain (Nervous System)    fully expand to see all 2 entries
             Thalamus
     
     Heart (Cardiovascular System)
     
     Peripheral Nervous System (Nervous System)
    PRDM12 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    PRDM12 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.495311
        Custom PCR Arrays for PRDM12
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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)
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    This gene was present in the common ancestor of animals.

    Orthologs for PRDM12 gene from Selected species (see all 12)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Prdm121 , 5 PR domain containing 121, 5 91.42(n)1
    98.5(a)1
      2 (21.85 cM)5
    3813591  NM_001123362.11  NP_001116834.11 
     316400375 
    chicken
    (Gallus gallus)
    Aves PRDM121 PR domain containing 12 88.32(n)
    93.66(a)
      417183  XM_415465.3  XP_415465.2 
    African clawed frog
    (Xenopus laevis)
    Amphibia MGC689442 hypothetical protein MGC68944 80.57(n)    BC056019.1 
    zebrafish
    (Danio rerio)
    Actinopterygii prdm12b1 PR domain containing 12b 79.38(n)
    88.29(a)
      492816  NM_001007457.2  NP_001007458.1 
    worm
    (Caenorhabditis elegans)
    Secernentea set-176
    Protein SET-17 (set-17) mRNA, complete cds
    14(a)
    1 → many
    II(8939057-8940488) WBGene00011887


    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)
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    Paralogs for PRDM12 gene
    PRDM62  PRDM142  PRDM72  PRDM112  PRDM42  

    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), 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 PRDM12 (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

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing PRDM12
    DNA2.0 Custom Variant and Variant Library Synthesis for PRDM12

    (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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    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)
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    PubMed articles for PRDM12 gene integrated from 10 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. (Leukemia 2004)
    2. DNA sequence and analysis of human chromosome 9. (PubMed id 15164053)2 Humphray S.J.... Dunham I. (Nature 2004)
    3. SET domains and histone methylation. (PubMed id 14675547)1 Xiao B....Gamblin S.J. (Curr. Opin. Struct. Biol. 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. (J. Biol. Chem. 2001)
    5. The yin-yang of PR-domain family genes in tumorigenesis. (PubMed id 10668202)1 Jiang G.L. and Huang S. (Histol. Histopathol. 2000)
    6. (PubMed id )2 

    (in PubMed, OMIM, and NCBI Bookshelf)
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     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)
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    Entrez Gene: 59335 HGNC: 13997 AceView: PRDM12 Ensembl:ENSG00000130711 euGenes: HUgn59335
    ECgene: PRDM12 H-InvDB: PRDM12

    (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)
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    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.)
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    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, 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
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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