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

HFM1 Gene

protein-coding   GIFtS: 52
GCID: GC01M091726

HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae)

(Previous name: SEC63 domain containing 1 )
(Previous symbol: SEC63D1)
 Explore 9 diseases affiliated with
HFM1 via our new
 Human Malady Compendium 
Biological research products
for HFM1
    

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

Aliases
HFM1, ATP-Dependent DNA Helicase Homolog (S. Cerevisiae)1 2     Si-11-62
MER31 2     Helicase1
SEC63D11 2     Helicase-Like Protein HFM12
SEC63 Domain Containing 11 2     Probable ATP-Dependent DNA Helicase HFM12
SEC63 Domain-Containing Protein 12 3     EC 3.6.4.123
FLJ367601     SEC3D13
FLJ390111     DSS15
RP11-539G11.12     EC 3.6.18
Si-112     

External Ids:    HGNC: 201931   Entrez Gene: 1640452   Ensembl: ENSG000001626697   OMIM: 6012855   UniProtKB: A2PYH43   

Export aliases for HFM1 gene to outside databases

Previous GC identifers: GC01M091556 GC01M091499 GC01M089845


(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_000001.10  NC_018912.1  NT_032977.9  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the HFM1 gene promoter:
         Nkx3-1 v4   Sox5   Brachyury   FOXD3   HNF-3beta   MEF-2A   IRF-7A   aMEF-2   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidHFM1 promoter sequence
   Search SABiosciences Chromatin IP Primers for HFM1

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat HFM1


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

Entrez Gene cytogenetic band: 1p22.2   Ensembl cytogenetic band:  1p22.2   HGNC cytogenetic band: 1p22.2

HFM1 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
HFM1 gene location

GeneLoc information about chromosome 1         GeneLoc Exon Structure

GeneLoc location for GC01M091726:  view genomic region     (about GC identifiers)

Start:
91,726,323 bp from pter      End:
91,870,426 bp from pter
Size:
144,104 bases      Orientation:
minus 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: HFM1_HUMAN, A2PYH4 (See protein sequence)
Recommended Name: Probable ATP-dependent DNA helicase HFM1  
Size: 1435 amino acids; 162610 Da
Secondary accessions: B1B0B6 Q8N9Q0
Alternative splicing: 2 isoforms:  A2PYH4-1   A2PYH4-2   

Explore the universe of human proteins at neXtProt for HFM1: NX_A2PYH4

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_A2PYH4

  • 3 DME Specific Peptides for HFM1 (A2PYH4)
     QMIGRAGR  APTGSGKT  GRAGRPQF 

    HFM1 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins: NP_001017975.3  
    ENSEMBL proteins: 
     ENSP00000359454   ENSP00000387661   ENSP00000397369   ENSP00000388900   ENSP00000409827  
     ENSP00000359453   ENSP00000294696  

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    Uscn Proteins for HFM1


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    Uscn Antibodies for HFM1
    ThermoFisher Antibodies for HFM1

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    Uscn ELISAs and CLIAs for HFM1


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

    HFM1 for domains           About GeneDecksing

    4 InterPro domains/families:
     IPR011545 DNA/RNA_helicase_DEAD/DEAH_N
     IPR004179 Sec63-dom
     IPR014001 Helicase_ATP-bd
     IPR001650 Helicase_C

    Graphical View of Domain Structure for InterPro Entry A2PYH4

    ProtoNet protein and cluster: A2PYH4

    UniProtKB/Swiss-Prot: HFM1_HUMAN, A2PYH4
    Similarity: Belongs to the helicase family. SKI2 subfamily
    Similarity: Contains 1 helicase ATP-binding domain
    Similarity: Contains 1 helicase C-terminal domain
    Similarity: Contains 1 SEC63 domain


    (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: HFM1_HUMAN, A2PYH4
    Catalytic activity: ATP + H(2)O = ADP + phosphate

    Enzyme Numbers (IUBMB): EC 3.6.12 EC 3.6.4.121

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    Inhib. RNA
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    OriGene shRNA RFP: HFM1
    OriGene siRNA: HFM1
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for HFM1

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003676nucleic acid binding IEA--
    GO:0005524ATP binding IEA--
    GO:0008026ATP-dependent helicase activity IEA--


    HFM1 for ontologies           About GeneDecksing


    1 GenomeRNAi human phenotype for HFM1:
     Decreased Wnt reporter activit 


    (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 HFM1

    STRING Interaction Network Preview (showing 1 interactants - click image to see more details)

    5/10 Interacting proteins for HFM1 (A2PYH43 ENSP000003594544) via UniProtKB, MINT, STRING, and/or I2D (see all 10)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    PLRG1O436603I2D: score=2 
    EEF2P136393I2D: score=1 
    ENO3P139293I2D: score=1 
    EXOSC10Q017803I2D: score=1 
    HSPH1Q925983I2D: score=1 
    About this table

    (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 HFM1
    Search CenterWatch for drugs/clinical trials and news about HFM1 

    (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 HFM1 gene: 
    NM_001017975.3  

    Unigene Cluster for HFM1:

    HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae)
    Hs.454818  [show with all ESTs]
    Unigene Representative Sequence: AB204867
    11 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000462405 ENST00000370425(uc009wdb.3 uc001doa.4 uc010osu.2)
    ENST00000430465(uc001dob.4) ENST00000497520 ENST00000481900(uc001doc.1)
    ENST00000488023 ENST00000448819 ENST00000427444 ENST00000455133 ENST00000370424
    ENST00000294696(uc010osv.1)

    miRNA
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    OriGene 3'-UTR Clone: HFM1
    Browse OriGene MicroRNA Expression Plasmids
    QIAGEN Custom miScript Target Protector blocks miRNA-binding site of human, mouse, rat HFM1
    Search QIAGEN for miScript miRNA Assays for microRNAs that regulate HFM1
    SwitchGear 3'UTR luciferase reporter plasmidHFM1 3' UTR sequence
    Inhib. RNA
    Products:
         
    Browse for Gene Knock-down Tools from EMD Millipore
    OriGene 29mer shRNA kits in GFP-retroviral vector in human, mouse, rat for HFM1 (see all 4)
    OriGene shRNA RFP: HFM1
    OriGene siRNA: HFM1
    QIAGEN FlexiTube/FlexiPlate siRNA for gene silencing in human, mouse, rat HFM1
    Clone
    Products:
         
    OriGene Myc/DDK tagged cDNA clones in CMV expression vector in human, mouse, rat for HFM1 (see all 2)
    OriGene untagged cDNA clones in CMV expression vector in human, mouse, rat for HFM1
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    GenScript: all cDNA clones in your preferred vector: HFM1 (NM_006304)
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      QIAGEN QuantiTect SYBR Green Assays in human, mouse, rat HFM1
      QIAGEN QuantiFast Probe-based Assays in human, mouse, rat HFM1

    Additional cDNA sequence: 

    AB044787.1 AB044788.1 AB058636.1 AB058637.1 AB074274.1 AB204867.1 AK294754.1 AK302582.1 
    BC062793.1 BC130525.1 BC144172.1 BC144198.1 BX649037.1 

    8 DOTS entries:

    DT.105340  DT.97796872  DT.100730550  DT.121390752  DT.121390755  DT.121390757  DT.99930630  DT.102821192 

    2 AceView cDNA sequences:

    BX481571 AK096330 

    GeneLoc Exon Structure

    2 Alternative Splicing Database (ASD) splice patterns (SP) for HFM1    About this scheme

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


    ECgene alternative splicing isoforms for HFM1

    (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

    HFM1 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: TATTTTGTTT

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

    About this image

    HFM1 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
    Posterior foregut-like cells (A scalable, suspensi...)
    Expression: Positive    Negative     Selective marker
    Experimental details: Curated     Microarrays     In-situ hybridization

    See HFM1 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for HFM1

    SOURCE GeneReport for Unigene cluster: Hs.454818
        SABiosciences Custom PCR Arrays for HFM1
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for HFM1

    (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 HFM1 gene from 6/21 species (see all 21)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves HFM11 HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae) 70.14(n)
    63.58(a)
      424509  XM_422349.3  XP_422349.3 
    lizard
    (Anolis carolinensis)
    Reptilia HFM16
    --
    71(a)
    1 ↔ 1
    4(94600182-94647546)
    zebrafish
    (Danio rerio)
    Actinopterygii hfm11 HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae) 62.47(n)
    58.38(a)
      557052  XM_001919520.3  XP_001919555.3 
    mosquito
    (Anopheles gambiae)
    Insecta AgaP_AGAP0090601 AGAP009060-PA 45.1(n)
    37.53(a)
      3291892  XM_552976.3  XP_552976.3 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons RCK1 rock-N-rollers protein 50.48(n)
    42.48(a)
      822395  NM_113689.2  NP_189410.2 
    rice
    (Oryza sativa)
    Liliopsida Os02g06175001 hypothetical protein 52.17(n)
    45.77(a)
      4329993  NM_001053977.1  NP_001047442.1 


    ENSEMBL Gene Tree for HFM1 (if available)
    TreeFam Gene Tree for HFM1 (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

    10/2430 NCBI SNPs in HFM1 are shown (see all 2430    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 1 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1847694471,2
    --91725904(+) AACAAC/TAGACA 1 -- int10--------
    rs1456054561,2
    --91725912(+) ACACTA/GGGGCC 1 -- int10--------
    rs1156789211,2
    --91726109(+) TTTCTA/GAAAGT 1 -- int11Minor allele frequency- G:0.01NA 120
    rs1883676871,2
    --91726197(+) ACTTAA/TCAATA 1 -- int10--------
    rs1915301311,2
    --91726245(+) AATATA/CTTTTT 1 -- int10--------
    rs412867691,2
    C,--91726288(+) GACAAC/GATTGA 1 -- int13Minor allele frequency- G:0.16NA WA 240
    rs1152850151,2
    C,F,--91726448(+) CCATAC/TAATAA 1 -- ut311Minor allele frequency- T:0.02WA 118
    rs1423633031,2
    --91726539(+) CATTGC/GTTCTT 1 -- ut310--------
    rs412867711,2
    --91726637(+) AACAAA/TGCCAC 1 -- ut310--------
    rs412867731,2
    F,--91726679(+) AATGGG/AAAAAT 1 -- ut311Minor allele frequency- A:0.04NA 120

    HapMap Linkage Disequilibrium report for HFM1 (91726323 - 91870426 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 3 variations for HFM1
         1 CNV: 1547
         2 Indels: 59942 59941

    SABiosciences Cancer Mutation PCR Assays
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    DNA2.0 Custom Variant and Variant Library Synthesis for HFM1

    (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

    HFM1 for disorders           About GeneDecksing

    OMIM gene information: 601285    OMIM disorders: --

    9 diseases for HFM1:    About MalaCards
    fukuyama congenital muscular dystrophy    spastic hemiplegia    hemiplegia    congenital muscular dystrophy
    epicondylitis    muscular dystrophy    spasticity    tuberculosis
    mycobacterium tuberculosis

    2 diseases from the University of Copenhagen DISEASES database for HFM1:
    Spastic hemiplegia     Epicondylitis
    Human Genome Epidemiology (HuGE) Navigator: HFM1 (2 documents)

    Export disorders for HFM1 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 HFM1 gene integrated from 9 sources:
    (articles sorted by number of sources associating them with HFM1)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. HFM1, the human homologue of yeast Mer3, encodes a putative DNA helicase expressed specifically in germ-line cells. (PubMed id 17286053)1, 2, 3, 9 Tanaka K....Ikeda J.E. (2006)
    2. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2, 3 Ota T.... Sugano S. (2004)
    3. Investigation of genetic susceptibility factors for h uman longevity - A targeted nonsynonymous SNP study. (PubMed id 20800603)1 Flachsbart F....Nebel A. (2010)
    4. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PubMed id 20379614)1 Rose J.E....Uhl G.R. (2010)
    5. The DNA sequence and biological annotation of human chromosome 1. (PubMed id 16710414)2 Gregory S.G.... Bentley D.R. (2006)
    6. 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. (2002)

    (in PubMed, OMIM, and NCBI Bookshelf)
    About This Section
     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)
    About This Section
    Entrez Gene: 164045 HGNC: 20193 AceView: LOC164045 Ensembl:ENSG00000162669 euGenes: HUgn164045
    ECgene: HFM1 H-InvDB: HFM1

    (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 HFM1 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 HFM1 gene:
    Search GeneIP for patents involving HFM1

    GeneCards and IP:
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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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