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

WDFY4 Gene

protein-coding   GIFtS: 44
GCID: GC10P049892

WDFY family member 4

(Previous name: chromosome 10 open reading frame 64 )
(Previous symbol: C10orf64)
 Explore 6 diseases affiliated with
WDFY4 via our new
 Human Malady Compendium 
Biological research products
for WDFY4
    

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

Aliases
WDFY Family Member 41 2     Chromosome 10 Open Reading Frame 641
C10orf641 2 3     WD Repeat- And FYVE Domain-Containing Protein 42
KIAA16071 3 5     EC 3.5.1.188
Em:AC060234.31     EC 3.6.3.128
FLJ457481     

External Ids:    HGNC: 293231   Entrez Gene: 577052   Ensembl: ENSG000001288157   OMIM: 6133165   UniProtKB: Q6ZS813   

Export aliases for WDFY4 gene to outside databases

Previous GC identifers: GC10P049313 GC10U900444 GC10P049563 GC10P044158


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

  --

(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_000010.10  NC_018921.1  NT_030059.13  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the WDFY4 gene promoter:
         AML1a   FOXD3   STAT3   Pax-4a   FOXL1   C/EBPalpha   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for WDFY4

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat WDFY4


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

Entrez Gene cytogenetic band: 10q11.23   Ensembl cytogenetic band:  10q11.22   HGNC cytogenetic band: 10q11.23

WDFY4 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
WDFY4 gene location

GeneLoc information about chromosome 10         GeneLoc Exon Structure

GeneLoc location for GC10P049892:  view genomic region     (about GC identifiers)

Start:
49,892,921 bp from pter      End:
50,191,001 bp from pter
Size:
298,081 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: WDFY4_HUMAN, Q6ZS81 (See protein sequence)
Recommended Name: WD repeat- and FYVE domain-containing protein 4  
Size: 3184 amino acids; 353610 Da
Subcellular location: Membrane; Multi-pass membrane protein (Potential)
Secondary accessions: B9ZVP2 Q86WZ4 Q8N4A3 Q8TEN7 Q96BE1 Q9H7H8 Q9HCG5
Alternative splicing: 5 isoforms:  Q6ZS81-1   Q6ZS81-2   Q6ZS81-3   Q6ZS81-4   Q6ZS81-5   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for WDFY4: NX_Q6ZS81

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q6ZS81

  • 3 DME Specific Peptides for WDFY4 (Q6ZS81)
     GQVIGSA  LTFFPAL  STVEGLQ 

    WDFY4 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_065996.1  
    ENSEMBL proteins: 
     ENSP00000354141   ENSP00000407881   ENSP00000309314   ENSP00000363276   ENSP00000265453  
     ENSP00000320563   ENSP00000403789  

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    Uscn Proteins for WDFY4

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0016021integral to membrane IEA--


    WDFY4 for ontologies           About GeneDecksing



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    Uscn ELISAs and CLIAs for WDFY4


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

    WDFY4 for domains           About GeneDecksing

    5/8 InterPro domains/families (see all 8):
     IPR000409 BEACH_dom
     IPR011989 ARM-like
     IPR019775 WD40_repeat_CS
     IPR001680 WD40_repeat
     IPR017986 WD40_repeat_dom

    Graphical View of Domain Structure for InterPro Entry Q6ZS81

    ProtoNet protein and cluster: Q6ZS81

    UniProtKB/Swiss-Prot: WDFY4_HUMAN, Q6ZS81
    Similarity: Contains 1 BEACH domain
    Similarity: Contains 5 WD repeats


    (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

    Enzyme Numbers (IUBMB): EC 3.6.3.122 EC 3.5.1.182

    miRNA
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    (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 WDFY4

    (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 WDFY4
    Search CenterWatch for drugs/clinical trials and news about WDFY4 

    (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 WDFY4 gene: 
    NM_020945.1  

    Unigene Cluster for WDFY4:

    WDFY family member 4
    Hs.287379  [show with all ESTs]
    Unigene Representative Sequence: NM_020945
    10 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000360890(uc001jgy.3) ENST00000454161 ENST00000312002 ENST00000374161(uc001jhb.1)
    ENST00000265453(uc009xob.3 uc010qgn.1) ENST00000465910 ENST00000497480
    ENST00000490507 ENST00000325239(uc001jha.4) ENST00000413659

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    hsa-miR-3163 hsa-miR-152 hsa-miR-148b hsa-miR-548u hsa-miR-148a
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    Inhib. RNA
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    OriGene shRNA RFP: WDFY4
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat WDFY4
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat WDFY4

    Additional cDNA sequence: 

    AB046827.1 AK074085.1 AK074443.1 AK093607.1 AK127650.1 AK301736.1 AL833669.1 BC015694.2 
    BC032420.1 BC034937.1 BC047574.1 

    11 DOTS entries:

    DT.207837  DT.86853800  DT.100746825  DT.99928057  DT.91862719  DT.101958248  DT.97803385  DT.100865949 
    DT.121230791  DT.97814933  DT.40311322 

    GeneLoc Exon Structure

    5/12 Alternative Splicing Database (ASD) splice patterns (SP) for WDFY4 (see all 12)    About this scheme

    ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12a · 12b ^ 13 ^ 14 ^ 15a · 15b ^ 16 ^ 17a · 17b ^ 18 ^ 19 ^ 20 ^ 21a · 21b · 21c ^
    SP1:                                                                                                                                                            
    SP2:                                                                                                                                                            
    SP3:                                                                          -                                                                                 
    SP4:                                                                                                                                                            
    SP5:        -                                                                                                                                                   

    ExUns: 22a · 22b ^ 23 ^ 24 ^ 25 ^ 26 ^ 27 ^ 28 ^ 29 ^ 30 ^ 31 ^ 32 ^ 33 ^ 34 ^ 35 ^ 36a · 36b ^ 37 ^ 38 ^ 39 ^ 40 ^ 41 ^ 42 ^ 43 ^ 44 ^ 45 ^
    SP1:                                -                                                                             -                             -               
    SP2:                                                                                                              -                             -               
    SP3:                                                                                                                                                            
    SP4:                                                                                                                                                            
    SP5:                                                                                                                                                            

    ExUns: 46a · 46b ^ 47 ^ 48 ^ 49a · 49b ^ 50 ^ 51 ^ 52 ^ 53 ^ 54a · 54b ^ 55 ^ 56 ^ 57 ^ 58 ^ 59 ^ 60a · 60b ^ 61 ^ 62 ^ 63 ^ 64a · 64b ^ 65 ^ 66a ·
    SP1:                          -                                                                             -                                                   
    SP2:                          -                                                                             -                                                   
    SP3:                                                                                                                                                            
    SP4:                                                                                                                                                            
    SP5:                                                                                                                                                            


    ECgene alternative splicing isoforms for WDFY4

    (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

    WDFY4 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: --

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

    About this image

    WDFY4 expression in embryonic tissues and stem cells
    Expression by the Database of Embryonic development, Stem cell research, and Regenerative medicine    About this table
    Stem Cell Differentiation: 1 LifeMap Cell 
    NameCategory
    Blimp1- mVenus and stella-ECFP genetically modified stem cells (Embryonic Stem Cell)Early Embryo, Inner Cell Mass
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See WDFY4 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for WDFY4

    SOURCE GeneReport for Unigene cluster: Hs.287379
        SABiosciences Custom PCR Arrays for WDFY4
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for WDFY4

    (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 WDFY4 gene from 6/14 species (see all 14)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Wdfy41 , 5 WD repeat and FYVE domain containing 41, 5 82.72(n)1
    82.53(a)1
      14 (19.44 cM)5
    5450301  NM_001146022.11  NP_001139494.11 
     329595705 
    chicken
    (Gallus gallus)
    Aves WDFY41 WDFY family member 4 64.22(n)
    59.65(a)
      423781  XM_003641478.1  XP_003641526.1 
    African clawed frog
    (Xenopus laevis)
    Amphibia CD326631.12   -- 73.82(n)    CD326631.1 
    zebrafish
    (Danio rerio)
    Actinopterygii wdfy41 WDFY family member 4 53.43(n)
    43.41(a)
      572477  XM_696196.5  XP_701288.5 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons SPI6
    AT4G026606
    Beige/BEACH and WD40 domain-containing protein
    16(a)
    16(a)
    many ↔ many
    many ↔ many
    1(712473-726891)
    4(1159667-1174321)
    rice
    (Oryza sativa)
    Liliopsida --
    WD domain containing protein, putative, expressed
    16(a)
    1 → many
    3(30557073-30574933)


    ENSEMBL Gene Tree for WDFY4 (if available)
    TreeFam Gene Tree for WDFY4 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for WDFY4 gene
    NSMAF2  LYST2  LRBA2  NBEAL12  NBEA2  WDFY32  NBEAL22  
    3 SIMAP similar genes for WDFY4 using alignment to 7 protein entries:     WDFY4_HUMAN (see all proteins):
    WDFY3    NBEA    DKFZp686K03100

    WDFY4 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

    10/6111 NCBI SNPs in WDFY4 are shown (see all 6111    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 10 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1113188491,2
    --44282775(+) ACCATC/AATTAT 1 -- int12Minor allele frequency- A:0.25CSA WA 120
    rs1998450321,2
    C--44382247(+) TTTTTA/TANNNN 1 -- int10--------
    rs1906054911,2
    --49891593(+) GGTGGA/GCCCTC 1 -- us2k10--------
    rs1115361271,2
    C,--49891719(+) CCTCTG/-GTCTA 1 -- us2k11Minor allele frequency- -:0.00CSA 2
    rs113735351,2
    C--49891720(+) CTCTG-/GTCTAA 1 -- us2k10--------
    rs775758161,2
    C,--49891728(+) TAATCC/AGCTCT 1 -- us2k14Minor allele frequency- A:0.08NA WA 242
    rs1432645871,2
    --49891731(+) TCCGCC/TCTTAC 1 -- us2k10--------
    rs1505853751,2
    --49892120(+) GCCTC-/TCA   
       GTCAG
    TCATG
    1 -- us2k10--------
    rs1823261031,2
    --49892138(+) CATGGG/TCCACT 1 -- us2k10--------
    rs727872781,2
    C,F,--49892166(+) ACAAGC/AGATGA 1 -- us2k12Minor allele frequency- A:0.12NA EA 240

    HapMap Linkage Disequilibrium report for WDFY4 (49892921 - 50142921 bp, first 250kb of WDFY4)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 11 variations for WDFY4
         4 CNVs: 48562 6869 100941 48561
         7 Indels: 42369 61019 60012 48560 44755 39748 24505
    Human Gene Mutation Database (HGMD): WDFY4

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    (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

    WDFY4 for disorders           About GeneDecksing

    OMIM gene information: 613316    OMIM disorders: --

    6 diseases for WDFY4:    About MalaCards
    chediak-higashi syndrome    systemic lupus erythematosus    lupus erythematosus    alzheimer's disease
    atherosclerosis    malaria

    Human Genome Epidemiology (HuGE) Navigator: WDFY4 (5 documents)

    Export disorders for WDFY4 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 WDFY4 gene, integrated from 9 sources (see all 18):
    (articles sorted by number of sources associating them with WDFY4)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Prediction of the coding sequences of unidentified human genes. XVIII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PubMed id 10997877)1, 2, 3 Nagase T.... Ohara O. (2000)
    2. 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)
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (2004)
    4. Pharmacogenomic study of side-effects for antidepressa nt treatment options in STAR*D. (PubMed id 22041458)1 Clark S.L....van den Oord E.J. (2012)
    5. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (2011)
    6. A proteome-wide, quantitative survey of in vivo ubiqui tylation sites reveals widespread regulatory roles. (PubMed id 21890473)1 Wagner S.A....Choudhary C. (2011)
    7. Genome-wide association study in Asian populations id entifies variants in ETS1 and WDFY4 associated with systemic lupus erythematosu s. (PubMed id 20169177)1 Yang W....Lau Y.L. (2010)
    8. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1 Rose J.E....Uhl G.R. (2010)
    9. Genome-wide association study in a Chinese Han popula tion identifies nine new susceptibility loci for systemic lupus erythematosus. (PubMed id 19838193)1 Han J.W....Zhang X.J. (2009)
    10. Molecular genetics of successful smoking cessation: convergent genome-wide association study results. (PubMed id 18519826)1 Uhl G.R....Lerman C. (2008)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
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    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
    About This Section
    Entrez Gene: 57705 HGNC: 29323 Ensembl:ENSG00000128815 euGenes: HUgn57705 ECgene: WDFY4
    H-InvDB: WDFY4

    (According to HUGE)
    About This Section
    HUGE: KIAA1607

    (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 WDFY4 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 WDFY4 gene:
    Search GeneIP for patents involving WDFY4

    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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