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

VPS11 Gene

protein-coding   GIFtS: 52
GCID: GC11P118938

vacuolar protein sorting 11 homolog (S. cerevisiae)

(Previous name: vacuolar protein sorting 11 (yeast homolog) )
 Explore 4 diseases affiliated with
VPS11 via our new
 Human Malady Compendium 
Biological research products
for VPS11
    

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

Aliases
Vacuolar Protein Sorting 11 Homolog (S. Cerevisiae)1 2     Vacuolar Protein Sorting 11 (Yeast Homolog)1
RNF1081 2 3     END12
PEP51 2     Vacuolar Protein Sorting Protein 112
HVPS111     Vacuolar Protein Sorting-Associated Protein 11 Homolog2
RING Finger Protein 1082 3     

External Ids:    HGNC: 145831   Entrez Gene: 558232   Ensembl: ENSG000001606957   OMIM: 6085495   UniProtKB: Q9H2703   

Export aliases for VPS11 gene to outside databases

Previous GC identifers: GC11P135438 GC11P120450 GC11P118972 GC11P118476 GC11P118443 GC11P114878


(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 VPS11:
Vesicle mediated protein sorting plays an important role in segregation of intracellular molecules into distinct
organelles. Genetic studies in yeast have identified more than 40 vacuolar protein sorting (VPS) genes involved in
vesicle transport to vacuoles. This gene encodes the human homolog of yeast class C Vps11 protein. The mammalian class
C Vps proteins are predominantly associated with late endosomes/lysosomes, and like their yeast counterparts, may
mediate vesicle trafficking steps in the endosome/lysosome pathway. (provided by RefSeq, Jul 2008)

UniProtKB/Swiss-Prot: VPS11_HUMAN, Q9H270
Function: May play a role in vesicle-mediated protein trafficking to lysosomal compartments and in membrane
docking/fusion reactions of late endosomes/lysosomes

Gene Wiki entry for VPS11


(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_000011.9  NC_018922.1  NT_033899.8  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the VPS11 gene promoter:
         TBP   p53   TFIID   MyoD   Gfi-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidVPS11 promoter sequence
   Search SABiosciences Chromatin IP Primers for VPS11

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat VPS11


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

Entrez Gene cytogenetic band: 11q23   Ensembl cytogenetic band:  11q23.3   HGNC cytogenetic band: 11q23

VPS11 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
VPS11 gene location

GeneLoc information about chromosome 11         GeneLoc Exon Structure

GeneLoc location for GC11P118938:  view genomic region     (about GC identifiers)

Start:
118,938,403 bp from pter      End:
118,952,688 bp from pter
Size:
14,286 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: VPS11_HUMAN, Q9H270 (See protein sequence)
Recommended Name: Vacuolar protein sorting-associated protein 11 homolog  
Size: 941 amino acids; 107837 Da
Subunit: Part of large heterooligomeric complex together with VPS16, VPS18 and VPS33A. Interacts with STX7. Interacts
with ECM29
Subcellular location: Late endosome membrane; Peripheral membrane protein; Cytoplasmic side. Lysosome membrane;
Peripheral membrane protein; Cytoplasmic side. Cytoplasmic vesicle
Sequence caution: Sequence=AAG23761.1; Type=Frameshift; Positions=439, 924; Sequence=BAB15320.1; Type=Erroneous
initiation; Note=Translation N-terminally extended;
Secondary accessions: Q8WY89 Q96EP8 Q9H6D9 Q9HCS6

Explore the universe of human proteins at neXtProt for VPS11: NX_Q9H270

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q9H270

  • VPS11 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_068375.3  
    Human Recombinant Protein Products: 
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    Uscn Proteins for VPS11

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005765lysosomal membrane IEA--
    GO:0005768endosome IDA--
    GO:0030139endocytic vesicle IDA--
    GO:0030897HOPS complex IDA19109425
    GO:0031902late endosome membrane IEA--


    VPS11 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

    VPS11 for domains           About GeneDecksing

    5/7 InterPro domains/families (see all 7):
     IPR001841 Znf_RING
     IPR024763 VPS11_C
     IPR016528 VPS11
     IPR017986 WD40_repeat_dom
     IPR013083 Znf_RING/FYVE/PHD

    Graphical View of Domain Structure for InterPro Entry Q9H270

    ProtoNet protein and cluster: Q9H270

    1 Blocks protein family: IPB001841 Zn-finger

    UniProtKB/Swiss-Prot: VPS11_HUMAN, Q9H270
    Similarity: Belongs to the VPS11 family
    Similarity: Contains 1 clathrin repeat
    Similarity: Contains 1 RING-type zinc finger


    (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: VPS11_HUMAN, Q9H270
    Function: May play a role in vesicle-mediated protein trafficking to lysosomal compartments and in membrane
    docking/fusion reactions of late endosomes/lysosomes

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000166nucleotide binding IEA--
    GO:0005515protein binding IPI--
    GO:0008270zinc ion binding IEA--


    VPS11 for ontologies           About GeneDecksing


    1 GenomeRNAi human phenotype for VPS11:
     Increased gamma-H2AX phosphory 


    (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 VPS11

    5/57 Interacting proteins for VPS11 (Q9H2701, 2, 3) via UniProtKB, MINT, STRING, and/or I2D (see all 57)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    MARK3P274482, 3MINT-63626 I2D: score=5 
    TFAP2BQ924812, 3MINT-65489 I2D: score=4 
    VPS18Q9P2533I2D: score=9 
    VPS16Q9H2693I2D: score=7 
    BCAR1P569453I2D: score=4 
    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:0006886intracellular protein transport IEA--
    GO:0016192vesicle-mediated transport IEA--


    VPS11 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 VPS11
    Search CenterWatch for drugs/clinical trials and news about VPS11 

    (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 VPS11 gene: 
    NM_021729.4  

    Unigene Cluster for VPS11:

    Vacuolar protein sorting 11 homolog (S. cerevisiae)
    Hs.234282  [show with all ESTs]
    Unigene Representative Sequence: AK302973
    10 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000531528 ENST00000527798(uc010ryy.2) ENST00000529838 ENST00000529545
    ENST00000526829 ENST00000530809 ENST00000534551 ENST00000524454 ENST00000300793(uc010ryx.2)
    ENST00000443691

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    Additional cDNA sequence: 

    AB027508.2 AF258558.1 AF308800.1 AK023279.1 AK026012.1 AK223158.1 AK302973.1 AL834218.1 
    BC012051.1 BC065563.1 

    10 DOTS entries:

    DT.216063  DT.100791149  DT.120685704  DT.95276364  DT.97845938  DT.120685716  DT.91990434  DT.100791144 
    DT.120685697  DT.91838291 

    24/262 AceView cDNA sequences (see all 262):

    NM_021729 BQ219690 BQ018833 AL042680 BM995369 CA414301 BX345388 BU740468 
    CB321845 AA911852 AA917367 BE672488 BE908869 BF437133 CK823127 BF002246 
    BQ694057 BE552300 CO393555 AI656106 AW138324 Z40836 CB528438 CD370480 

    GeneLoc Exon Structure

    5/8 Alternative Splicing Database (ASD) splice patterns (SP) for VPS11 (see all 8)    About this scheme

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

    ExUns: 14 ^ 15 ^ 16a · 16b
    SP1:                        
    SP2:                        
    SP3:                        
    SP4:                        
    SP5:                        


    ECgene alternative splicing isoforms for VPS11

    (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

    VPS11 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: CCCAGGGCTC

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

    About this image
    See VPS11 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for VPS11

    SOURCE GeneReport for Unigene cluster: Hs.234282

    UniProtKB/Swiss-Prot: VPS11_HUMAN, Q9H270
    Tissue specificity: Ubiquitous. Expression was highest in heart and low in lung

        SABiosciences Expression via Pathway-Focused PCR Array including VPS11: 
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    (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 VPS11 gene from 7/15 species (see all 15)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Vps111 , 5 vacuolar protein sorting 11 (yeast)1, 5 91.36(n)1
    97.56(a)1
      9 (24.84 cM)5
    717321  NM_027889.11  NP_082165.11 
     443481065 
    chicken
    (Gallus gallus)
    Aves VPS111 vacuolar protein sorting 11 homolog (S. cerevisiae) 75.28(n)
    84.5(a)
      419702  XM_417847.2  XP_417847.2 
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.79682 Xenopus laevis transcribed sequence with moderate similarity more 77.45(n)    BJ075021.1 
    zebrafish
    (Danio rerio)
    Actinopterygii vps111 vacuolar protein sorting 11 71.41(n)
    75.54(a)
      565852  NM_001037708.1  NP_001032797.1 
    mosquito
    (Anopheles gambiae)
    Insecta AgaP_AGAP0026651 AGAP002665-PA 51.79(n)
    41.75(a)
      1273295  XM_312259.4  XP_312259.4 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons VPS111 vacuolar protein sorting 11 protein 53.33(n)
    44.79(a)
      815065  NM_126544.2  NP_027676.1 
    rice
    (Oryza sativa)
    Liliopsida Os04g03827001 hypothetical protein 51.46(n)
    43.09(a)
      4335642  NM_001059144.1  NP_001052609.1 


    ENSEMBL Gene Tree for VPS11 (if available)
    TreeFam Gene Tree for VPS11 (if available) 

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

    (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

    10/341 NCBI SNPs in VPS11 are shown (see all 341    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 11 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1476863561,2
    --118936577(+) ATGACC/TAGTAT 1 -- us2k10--------
    rs1424520081,2
    --118936622(+) CGCTCC/GCATTT 1 -- us2k10--------
    rs1498212121,2
    --118936645(+) AACAGC/TTGGTA 1 -- us2k10--------
    rs1814097011,2
    --118936809(+) CCAGAC/TTGAGG 1 -- us2k10--------
    rs1175782231,2
    F,--118936829(+) GATAAG/AAGGAG 1 -- us2k11Minor allele frequency- A:0.03EA 120
    rs4710001,2
    C,F,H,--118936910(+) ACAGTC/TACGGT 1 -- us2k130Minor allele frequency- T:0.10NS EA NA MN WA CSA 2849
    rs1129146221,2
    C,--118936912(+) AGTTAC/TGGTAC 1 -- us2k11Minor allele frequency- T:0.50NA 2
    rs1919713631,2
    --118936931(+) GCCCCC/TGCTCT 1 -- us2k10--------
    rs1818123821,2
    --118936999(+) GGGCCA/GGGTGC 1 -- us2k10--------
    rs1123605211,2
    --118937014(+) GCTCAT/CGCCTG 1 -- us2k12Minor allele frequency- C:0.33CSA 3

    HapMap Linkage Disequilibrium report for VPS11 (118938403 - 118952688 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
          Database of Genomic Variants (DGV) variations for VPS11: --

    SABiosciences Cancer Mutation PCR Assays
    QIAGEN SeqTarget long-range PCR primers in human, mouse, rat for resequencing VPS11
    DNA2.0 Custom Variant and Variant Library Synthesis for VPS11

    (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

    VPS11 for disorders           About GeneDecksing

    OMIM gene information: 608549    OMIM disorders: --

    4 diseases for VPS11:    About MalaCards
    chronic apical periodontitis    acute intermittent porphyria    porphyria    periodontitis

    1 disease from the University of Copenhagen DISEASES database for VPS11:
    Chronic apical periodontitis
    Human Genome Epidemiology (HuGE) Navigator: VPS11 (3 documents)

    Export disorders for VPS11 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 VPS11 gene, integrated from 9 sources (see all 28):
    (articles sorted by number of sources associating them with VPS11)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. A protein interaction network for Ecm29 links the 26 S proteasome to molecular motors and endosomal components. (PubMed id 20682791)1, 2 Gorbea C.... Rechsteiner M. (2010)
    2. Large-scale cDNA transfection screening for genes related to cancer development and progression. (PubMed id 15498874)1, 2 Wan D....Gu J. (2004)
    3. 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)
    4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    5. Molecular characterization of mammalian homologues of class c Vps proteins that interact with syntaxin-7. (PubMed id 11382755)1, 2 Kim B.Y....Akazawa C. (2001)
    6. Molecular cloning and characterization of human VPS18, VPS11, VPS16, and VPS33. (PubMed id 11250079)1, 2 Huizing M.... Kraemer H. (2001)
    7. Systematic analysis of dimeric E3-RING interactions re veals increased combinatorial complexity in human ubiquitination networks. (PubMed id 22493164)1 Woodsmith J....Sanderson C.M. (2012)
    8. A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (2012)
    9. NOTCH1 nuclear interactome reveals key regulators of i ts transcriptional activity and oncogenic function. (PubMed id 23022380)1 Yatim A....Benkirane M. (2012)
    10. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (2011)

    (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)
    About This Section
    Entrez Gene: 55823 HGNC: 14583 AceView: VPS11 Ensembl:ENSG00000160695 euGenes: HUgn55823
    ECgene: VPS11 H-InvDB: VPS11

    (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 VPS11 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 VPS11 gene:
    Search GeneIP for patents involving VPS11

    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 , 27 Apr 2013

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