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

PRDM7 Gene

protein-coding   GIFtS: 47
GCID: GC16M090122

PR domain containing 7
 Explore 1 disease affiliated with
PRDM7 via
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Biological research products
for PRDM7    

Aliases
for PRDM7 gene

(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 71 2     PR Domain-Containing Protein 72 3
ZNF9101 2     EC 2.1.1.433 8
PFM42 3     PR-Domain Family Protein 42
PR Domain Zinc Finger Protein 72 3     Probable Histone-Lysine N-Methyltransferase PRDM72

External Ids:    HGNC: 93511   Entrez Gene: 111052   Ensembl: ENSG000001268567   OMIM: 6097595   UniProtKB: Q9NQW53   

Export aliases for PRDM7 gene to outside databases

Previous GC identifers: GC16M081443 GC16M091111 GC16M089824 GC16M089865 GC16M088650 GC16M075814


Summaries
for PRDM7 gene

(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section
Entrez Gene summary for PRDM7:
The protein encoded by this gene is a transcription factor of the PR-domain protein family. It contains a PR-domain and
multiple zinc finger motifs. Transcription factors of the PR-domain family are known to be involved in cell
differentiation and tumorigenesis. Alternative splicing results in multiple transcript variants encoding distinct
isoforms. (provided by RefSeq, Jul 2008)

UniProtKB/Swiss-Prot: PRDM7_HUMAN, Q9NQW5
Function: Probable histone methyltransferase (By similarity)




Genomic Views
for PRDM7 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 69), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000016.9  NC_018927.1  NT_010542.15  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the PRDM7 gene promoter:
         SRF   RFX1   Tal-1   p53   SRF (504 AA)   ZID   LCR-F1   E47   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmid: PRDM7 promoter sequence
   Search SABiosciences Chromatin IP Primers for PRDM7

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat PRDM7


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

Entrez Gene cytogenetic band: 16q24.3   Ensembl cytogenetic band:  16q24.3   HGNC cytogenetic band: 16q24.3

PRDM7 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PRDM7 gene location

GeneLoc information about chromosome 16         GeneLoc Exon Structure

GeneLoc location for GC16M090122:  view genomic region     (about GC identifiers)

Start:
 90,122,974 bp from pter      End:
 90,158,480 bp from pter
Size:
 35,507 bases      Orientation:
 minus strand

Proteins
for PRDM7 gene

(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: PRDM7_HUMAN, Q9NQW5 (See protein sequence)
Recommended Name: Probable histone-lysine N-methyltransferase PRDM7  
Size: 492 amino acids; 55777 Da
Subcellular location: Nucleus (Potential). Chromosome (Potential)
Miscellaneous: The mouse orthologous protein seems not to exist. According to PubMed:17916234, human PRDM7 and PRDM9
genes, a pair of close paralogs corresponding to a single mouse gene Prdm9, were generated by a recent gene
duplication event after the divergence of the ancestors of human and mouse
Secondary accessions: A4Q9G8 Q08EM4 Q9NQW4
Alternative splicing: 3 isoforms:  Q9NQW5-3   Q9NQW5-2   Q9NQW5-1   (May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay)

Explore the universe of human proteins at neXtProt for PRDM7: NX_Q9NQW5

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q9NQW5

    • 2 DME Specific Peptides for PRDM7 (Q9NQW5)
     EQNLVAFQ  GDEYGQELGI 

    PRDM7 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins (2 alternative transcripts): 
    NP_001091643.1  NP_443722.2  

    ENSEMBL proteins: 
     ENSP00000315512   ENSP00000396732   ENSP00000455390   ENSP00000457667   ENSP00000385121  

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    Uscn Proteins for PRDM7

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005622intracellular ----
    GO:0005634nucleus IEA--
    GO:0005694chromosome IEA--


    PRDM7 for ontologies           About GeneDecksing



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    Protein Domains /
    Families
    for PRDM7 gene

    (According to InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
    About This Section
    PRDM7 for domains           About GeneDecksing

    4 InterPro domains/families:
     IPR003655 Krueppel-associated_box-rel
     IPR019041 SSXRD_motif
     IPR001214 SET_dom
     IPR001909 Krueppel-associated_box

    Graphical View of Domain Structure for InterPro Entry Q9NQW5

    ProtoNet protein and cluster: Q9NQW5

    1 Blocks protein family: IPB007086 C2H2-type zinc finger signature

    UniProtKB/Swiss-Prot: PRDM7_HUMAN, Q9NQW5
    Similarity: Contains 1 KRAB-related domain
    Similarity: Contains 1 SET domain


    Function
    for PRDM7 gene

    (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: PRDM7_HUMAN, Q9NQW5
    Function: Probable histone methyltransferase (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 2

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    hsa-miR-515-5p hsa-miR-3158-3p hsa-miR-629* hsa-miR-331-3p hsa-miR-4276 hsa-miR-3909 hsa-miR-548q hsa-miR-519e*
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    Gene Editing
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    Clone
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    In Situ Assay
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    Gene Ontology (GO): 4 molecular function terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003676nucleic acid binding IEA--
    GO:0018024histone-lysine N-methyltransferase activity IEA--
    GO:0042800histone methyltransferase activity (H3-K4 specific) ----
    GO:0043565sequence-specific DNA binding ----


    PRDM7 for ontologies           About GeneDecksing


    3 GenomeRNAi human phenotypes for PRDM7:
     Decreased NANOG protein expres  Decreased OCT4 protein express  Decreased POU5F1-GFP protein e 


    Pathways & Interactions
    for PRDM7 gene

    (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 PRDM7

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006355regulation of transcription, DNA-dependent IEA--
    GO:0007128meiotic prophase I ----
    GO:0007283spermatogenesis ----
    GO:0010520regulation of reciprocal meiotic recombination ----
    GO:0045944positive regulation of transcription from RNA polymerase II promoter ----


    PRDM7 for ontologies           About GeneDecksing



    Drugs & Compounds
    for PRDM7 gene

    (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 PRDM7
    Search CenterWatch for drugs/clinical trials and news about PRDM7 

    Transcripts
    for PRDM7 gene

    (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,
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    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 PRDM7 gene (2 alternative transcripts): 
    NM_001098173.1  NM_052996.2  

    Unigene Cluster for PRDM7:

    PR domain containing 7
    Hs.406695  [show with all ESTs]
    Unigene Representative Sequence: NM_001098173
    6 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000325921(uc002fqo.3) ENST00000449207(uc010cjg.1 uc010cjh.1)
    ENST00000568473 ENST00000564210 ENST00000569206 ENST00000407825(uc010cje.3 uc010cjf.3)


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    8 QIAGEN miScript miRNA Assays for microRNAs that regulate PRDM7:
    hsa-miR-515-5p hsa-miR-3158-3p hsa-miR-629* hsa-miR-331-3p hsa-miR-4276 hsa-miR-3909 hsa-miR-548q hsa-miR-519e*
    Browse SwitchGear 3'UTR luciferase reporter plasmids
    Inhib. RNA
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    OriGene shRNA RFP: PRDM7
    OriGene siRNA: PRDM7
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    Clone
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    Primer
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      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat PRDM7

    Additional cDNA sequence: 

    AF274347.1 AF274348.1 AL137711.1 AM690991.1 AM690992.1 AM690993.1 BC107033.2 

    1 DOTS entry:

    DT.92414282 

    6 AceView cDNA sequences:

    NM_052996 AF274348 AF274347 AL137711 BU194881 BF978710 

    GeneLoc Exon Structure


    Expression
    for PRDM7 gene

    (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

    PRDM7 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: CAGCCCCTGT

    Microarray
    RNAseq (Illumina Body Map)
    (100×FPKM)½
    SAGE (Serial Analysis of Gene Expression)
    About this image
    See PRDM7 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for PRDM7

    SOURCE GeneReport for Unigene cluster: Hs.406695
        SABiosciences Custom PCR Arrays for PRDM7
    Primer
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    In Situ
    Assay Products:     
         		Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PRDM7

    Orthologs
    for PRDM7 gene

    (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
    		   --

    ENSEMBL Gene Tree for PRDM7 (if available)
    TreeFam Gene Tree for PRDM7 (if available) 

    Paralogs
    for PRDM7 gene

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for PRDM7 gene
    PRDM62  PRDM92  PRDM122  PRDM142  PRDM112  PRDM42  
    3 SIMAP similar genes for PRDM7 using alignment to 2 protein entries:     PRDM7_HUMAN (see all proteins):
    PRDM7_V2    PRDM7_V3    PRDM9

    PRDM7 for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for PRDM7
    PGOHUM00000238374


    Genomic Variants
    for PRDM7 gene

    (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

    10/424 NCBI SNPs in PRDM7 are shown (see all 424)     About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance    		Chr 16 posSequence#AA
    Chg    		TypeMore#Allele
    freq    		PopTotal
    sample    		More
    ----------
    rs1812431311,2
    		--90122496(+) TAGAAG/TAAAAG 2 -- ds50010--------
    rs1490272511,2
    		--90122521(+) GGTGCA/GGTGGC 2 -- ds50010--------
    rs110766641,2
    		C,F,A,H,--90122562(+) CTGAGG/ATGGGT 2 -- ds50016Minor allele frequency- A:0.31NA CSA 13
    rs1858901541,2
    		--90122603(+) CTGGCC/TAACAT 2 -- ds50010--------
    rs1905547831,2
    		--90122605(+) GGCCAA/TCATGG 2 -- ds50010--------
    rs1821268991,2
    		--90122947(+) TGAGCC/TGCAGA 2 -- ds50010--------
    rs1403652001,2
    		--90122948(+) GAGCCA/GCAGAC 2 -- ds50010--------
    rs1454533511,2
    		--90122983(+) AGAAGA/GAAGCG 2 -- ut310--------
    rs1870574281,2
    		--90123043(+) TCCCCA/GAGTGA 2 -- ut310--------
    rs1464742621,2
    		--90123095(+) TCCACA/GTGAGA 2 -- ut310--------

    HapMap Linkage Disequilibrium report for PRDM7 (90122974 - 90158480 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 10 variations for PRDM7
         10 CNVs: 88276 0200 67089 102366 43938 32145 88278 77468 35423 88277

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    Disorders / Diseases
    for PRDM7 gene

    (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
    PRDM7 for disorders           About GeneDecksing

    OMIM gene information: 609759    OMIM disorders: --

    1 disease for PRDM7:    About MalaCards
    homocysteine

    Human Genome Epidemiology (HuGE) Navigator: PRDM7 (1 document)

    Export disorders for PRDM7 gene to outside databases

    Publications
    for PRDM7 gene

    (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 PRDM7 gene integrated from 9 sources:
    (articles sorted by number of sources associating them with PRDM7)    		    Utopia: connect your pdf to the dynamic
    world of online information

    1. Family expansion and gene rearrangements contributed to the functional specialization of PRDM genes in vertebrates. (PubMed id 17916234)1, 2, 3 Fumasoni I....Ciccarelli F.D. (2007)
    2. An unappreciated role for RNA surveillance. (PubMed id 14759258)1, 2 Hillman R.T.... Brenner S.E. (2004)
    3. The yin-yang of PR-domain family genes in tumorigenesis. (PubMed id 10668202)1, 2 Jiang G.L. and Huang S. (2000)
    4. Genome-wide survey and developmental expression mapping of zebrafish SET domain-containing genes. (PubMed id 18231586)1 Sun X.J....Chen Z. (2008)
    5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S....Malek J. (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)

    External Searches for PRDM7 gene

    (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)

    Genome Databases showing PRDM7 gene

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 11105 HGNC: 9351 AceView: PRDM7 Ensembl:ENSG00000126856 euGenes: HUgn11105
    ECgene: PRDM7 H-InvDB: PRDM7

    Other Databases showing PRDM7 gene

    (According to HUGE)
    About This Section
    		   --

    Specialized Databases showing PRDM7 gene

    (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 PRDM7 Pharmacogenomics, SNPs, Pathways
    ATLAS Chromosomes in Cancer entry for PRDM7 Genetics and Cytogenetics in Oncology and Haematology

    Intellectual Property
    for PRDM7 gene

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section
    		Patent Information for PRDM7 gene:
    Search GeneIP for patents involving PRDM7

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    Products
    for PRDM7 gene

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    Advanced Cell Diagnostics
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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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    von Willebrand factor
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