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ABCC13 Gene

pseudogene   GIFtS: 39
GCID: GC21P015647

ATP-Binding Cassette, Sub-Family C (CFTR/MRP), Member 13,...

(Previous names: ATP-binding cassette, sub-family C (CFTR/MRP), member 13)
  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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This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
ATP-Binding Cassette, Sub-Family C (CFTR/MRP), Member 13,
Pseudogene1 2
C21orf732 3
PRED62 3
ATP-Binding Cassette, Sub-Family C (CFTR/MRP), Member 131
ATP-Binding Cassette Protein C132

External Ids:    HGNC: 160221   Entrez Gene: 1500002   Ensembl: ENSG000002430647   OMIM: 6088355   UniProtKB: Q9NSE73   
ORGUL members:         

Export aliases for ABCC13 gene to outside databases

Previous GC identifers: GC21P012310 GC21P014567 GC21P001016


(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 ABCC13 Gene:
This gene is a member of the superfamily of genes encoding ATP-binding cassette (ABC) transporters. ABC proteins
transport various molecules across extra- and intra-cellular membranes. ABC genes are divided into seven distinct
subfamilies (ABC1, MDR/TAP, MRP, ALD, OABP, GCN20, and White). This family member is part of the MRP subfamily,
which is involved in multi-drug resistance, but the human locus is now thought to be a pseudogene incapable of
encoding a functional ABC protein. Alternative splicing results in multiple transcript variants; however, not all
variants have been fully described. (provided by RefSeq, Jul 2008)

GeneCards Summary for ABCC13 Gene:
ABCC13 (ATP-binding cassette, sub-family C (CFTR/MRP), member 13, pseudogene) is a pseudogene, and is affiliated with the lncRNA class. Diseases associated with ABCC13 include down syndrome, and hepatitis. GO annotations related to this gene include ATPase activity, coupled to transmembrane movement of substances.

Gene Wiki entry for ABCC13 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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000021.9  NC_018932.2  NT_011512.12  
Regulatory elements:
   Regulatory transcription factor binding sites in the ABCC13 gene promoter:
         STAT1   Brachyury   E4BP4   GATA-1   HNF-1A   POU2F1   POU2F1a   HNF-1   Sox9   Pax-4a   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat ABCC13


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

Entrez Gene cytogenetic band: 21q11.2   Ensembl cytogenetic band:  21q11.2   HGNC cytogenetic band: 21q11.2

ABCC13 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
ABCC13 gene location

GeneLoc information about chromosome 21         GeneLoc Exon Structure

GeneLoc location for GC21P015647:  view genomic region     (about GC identifiers)

Start:
15,608,527 bp from pter      End:
15,735,075 bp from pter
Size:
126,549 bases      Orientation:
plus 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, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: ABCCD_HUMAN, Q9NSE7 (See protein sequence)
Recommended Name: Putative ATP-binding cassette sub-family C member 13  
Size: 274 amino acids; 30831 Da
Caution: Contains sequences related to the ABC transporters of subfamily C, but lacks Walker A, Walker B, and
signature C motifs, indicating that it is a nonfunctional ABC transporter. Translation of the cDNA in a different
reading frame predicts a 93 amino acid peptide with signature C and Walker B motifs, but no Walker A motif
Secondary accessions: Q8N6A4 Q8N6A5
Alternative splicing: 5 isoforms:  Q9NSE7-1   Q9NSE7-2   Q9NSE7-3   Q9NSE7-4   Q9NSE7-5   (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 ABCC13: NX_Q9NSE7

Explore proteomics data for ABCC13 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See ABCC13 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB


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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:
    ABCC: ATP binding cassette transporters / subfamily C

    2 InterPro protein domains:
     IPR001140 ABC_transptr_TM_dom
     IPR011527 ABC1_TM_dom

    Graphical View of Domain Structure for InterPro Entry Q9NSE7

    ProtoNet protein and cluster: Q9NSE7

    UniProtKB/Swiss-Prot: ABCCD_HUMAN, Q9NSE7
    Similarity: Belongs to the binding-protein-dependent transport system permease family
    Similarity: Contains 1 ABC transmembrane type-1 domain


    ABCC13 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: ABCCD_HUMAN, Q9NSE7
    Induction: Down-regulated by cell differentiation in certain leukemia cells

         Gene Ontology (GO): 2 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005524ATP binding IEA--
    GO:0042626ATPase activity, coupled to transmembrane movement of substances IEA--
         
    ABCC13 for ontologies           About GeneDecksing


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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 UniProtKB/Swiss-Prot
    ABCCD_HUMAN, Q9NSE7: Membrane; Multi-pass membrane protein (Potential)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    plasma membrane3
    peroxisome2

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016021integral component of membrane IEA--

    ABCC13 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 ABCC13
    Interactions:

        Search GeneGlobe Interaction Network for ABCC13

    (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
      Browse compounds at ApexBio 

    Browse Tocris compounds for ABCC13 (ABCCD)



    (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,
    Conferences by KenesGroup, 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 ABCC13 gene (4 alternative transcripts): 
    NM_138726.2  NM_172024.1  NM_172025.1  NM_172026.1  

    Unigene Cluster for ABCC13:

    ATP-binding cassette, sub-family C (CFTR/MRP), member 13, pseudogene
    Hs.366575  [show with all ESTs]
    Unigene Representative Sequence: AY063515
    8 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000429114 ENST00000482980(uc002yjs.3) ENST00000481582(uc002yjq.3)
    ENST00000467409(uc002yjr.3 uc010gkx.3) ENST00000471902 ENST00000463099
    ENST00000400574 ENST00000400571
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    Additional mRNA sequence: 

    AF418600.1 AF518320.1 AF518321.1 AY063514.1 AY063515.1 AY344117.1 BC054020.1 BC144077.1 
    NR_003087.1 NR_003088.1 

    4 DOTS entries:

    DT.97835312  DT.100020806  DT.97835311  DT.100744643 

    23 AceView cDNA sequences:

    AI076090 NM_172024 NM_172025 AY344117 NM_138726 NM_172026 AF518320 AA699859 
    AY063514 AY063515 AF518321 AF418600 AA677543 BX101893 H47929 BU570227 
    H47627 N58518 N72630 N78108 BC054020 BU588880 N54854 

    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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    ABCC13 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: CAATTGCACT
    ABCC13 Expression
    About this image

    ABCC13 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    ABCC13 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.366575

    UniProtKB/Swiss-Prot: ABCCD_HUMAN, Q9NSE7
    Tissue specificity: Highest expression in fetal liver and fetal spleen. In the adult, highest levels are found in
    the colon ascending and transverse. Also expressed in brain, placenta, lung, liver, pancreas and ovary. In bone
    marrow cells, levels are several fold higher than in peripheral blood leukocytes

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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)
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    ENSEMBL Gene Tree for ABCC13 (if available)
    TreeFam Gene Tree for ABCC13 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for ABCC13 gene
    4 SIMAP similar genes for ABCC13 using alignment to 1 protein entry:     ABCCD_HUMAN:
    ABCC1    MRP    ABCC3    MRP3

    ABCC13 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 ABCC13 (see all 754)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 21 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs795366771,2
    F--15644128(+) AGGCTC/TTCCTC 2 -- us2k11Minor allele frequency- T:0.01EA 120
    rs1904086601,2
    --15644150(+) AAGGAC/TGACGT 2 -- us2k10--------
    rs1474670761,2
    --15644162(+) CCATAA/CCTGCA 2 -- us2k10--------
    rs731636251,2
    C--15644229(+) TGTGGC/TACAGA 2 -- us2k14Minor allele frequency- T:0.17NA WA 242
    rs72770331,2
    C,F,A,H--15644339(+) TAGCAC/TGATAA 2 -- us2k115Minor allele frequency- T:0.45NS EA WA NA CSA 742
    rs21101531,2
    C,F,A,H--15644351(-) TGACTC/TGCTGA 2 -- us2k195Minor allele frequency- T:0.18NS NA EA PA EU CA WA CSA 4802
    rs1813104661,2
    --15644384(+) TTTTGC/GGAATA 2 -- us2k10--------
    rs1859153941,2
    --15644432(+) CAAATC/GTGAGT 2 -- us2k10--------
    rs1398650041,2
    --15644465(+) TAGGCA/CTTGAA 2 -- us2k10--------
    rs1919339071,2
    --15644528(+) CTTATC/TTTGCA 2 -- us2k10--------

    HapMap Linkage Disequilibrium report for ABCC13 (15608527 - 15735075 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 6 variations for ABCC13:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv272254CNV Insertion20981092
    esv2446530CNV Insertion19546169
    esv269832CNV Insertion20981092
    nsv470878CNV Gain18288195
    nsv520538CNV Gain19592680
    nsv459095CNV Gain19166990

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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 608835    OMIM disorders: --

    3 diseases for ABCC13:    
    About MalaCards
    down syndrome    hepatitis    leukemia


    ABCC13 for disorders           About GeneDecksing

    Genetic Association Database (GAD): ABCC13

    Export disorders for ABCC13 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 ABCC13 gene, integrated from 10 sources (see all 15):
    (articles sorted by number of sources associating them with ABCC13)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Degeneration of an ATP-binding cassette transporter gene, ABCC13, in different mammalian lineages. (PubMed id 15203202)1, 2 Annilo T. and Dean M. (Genomics 2004)
    2. An unappreciated role for RNA surveillance. (PubMed id 14759258)1, 2 Hillman R.T.... Brenner S.E. (Genome Biol. 2004)
    3. Juxtacentromeric region of human chromosome 21: a boundary between centromeric heterochromatin and euchromatic chromosome arms. (PubMed id 12909339)1, 2 Brun M.-E.... De Sario A. (Gene 2003)
    4. Annotation of human chromosome 21 for relevance to Down syndrome: gene structure and expression analysis. (PubMed id 12036298)1, 2 Gardiner K.... Davisson M. (Genomics 2002)
    5. ABCC13, an unusual truncated ABC transporter, is highly expressed in fetal human liver. (PubMed id 12445816)1, 2 Yabuuchi H....Ishikawa T. (Biochem. Biophys. Res. Commun. 2002)
    6. The DNA sequence of human chromosome 21. (PubMed id 10830953)1, 2 Hattori M.... Yaspo M.-L. (Nature 2000)
    7. Molecular cloning of mouse Lrp7(Lr3) cDNA and chromosomal mapping of orthologous genes in mouse and human. (PubMed id 10049586)1, 3 Chen D....Dong Y. (Genomics 1999)
    8. A genome-wide association study for reading and language abilities in two population cohorts. (PubMed id 23738518)1 Luciano M....Bates T.C. (Genes Brain Behav. 2013)
    9. Toward an understanding of the protein interaction network of the human liver. (PubMed id 21988832)1 Wang J....Yang X. (Mol. Syst. Biol. 2011)
    10. MRP class of human ATP binding cassette (ABC) transporters: historical background and new research directions. (PubMed id 18668432)1 Toyoda Y....Ishikawa T. ( the fate of foreign compounds in biological systems 2008)

    (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: 150000 HGNC: 16022 AceView: ABCC13 Ensembl:ENSG00000243064 euGenes: HUgn150000
    ECgene: ABCC13 H-InvDB: ABCC13

    (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)
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    NameDescription
    PharmGKB entry for ABCC13 Pharmacogenomics, SNPs, Pathways
    ABCMdbhttp://abcmutations.hegelab.org/proteinDetails?uniprot_id=Q9NSE7

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for ABCC13 gene:
    Search GeneIP for patents involving ABCC13

    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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