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

PRPF40B Gene

protein-coding   GIFtS: 49
GCID: GC12P049963

PRP40 pre-mRNA processing factor 40 homolog B (S. cerevisiae)

(Previous name: PRP40 pre-mRNA processing factor 40 homolog B (yeast) )
 Explore 4 diseases affiliated with
PRPF40B via our new
 Human Malady Compendium 
Biological research products
for PRPF40B
    

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

Aliases
PRP40 Pre-MRNA Processing Factor 40 Homolog B (S. Cerevisiae)1 2     Huntingtin Interacting Protein C2
HYPC1 2 3     Pre-MRNA-Processing Factor 40 Homolog B2
Huntingtin Yeast Partner C2 3     Huntingtin-Interacting Protein C3
PRP40 Pre-MRNA Processing Factor 40 Homolog B (Yeast)1     

External Ids:    HGNC: 250311   Entrez Gene: 257662   Ensembl: ENSG000001108447   UniProtKB: Q6NWY93   

Export aliases for PRPF40B gene to outside databases

Previous GC identifers: GC12P048304 GC12P050017 GC12P047049


(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 PRPF40B:
This gene encodes a WW-domain containing protein similar to yeast splicing factor PRP40. This protein has been shown to
interact with Huntingtin and MeCP2. Alternative splicing results in different transcriptional variants. (provided by
RefSeq, Jun 2012)

UniProtKB/Swiss-Prot: PR40B_HUMAN, Q6NWY9
Function: May be involved in pre-mRNA splicing




(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_000012.11  NC_018923.1  NT_029419.12  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the PRPF40B gene promoter:
         POU2F1   Egr-1   AP-2beta   AP-2gamma   AP-2alpha   AP-2alphaA   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidPRPF40B promoter sequence
   Search SABiosciences Chromatin IP Primers for PRPF40B

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat PRPF40B


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

Entrez Gene cytogenetic band: 12q   Ensembl cytogenetic band:  12q13.12   HGNC cytogenetic band: 12q13.12

PRPF40B Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PRPF40B gene location

GeneLoc information about chromosome 12         GeneLoc Exon Structure

GeneLoc location for GC12P049963:  view genomic region     (about GC identifiers)

Start:
49,962,001 bp from pter      End:
50,038,449 bp from pter
Size:
76,449 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: PR40B_HUMAN, Q6NWY9 (See protein sequence)
Recommended Name: Pre-mRNA-processing factor 40 homolog B  
Size: 871 amino acids; 99358 Da
Subunit: Interacts with the N-terminus of HD
Subcellular location: Nucleus speckle
Sequence caution: Sequence=AAH50398.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A
sequence; Sequence=BAB15662.1; Type=Frameshift; Positions=537, 851;
Secondary accessions: O75401 Q6PI09 Q6ZWB3 Q8NCZ1 Q9H5G4 Q9NT95
Alternative splicing: 4 isoforms:  Q6NWY9-1   Q6NWY9-2   Q6NWY9-3   Q6NWY9-4   

Explore the universe of human proteins at neXtProt for PRPF40B: NX_Q6NWY9

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q6NWY9

  • PRPF40B Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_001026868.2  
    ENSEMBL proteins: 
     ENSP00000449569   ENSP00000448073   ENSP00000261897   ENSP00000369634   ENSP00000449485  

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    Uscn Proteins for PRPF40B

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016607nuclear speck IEA--


    PRPF40B for ontologies           About GeneDecksing



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

    PRPF40B for domains           About GeneDecksing

    2 InterPro domains/families:
     IPR002713 FF_domain
     IPR001202 WW_Rsp5_WWP

    Graphical View of Domain Structure for InterPro Entry Q6NWY9

    ProtoNet protein and cluster: Q6NWY9

    UniProtKB/Swiss-Prot: PR40B_HUMAN, Q6NWY9
    Similarity: Belongs to the PRPF40 family
    Similarity: Contains 2 FF domains
    Similarity: Contains 2 WW domains


    (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: PR40B_HUMAN, Q6NWY9
    Function: May be involved in pre-mRNA splicing

    miRNA
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    1 GenomeRNAi human phenotype for PRPF40B:
     Decreased homologous recombina 


    (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

    Unified GeneCards pathways  About this table 
    See pathways by source

    Super-pathwaycontained gene-specific pathways
    1mRNA Splicing - Major Pathway
    Spliceosome0.31

    Pathway sources
    See GeneCards unified pathways
    Show all pathways



    1         Kegg Pathway  (Kegg details for PRPF40B):
        Spliceosome


    PRPF40B for pathways           About GeneDecksing

    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for PRPF40B

    STRING Interaction Network Preview (showing 5 interactants - click image to see 10)

    5/11 Interacting proteins for PRPF40B (Q6NWY93 ENSP000003696344) via UniProtKB, MINT, STRING, and/or I2D (see all 11)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    HTTP428583, ENSP000003471844I2D: score=2 STRING: ENSP00000347184
    HLA-DRAP019033, ENSP000003787864I2D: score=1 STRING: ENSP00000378786
    MECP2P516083, ENSP000003955354I2D: score=1 STRING: ENSP00000395535
    CDC42P609533I2D: score=2 
    PUF60ENSP000003220164STRING: ENSP00000322016
    About this table

    Gene Ontology (GO): 2 biological process terms (GO ID links to tree view):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006397mRNA processing IEA--
    GO:0008380RNA splicing IEA--


    PRPF40B 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 PRPF40B
    Search CenterWatch for drugs/clinical trials and news about PRPF40B / PR40B 

    (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 PRPF40B gene (2 alternative transcripts): 
    NM_001031698.2  NM_012272.1  

    Unigene Cluster for PRPF40B:

    PRP40 pre-mRNA processing factor 40 homolog B (S. cerevisiae)
    Hs.706827  [show with all ESTs]
    Unigene Representative Sequence: AL834216
    16 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000552301 ENST00000547764 ENST00000551063 ENST00000527253 ENST00000508736
    ENST00000551418 ENST00000548825 ENST00000548436 ENST00000261897(uc001ruq.1)
    ENST00000551111 ENST00000380281(uc001rup.1 uc001rur.1 uc001rus.1)
    ENST00000551320 ENST00000548399 ENST00000549547 ENST00000546626 ENST00000551269


    miRNA
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    Inhib. RNA
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    Additional cDNA sequence: 

    AF049525.1 AK027117.1 AL137459.1 AL834216.1 BC031917.1 BC050398.2 BC067364.1 NR_052006.1 

    16 DOTS entries:

    DT.111068  DT.97766348  DT.40297212  DT.100660166  DT.97817980  DT.408801  DT.121155666  DT.100738140 
    DT.100746293  DT.100763219  DT.101983531  DT.102822489  DT.91759955  DT.100701599  DT.100746292  DT.86857317 

    24/112 AceView cDNA sequences (see all 112):

    BX281346 BM691776 BU782786 BC031917 BM053144 BU553353 AL046450 BU846157 
    AK123353 BE392926 BQ877673 BF747904 BM713416 CD673751 BU854888 BQ082554 
    BM263931 AL137459 BM906064 BI966155 BC050398 BQ719821 AL834216 BM715151 

    GeneLoc Exon Structure

    5/8 Alternative Splicing Database (ASD) splice patterns (SP) for PRPF40B (see all 8)    About this scheme

    ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8a · 8b ^ 9a · 9b ^ 10a · 10b ^ 11 ^ 12a · 12b ^ 13 ^ 14 ^ 15a · 15b ^ 16a · 16b ^ 17a · 17b · 17c ^
    SP1:                                                                                                                                                            
    SP2:                                                                                -                                                                           
    SP3:                                                                                                                                                            
    SP4:                                                                                                                                                            
    SP5:                                                                                                                                                            

    ExUns: 18 ^ 19 ^ 20a · 20b
    SP1:                        
    SP2:                        
    SP3:                        
    SP4:                        
    SP5:                        


    ECgene alternative splicing isoforms for PRPF40B

    (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

    PRPF40B expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: GCCTTCGGAA

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

    About this image
    See PRPF40B Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for PRPF40B

    SOURCE GeneReport for Unigene cluster: Hs.706827

    UniProtKB/Swiss-Prot: PR40B_HUMAN, Q6NWY9
    Tissue specificity: Expressed in the striatum and cortex of the brain (at protein level). Highly expressed in testis,
    fetal kidney and fetal brain. Moderately expressed in pancreas, skeletal muscle, placenta, brain and heart. Weakly
    expressed in colon, ileum, ovary, prostate, spleen, kidney and fetal lung

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    In Situ
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PRPF40B

    (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 eukaryotes.

    Orthologs for PRPF40B gene from 5/24 species (see all 24)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    lizard
    (Anolis carolinensis)
    Reptilia PRPF40B6
    --
    65(a)
    1 ↔ 1
    2(94821606-94845923)
    fruit fly
    (Drosophila melanogaster)
    Insecta CG35426
    --
    41(a)
    1 → many
    2L(3023235-3026439)
    worm
    (Caenorhabditis elegans)
    Secernentea ZK1098.16
    WW domain-containing protein ZK1098.1
    34(a)
    1 → many
    III(9521991-9525370)
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons ATPRP40A6
    PRP40B6
    pre-mRNA-processing protein 40B
    21(a)
    19(a)
    many ↔ many
    many ↔ many
    1(16975604-16982965)
    3(6828062-6836582)
    rice
    (Oryza sativa)
    Liliopsida --
    protein binding protein, putative, expressed
    22(a)
    1 → many
    1(19176691-19184701)


    ENSEMBL Gene Tree for PRPF40B (if available)
    TreeFam Gene Tree for PRPF40B (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for PRPF40B gene
    PRPF40A2  TCERG12  TCERG1L2  
    3 SIMAP similar genes for PRPF40B using alignment to 3 protein entries:     PR40B_HUMAN (see all proteins):
    FNBP3    PRPF40A    TCERG1

    PRPF40B 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

    10/348 NCBI SNPs in PRPF40B are shown (see all 348    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 12 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1889950851,2
    --50015289(+) CTCCAA/GCAGTG 1 -- us2k10--------
    rs1478791231,2
    --50015537(+) GGTCCC/TAGGTA 2 -- us2k10--------
    rs1179453111,2
    F,--50015907(+) TGAAAA/TTCGCC 2 -- us2k11Minor allele frequency- T:0.03NA 120
    rs1815058551,2
    --50015920(+) AGCTGC/TGCTGG 2 -- us2k10--------
    rs740869111,2
    C,--50015942(+) CCCCCG/AGGGGA 2 -- us2k12Minor allele frequency- A:0.07WA NA 122
    rs1874573881,2
    --50016464(+) TCTCCC/GGAGTT 2 -- us2k10--------
    rs1415146511,2
    --50016675(+) CTCAGC/GCGCAC 2 -- us2k10--------
    rs1902118791,2
    --50016689(+) AAGCAC/TGTACC 2 -- us2k10--------
    rs1808992371,2
    --50016716(+) TGTCAA/GAGAGT 2 -- us2k10--------
    rs1472532201,2
    --50016836(+) TTTGT-/CTTTTT 2 -- us2k10--------

    HapMap Linkage Disequilibrium report for PRPF40B (49962001 - 50038449 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for PRPF40B: --

    1 SABiosciences Cancer Mutation PCR Assay for PRPF40B:
    Cosmic IdAA Change
    98000017P540S
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing PRPF40B
    DNA2.0 Custom Variant and Variant Library Synthesis for PRPF40B

    (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

    PRPF40B for disorders           About GeneDecksing

    4 diseases for PRPF40B:    About MalaCards
    rett syndrome    huntington's disease    malaria    prostatitis


    Export disorders for PRPF40B 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 PRPF40B gene, integrated from 9 sources (see all 12):
    (articles sorted by number of sources associating them with PRPF40B)
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    1. Huntingtin interacts with a family of WW domain proteins. (PubMed id 9700202)1, 2, 3, 9 Faber P.W....MacDonald M.E. (1998)
    2. Huntingtin's WW domain partners in Huntington's disease post-mortem brain fulfill genetic criteria for direct involvement in Huntington's disease pathogenesis. (PubMed id 10958656)1, 2 Passani L.A.... MacDonald M.E. (2000)
    3. A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (2012)
    4. System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation. (PubMed id 21406692)2 Rigbolt K.T....Blagoev B. (2011)
    5. Lysine acetylation targets protein complexes and co-regulates major cellular functions. (PubMed id 19608861)2 Choudhary C.... Mann M. (2009)
    6. The full-ORF clone resource of the German cDNA consortium. (PubMed id 17974005)2 Bechtel S.... Schupp I. (2007)
    7. 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)
    8. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)2 Ota T.... Sugano S. (2004)
    9. A WW domain binding region in methyl-CpG-binding protein MeCP2: impact on Rett syndrome. (PubMed id 14618241)1 Buschdorf J.P. and Stratling W.H. (2004)
    10. Transcriptome characterization elucidates signaling networks that control human ES cell growth and differentiation. (PubMed id 15146197)1 Brandenberger R.... Stanton L.W. (2004)

    (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: 25766 HGNC: 25031 AceView: HYPC Ensembl:ENSG00000110844 euGenes: HUgn25766
    ECgene: PRPF40B Kegg: 25766 H-InvDB: PRPF40B

    (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 PRPF40B 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 PRPF40B gene:
    Search GeneIP for patents involving PRPF40B

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



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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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