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

PRDM8 Gene

protein-coding   GIFtS: 44
GCID: GC04P081107

PR domain containing 8

  Search for PRDM8
in our new
 Human Malady Compendium 
Biological research products
for PRDM8
    

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, and/or 10fRNAdb)
About This Section

Aliases
PR Domain Containing 81 2
PFM52 3
PR Domain-Containing Protein 82 3
PR Domain Zinc Finger Protein 82
PR-Domain Containing Protein 82

External Ids:    HGNC: 139931   Entrez Gene: 569782   Ensembl: ENSG000001527847   UniProtKB: Q9NQV83   

Export aliases for PRDM8 gene to outside databases

Previous GC identifers: GC04P080993 GC04P081391 GC04P081498 GC04P081564 GC04P081565 GC04P081462 GC04P081325 GC04P076850


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

UniProtKB/Swiss-Prot: PRDM8_HUMAN, Q9NQV8
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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000004.11  NC_018915.1  NT_016354.19  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the PRDM8 gene promoter:
         C/EBPbeta   Nkx2-5   CUTL1   AP-2gamma   GATA-1   c-Myb   AP-2beta   AP-2alpha   AP-2alphaA   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmids (see all 2): PRDM8 promoter sequence
   Search SABiosciences Chromatin IP Primers for PRDM8

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat PRDM8


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

Entrez Gene cytogenetic band: 4q21   Ensembl cytogenetic band:  4q21.21   HGNC cytogenetic band: 4q21

PRDM8 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PRDM8 gene location

GeneLoc information about chromosome 4         GeneLoc Exon Structure

GeneLoc location for GC04P081107:  view genomic region     (about GC identifiers)

Start:
81,105,033 bp from pter      End:
81,125,483 bp from pter
Size:
20,451 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to 2PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE MOPED and PaxDb, 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 Uscn,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Uscn, Ontologies according to Gene Ontology Consortium 01 Mar 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, and/or Uscn)
About This Section

UniProtKB/Swiss-Prot: PRDM8_HUMAN, Q9NQV8 (See protein sequence)
Recommended Name: PR domain zinc finger protein 8  
Size: 689 amino acids; 71663 Da
Subcellular location: Nucleus (By similarity)
Sequence caution: Sequence=AAF87241.1; Type=Frameshift; Positions=287;
Secondary accessions: A8K7X2 Q6IQ36
Alternative splicing: 2 isoforms:  Q9NQV8-1   Q9NQV8-2   

Explore the universe of human proteins at neXtProt for PRDM8: NX_Q9NQV8

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q9NQV8

  • PRDM8 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins (2 alternative transcripts): 
    NP_001092873.1  NP_064611.3  

    ENSEMBL proteins: 
     ENSP00000423985   ENSP00000425149   ENSP00000406998   ENSP00000339764  

    Human Recombinant Protein Products: 
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    Uscn Proteins for PRDM8

    Gene Ontology (GO): 1 cellular component term (GO ID links to tree view):    About this table

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


    PRDM8 for ontologies           About GeneDecksing



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    Uscn ELISAs and CLIAs for PRDM8


    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section

    PRDM8 for domains           About GeneDecksing

    3 InterPro domains/families:
     IPR001214 SET_dom
     IPR015880 Znf_C2H2-like
     IPR007087 Znf_C2H2

    Graphical View of Domain Structure for InterPro Entry Q9NQV8

    ProtoNet protein and cluster: Q9NQV8

    UniProtKB/Swiss-Prot: PRDM8_HUMAN, Q9NQV8
    Similarity: Contains 3 C2H2-type zinc fingers
    Similarity: Contains 1 SET domain


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013,
    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, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Mar 2013 via Entrez Gene.)
    About This Section

    Function Summary:

         UniProtKB/Swiss-Prot: PRDM8_HUMAN, Q9NQV8
    Function: May be involved in transcriptional regulation

    miRNA
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    OriGene 3'-UTR Clone (see all 2): PRDM8
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    8/31 QIAGEN miScript miRNA Assays for microRNAs that regulate PRDM8 (see all 31):
    hsa-miR-142-5p hsa-miR-875-3p hsa-miR-302d hsa-miR-520e hsa-miR-520f hsa-miR-16-2* hsa-miR-938 hsa-miR-944
    SwitchGear 3'UTR luciferase reporter plasmidPRDM8 3' UTR sequence
    Inhib. RNA
    Products:
        
    Browse for Gene Knock-down Tools from EMD Millipore
    OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for PRDM8 (see all 7)
    OriGene shRNA RFP: PRDM8
    OriGene siRNA: PRDM8
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat PRDM8

    Gene Editing
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    DNA2.0 Custom Protein Engineering Service for PRDM8

    Clone
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    Browse Clones for the Expression of Recombinant Proteins Available from EMD Millipore
    OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for PRDM8 (see all 3)
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    Browse Sino Biological Human cDNA Clones
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    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat PRDM8 

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    Search LifeMap BioReagents cell lines for PRDM8

    In Situ Assay
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PRDM8

    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:0003682chromatin binding IEA--
    GO:0003714transcription corepressor activity IEA--
    GO:0008270zinc ion binding IEA--
    GO:0046974histone methyltransferase activity (H3-K9 specific) IEA--


    PRDM8 for ontologies           About GeneDecksing


    1 GenomeRNAi human phenotype for PRDM8:
     High actin ratio cells 

    Animal Models:
         4 MGI mutant phenotypes (inferred from 1 allele(MGI details for Prdm8):
     behavior/neurological  cellular  integument  nervous system 

    PRDM8 for phenotypes           About GeneDecksing


    (Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, 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 Mar 2013 via Entrez Gene).
    About This Section



    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for PRDM8

    Gene Ontology (GO): 5/6 biological process terms (GO ID links to tree view) (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006351transcription, DNA-dependent IEA--
    GO:0006355regulation of transcription, DNA-dependent ----
    GO:0021540corpus callosum morphogenesis IEA--
    GO:0021957corticospinal tract morphogenesis IEA--
    GO:0022008neurogenesis ----


    PRDM8 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, 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 PRDM8
    Search CenterWatch for drugs/clinical trials and news about PRDM8 

    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 235 Homo sapiens; Mar 10 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,
    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, Primers from OriGene, SABiosciences, and/or QIAGEN )
    About This Section

    REFSEQ mRNAs for PRDM8 gene (2 alternative transcripts): 
    NM_001099403.1  NM_020226.3  

    Unigene Cluster for PRDM8:

    PR domain containing 8
    Hs.373642  [show with all ESTs]
    Unigene Representative Sequence: NM_020226
    11 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000508965 ENST00000509375 ENST00000506547 ENST00000511825 ENST00000504452(uc010ijo.3)
    ENST00000508061 ENST00000511197 ENST00000515013 ENST00000507025 ENST00000415738(uc003hmc.4)
    ENST00000339711(uc003hmb.4)

    miRNA
    Products:
         
    OriGene 3'-UTR Clone (see all 2): PRDM8
    Browse OriGene MicroRNA Expression Plasmids
    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat PRDM8
    8/31 QIAGEN miScript miRNA Assays for microRNAs that regulate PRDM8 (see all 31):
    hsa-miR-142-5p hsa-miR-875-3p hsa-miR-302d hsa-miR-520e hsa-miR-520f hsa-miR-16-2* hsa-miR-938 hsa-miR-944
    SwitchGear 3'UTR luciferase reporter plasmidPRDM8 3' UTR sequence
    Inhib. RNA
    Products:
         
    Browse for Gene Knock-down Tools from EMD Millipore
    OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for PRDM8 (see all 7)
    OriGene shRNA RFP: PRDM8
    OriGene siRNA: PRDM8
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat PRDM8
    Clone
    Products:
         
    OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for PRDM8 (see all 3)
    OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for PRDM8 (see all 3)
    OriGene custom cloning services – gene synthesis, subcloning, mutagenesis, variant library, vector shuttling 
    GenScript: all cDNA clones in your preferred vector (see all 2): PRDM8 (NM_001099403)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for PRDM8
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat PRDM8 
    Primer
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    Browse OriGene validated miRNA SYBR primer pairs
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat PRDM8
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat PRDM8

    Additional cDNA sequence: 

    AF275815.1 AK292137.1 BC027929.1 BC058908.1 BC071584.1 

    7 DOTS entries:

    DT.75133058  DT.426473  DT.456119  DT.91755370  DT.121260204  DT.95258339  DT.100707153 

    24/72 AceView cDNA sequences (see all 72):

    BP360245 AI738440 BG059660 BC027929 BC058908 CR597213 AI738426 NM_020226 
    F09774 F05284 AW161646 AW160888 AI762043 AI079265 AW197623 C01405 
    H84086 AA000993 BX092578 BP349591 BI489104 AI436578 BE676846 BI913179 

    GeneLoc Exon Structure

    5/7 Alternative Splicing Database (ASD) splice patterns (SP) for PRDM8 (see all 7)    About this scheme

    ExUns: 1a · 1b · 1c ^ 2a · 2b ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8a · 8b · 8c ^ 9a · 9b ^ 10 ^ 11 ^ 12a · 12b ^ 13
    SP1:                                                                                                                    -         
    SP2:                                -     -     -     -           -                                                     -         
    SP3:                                      -                                                                                       
    SP4:                    -     -     -     -     -                 -                                                               
    SP5:                                                                                                                              


    ECgene alternative splicing isoforms for PRDM8

    (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

    PRDM8 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: TATAATGAAA

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)

    About this image

    PRDM8 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    1 LifeMap In Vivo Development Anatomical Compartment/Cell 
    Tissue Anatomical Compartment CellCategory (developmental path)
    BrainBlood Brain BarrierEndothelial CellsBlood Brain Barrier, Endothelium
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization
    Stem Cell Differentiation: 5 LifeMap Cells 
    NameCategory
    PureStem™ myogenic progenitor Z11 (Embryonic Progenitor Cell)Heart, Myocardium, Smooth Muscle
    PureStem™ mesenchymal progenitor SM30 (Embryonic Progenitor Cell)Adipose, Bone, Cartilage
    PureStem™ mesenchymal progenitor 7SMOO32 (Embryonic Progenitor Cell)Adipose, Bone, Cartilage
    PureStem™ mesenchymal progenitor 4D20.8 (Embryonic Progenitor Cell)Lateral Plate Mesoderm, Neural Crest
    PureStem™ progenitor EN27 (Embryonic Progenitor Cell)

    See PRDM8 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for PRDM8

    SOURCE GeneReport for Unigene cluster: Hs.373642
        SABiosciences Custom PCR Arrays for PRDM8
    Primer
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    QIAGEN QuantiFast Probe-based Assays in human, mouse, rat PRDM8
    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PRDM8

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

    This gene was present in the common ancestor of animals.

    Orthologs for PRDM8 gene from 3/9 species (see all 9)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    lizard
    (Anolis carolinensis)
    Reptilia PRDM86
    --
    68(a)
    1 ↔ 1
    GL343425.1(373390-386287)
    zebrafish
    (Danio rerio)
    Actinopterygii prdm8b1 PR domain containing 8b 65.49(n)
    68.85(a)
      557162  NM_001105105.1  NP_001098575.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG132876
    --
    18(a)
    1 → many
    3L(5875404-5877190)


    ENSEMBL Gene Tree for PRDM8 (if available)
    TreeFam Gene Tree for PRDM8 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for PRDM8 gene
    ZNF4882  

    PRDM8 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, UniProtKB, 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

    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 1 variation for PRDM8
         1 Indel: 68756
    Human Gene Mutation Database (HGMD): PRDM8
    SABiosciences Cancer Mutation PCR Assays
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing PRDM8
    DNA2.0 Custom Variant and Variant Library Synthesis for PRDM8

    (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.)
    About This Section

    PRDM8 for disorders           About MalaCards

    PRDM8 for disorders           About GeneDecksing

    2 diseases from the University of Copenhagen DISEASES database for PRDM8:
    Unverricht-Lundborg syndrome     Lafora disease

    Export disorders for PRDM8 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 PRDM8 gene integrated from 9 sources:
    (articles sorted by number of sources associating them with PRDM8)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. 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. (2004)
    2. Early-onset Lafora body disease. (PubMed id 22961547)1 Turnbull J....Minassian B.A. (2012)
    3. Genome-wide association study identifies eight loci associated with blood pressure. (PubMed id 19430483)1 Newton-Cheh C....Munroe P.B. (2009)
    4. Sequence comparison of human and mouse genes reveals a homologous block structure in the promoter regions. (PubMed id 15342556)1 Suzuki Y.... Sugano S. (2004)
    5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)2 Ota T.... Sugano S. (2004)
    6. SET domains and histone methylation. (PubMed id 14675547)1 Xiao B....Gamblin S.J. (2003)
    7. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (2002)
    8. 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)
    9. 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: 56978 HGNC: 13993 AceView: PRDM8 Ensembl:ENSG00000152784 euGenes: HUgn56978
    ECgene: PRDM8 H-InvDB: PRDM8

    (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 PRDM8 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 PRDM8 gene:
    Search GeneIP for patents involving PRDM8

    GeneCards and IP:
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    GeneCards Homepage - Last full update: 19 Mar 2013 - Incrementals: 21 Mar 2013 , 15 Apr 2013 , 26 Apr 2013

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