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KRT39 Gene

protein-coding   GIFtS: 42
GCID: GC17M039114

Keratin 39

  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
Keratin 391 2     cytokeratin-392
Type I Hair Keratin Ka352 3     Keratin, Type I Cytoskeletal 392
CK-392 3     keratin-392
K392 3     Cytokeratin-393
KA352 3     Keratin-393

External Ids:    HGNC: 329711   Entrez Gene: 3907922   Ensembl: ENSG000001968597   UniProtKB: Q6A1633   

Export aliases for KRT39 gene to outside databases

Previous GC identifers: GC17M036369 GC17M034909


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for KRT39 Gene:
This gene encodes a member of the type I (acidic) keratin family, which belongs to the superfamily of intermediate
filament (IF) proteins. Keratins are heteropolymeric structural proteins which form the intermediate filament.
These filaments, along with actin microfilaments and microtubules, compose the cytoskeleton of epithelial cells.
The type I keratin genes are clustered in a region of chromosome 17q12-q21. (provided by RefSeq, Jul 2009)

GeneCards Summary for KRT39 Gene:
KRT39 (keratin 39) is a protein-coding gene. Diseases associated with KRT39 include visceral leishmaniasis, and leishmaniasis. GO annotations related to this gene include structural molecule activity. An important paralog of this gene is KRT34.

UniProtKB/Swiss-Prot: K1C39_HUMAN, Q6A163
Function: May play a role in late hair differentiation




(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_000017.11  NC_018928.2  NT_010783.16  
Regulatory elements:
   Regulatory transcription factor binding sites in the KRT39 gene promoter:
         AML1a   FOXF2   Pax-5   GCNF   FOXO3   FOXO3b   FAC1   GCNF-1   FOXO3a   GCNF-2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidKRT39 promoter sequence
   Search Chromatin IP Primers for KRT39

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat KRT39


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

Entrez Gene cytogenetic band: 17q21.2   Ensembl cytogenetic band:  17q21.2   HGNC cytogenetic band: 17q21.2

KRT39 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
KRT39 gene location

GeneLoc information about chromosome 17         GeneLoc Exon Structure

GeneLoc location for GC17M039114:  view genomic region     (about GC identifiers)

Start:
39,114,669 bp from pter      End:
39,123,144 bp from pter
Size:
8,476 bases      Orientation:
minus 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: K1C39_HUMAN, Q6A163 (See protein sequence)
Recommended Name: Keratin, type I cytoskeletal 39  
Size: 491 amino acids; 55651 Da
Subunit: Heterotetramer of two type I and two type II keratins
Developmental stage: During differentiation of the hair, it is one of the last keratins expressed
Miscellaneous: There are two types of cytoskeletal and microfibrillar keratin, I (acidic) and II (neutral to
basic) (40-55 and 56-70 kDa, respectively)
Secondary accessions: B2RXK6 Q6IFU6

Explore the universe of human proteins at neXtProt for KRT39: NX_Q6A163

Explore proteomics data for KRT39 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See KRT39 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_998821.3  
    ENSEMBL proteins: 
     ENSP00000347823   ENSP00000464180  

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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:
    IFF1: Intermediate filaments type I, keratins (acidic)

    3 InterPro protein domains:
     IPR018039 Intermediate_filament_CS
     IPR001664 IF
     IPR002957 Keratin_I

    Graphical View of Domain Structure for InterPro Entry Q6A163

    ProtoNet protein and cluster: Q6A163

    2 Blocks protein domains:
    IPB001664 Intermediate filament protein
    IPB002957 Type I keratin signature


    UniProtKB/Swiss-Prot: K1C39_HUMAN, Q6A163
    Similarity: Belongs to the intermediate filament family


    KRT39 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: K1C39_HUMAN, Q6A163
    Function: May play a role in late hair differentiation

         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005198structural molecule activity IEA--
         
    KRT39 for ontologies           About GeneDecksing


    Phenotypes:
         1 GenomeRNAi human phenotype for KRT39:
     Decreased POU5F1-GFP protein e 

    Animal Models:
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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 COMPARTMENTS: 

    CompartmentConfidence
    cytoskeleton3
    cytosol3
    nucleus2
    extracellular1
    peroxisome1

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005882intermediate filament IEA--

    KRT39 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 KRT39
    Interactions:

        Search GeneGlobe Interaction Network for KRT39

    (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
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    Browse Tocris compounds for KRT39 (K1C39)



    (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 KRT39 gene: 
    NM_213656.3  

    Unigene Cluster for KRT39:

    Keratin 39
    Hs.28467  [show with all ESTs]
    Unigene Representative Sequence: NM_213656
    3 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000355612(uc002hvo.1 uc010wfm.1) ENST00000578078 ENST00000578029

    miRNA
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    1 qRT-PCR Assays for microRNA that regulate KRT39:
    hsa-miR-20b*
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    Inhib. RNA
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      QuantiTect SYBR Green Assays in human, mouse, rat KRT39
      QuantiFast Probe-based Assays in human, mouse, rat KRT39

    Additional mRNA sequence: 

    AJ786657.1 BC157887.1 BC171907.1 

    2 DOTS entries:

    DT.102819723  DT.40110750 

    6 AceView cDNA sequences:

    BK004054 R63932 NM_213656 AJ786657 BX090195 R64023 

    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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    KRT39 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CTCCTGCCAG
    KRT39 Expression
    About this image

    KRT39 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    KRT39 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.28467

    UniProtKB/Swiss-Prot: K1C39_HUMAN, Q6A163
    Tissue specificity: Expressed in skin and scalp. In the hair follicle, it is present in the upper hair cuticle and
    the upper cortex. Also present in the in the upper portion of beard hairs (at protein level)

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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for KRT39

    (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 chordates.

    Orthologs for KRT39 gene from Selected species (see all 9)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Krt391 , 5 keratin 391, 5 79.86(n)1
    74.79(a)1
      11 (62.92 cM)5
    2379341  NM_213730.21  NP_998895.21 
     995141145 
    lizard
    (Anolis carolinensis)
    Reptilia --
    --
    Keratin aHA1; Uncharacterized protein
    49(a)
    40(a)
    many ↔ many
    many ↔ many
    6(70606275-70614367)
    6(70591466-70598937)
    zebrafish
    (Danio rerio)
    Actinopterygii cyt1l6
    zgc:1098686
    (see all 14)
    zgc:109868
    (see all 14)
    38(a)
    38(a)
    (see all 14)
    many ↔ many
    many ↔ many
    (see all 14)
    19(5980624-5982658) ENSDARG00000036832
    19(5974115-5976185) ENSDARG00000036834


    ENSEMBL Gene Tree for KRT39 (if available)
    TreeFam Gene Tree for KRT39 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for KRT39 gene
    KRT342  KRT172  KRT162  KRT312  KRT252  KRT402  KRT202  KRT372  
    KRT272  KRT322  KRT382  KRT362  KRT192  KRT282  KRT142  KRT132  
    KRT262  KRT102  KRT122  KRT352  KRT152  KRT242  KRT92  KRT33B2  
    KRT33A2  
    Selected SIMAP similar genes for KRT39 using alignment to 2 protein entries:     K1C39_HUMAN (see all proteins) (see all similar genes):
    KRT15    KRT14    KRT19    KRT33A    KRT34    K14
    KRT33B    KRT35    FLJ40504    KRT31    JUP    KRT32
    KRT17    KRT13    KRT36    KRT9    KRTHA7    KRT10

    KRT39 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 KRT39 (see all 327)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 17 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs105376431,2
    C--34912246(+) aaaag-/A/AA  
            
    aaaaa
    1 -- int12NA CSA 4
    rs1996968851,2
    C--34917182(+) GTGTA-/TGTG  
            
    TGTGT
    1 -- int10--------
    rs1889777001,2
    --34917183(+) TGTATC/GTGTGT 1 -- int10--------
    rs713000411,2
    C--39116961(-) GAGAAAGAG/-  
            
    AGAAA
    1 -- int11Minor allele frequency- -:0.50NA 2
    rs674957571,2
    C--39117388(+) AAAAG-/A/AA  
            
    AAAAA
    1 -- int10--------
    rs30676461,2
    C--39121022(+) TAAAATAAAA/
            
    AATCC
    1 -- int12Minor allele frequency- -:0.25NA CSA 4
    rs1124877111,2
    C--39121292(+) AAATAT/AAAAAA 1 -- int11Minor allele frequency- A:0.50WA 2
    rs348925831,2
    C--39122320(+) GTGTG-/TGTGTGT 1 -- int10--------
    rs58203781,2
    C--39123131(+) GTTTGT/-TTCCA 1 -- ut512Minor allele frequency- -:0.00CSA 6
    rs99078021,2
    C,F--39124706(+) ggattT/Gctggg 1 -- us2k12Minor allele frequency- G:0.33WA CSA 3

    HapMap Linkage Disequilibrium report for KRT39 (39114669 - 39123144 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 2 variations for KRT39:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv908230CNV Loss21882294
    nsv9550CNV Loss18304495

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing KRT39
    DNA2.0 Custom Variant and Variant Library Synthesis for KRT39

    (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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    2 diseases for KRT39:    
    About MalaCards
    visceral leishmaniasis    leishmaniasis

    1 disease from the University of Copenhagen DISEASES database for KRT39:
    Visceral leishmaniasis

    KRT39 for disorders           About GeneDecksing


    Export disorders for KRT39 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 KRT39 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with KRT39)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Novel type I hair keratins K39 and K40 are the last to be expressed in differentiation of the hair: completion of the human hair keratin catalog. (PubMed id 17301834)1, 2 Langbein L.... Schweizer J. (J. Invest. Dermatol. 2007)
    2. New consensus nomenclature for mammalian keratins. (PubMed id 16831889)1, 3 Schweizer J....Wright M.W. (J. Cell Biol. 2006)
    3. Comprehensive analysis of keratin gene clusters in humans and rodents. (PubMed id 15085952)1, 2 Hesse M.... Magin T.M. (Eur. J. Cell Biol. 2004)
    4. The human type I keratin gene family: characterization of new hair follicle specific members and evaluation of the chromosome 17q21.2 gene domain. (PubMed id 15617563)1, 2 Rogers M.A.... Schweizer J. (Differentiation 2004)
    5. DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage. (PubMed id 16625196)2 Zody M.C.... Nusbaum C. (Nature 2006)
    6. 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. (Genome Res. 2004)
    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. (Proc. Natl. Acad. Sci. U.S.A. 2002)

    (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: 390792 HGNC: 32971 AceView: KA35 Ensembl:ENSG00000196859 euGenes: HUgn390792
    ECgene: KRT39 H-InvDB: KRT39

    (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)
    About This Section

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    NameDescription
    PharmGKB entry for KRT39 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 KRT39 gene:
    Search GeneIP for patents involving KRT39

    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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    GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014

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