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

RPAP3 Gene

protein-coding   GIFtS: 46
GCID: GC12M048057

RNA polymerase II associated protein 3

 Explore 1 disease affiliated with
RPAP3 via our new
 Human Malady Compendium 
Biological research products
for RPAP3
    

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

Aliases
RNA Polymerase II Associated Protein 31 2
FLJ219081
Spag1
RNA Polymerase II-Associated Protein 32

External Ids:    HGNC: 261511   Entrez Gene: 796572   Ensembl: ENSG000000051757   OMIM: 6114775   UniProtKB: Q9H6T33   

Export aliases for RPAP3 gene to outside databases

Previous GC identifers: GC12M046344 GC12M045086


(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 RPAP3:
This gene encodes an RNA polymerase II-associated protein. The encoded protein may function in transcriptional
regulation and may also regulate apoptosis. Alternatively spliced transcript variants have been described. (provided
by RefSeq, Mar 2009)

UniProtKB/Swiss-Prot: RPAP3_HUMAN, Q9H6T3
Function: Forms an interface between the RNA polymerase II enzyme and chaperone/scaffolding protein, suggesting that it
is required to connect RNA polymerase II to regulators of protein complex formation




(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_000012.11  NC_018923.1  NT_029419.12  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the RPAP3 gene promoter:
         Nkx3-1   Nkx3-1 v4   AML1a   AP-1   Nkx3-1 v1   PPAR-alpha   Nkx3-1 v2   Nkx3-1 v3   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidRPAP3 promoter sequence
   Search SABiosciences Chromatin IP Primers for RPAP3

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat RPAP3


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

Entrez Gene cytogenetic band: 12q13.11   Ensembl cytogenetic band:  12q13.11   HGNC cytogenetic band: 12q13.11

RPAP3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
RPAP3 gene location

GeneLoc information about chromosome 12         GeneLoc Exon Structure

GeneLoc location for GC12M048057:  view genomic region     (about GC identifiers)

Start:
48,055,715 bp from pter      End:
48,099,844 bp from pter
Size:
44,130 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: RPAP3_HUMAN, Q9H6T3 (See protein sequence)
Recommended Name: RNA polymerase II-associated protein 3  
Size: 665 amino acids; 75719 Da
Subunit: Tightly associated with the RNA polymerase II complex
Secondary accessions: B4DRW9 Q6PHR5
Alternative splicing: 3 isoforms:  Q9H6T3-1   Q9H6T3-2   Q9H6T3-3   (No experimental confirmation available)

Explore the universe of human proteins at neXtProt for RPAP3: NX_Q9H6T3

Post-translational modifications:

  • View modification sites using PhosphoSitePlus2
  • View neXtProt modification sites for NX_Q9H6T3

  • RPAP3 Protein expression data from MOPED and PaxDb:    About this image 
    Estimated protein expression log10 (pmol).

    REFSEQ proteins (3 alternative transcripts): 
    NP_001139547.1  NP_001139548.1  NP_078880.2  

    ENSEMBL proteins: 
     ENSP00000005386   ENSP00000401823   ENSP00000370024  

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    Uscn Proteins for RPAP3


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    Uscn ELISAs and CLIAs for RPAP3


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

    RPAP3 for domains           About GeneDecksing

    5 InterPro domains/families:
     IPR001440 TPR-1
     IPR011990 TPR-like_helical
     IPR025986 RPAP3-like_C
     IPR013026 TPR-contain_dom
     IPR019734 TPR_repeat

    Graphical View of Domain Structure for InterPro Entry Q9H6T3

    ProtoNet protein and cluster: Q9H6T3

    UniProtKB/Swiss-Prot: RPAP3_HUMAN, Q9H6T3
    Similarity: Belongs to the RPAP3 family
    Similarity: Contains 7 TPR 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

    Function Summary:

         UniProtKB/Swiss-Prot: RPAP3_HUMAN, Q9H6T3
    Function: Forms an interface between the RNA polymerase II enzyme and chaperone/scaffolding protein, suggesting that it
    is required to connect RNA polymerase II to regulators of protein complex formation

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    hsa-miR-3146 hsa-miR-199b-3p hsa-miR-199a-3p hsa-miR-3129-5p hsa-miR-548x hsa-miR-3143 hsa-miR-3148 hsa-miR-548c-3p
    SwitchGear 3'UTR luciferase reporter plasmidRPAP3 3' UTR sequence
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RPAP3

    3 GenomeRNAi human phenotypes for RPAP3:
     Decreased Wnt reporter activit  G0/1 arrest  Increased G1 DNA content 


    (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 RPAP3

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    5/47 Interacting proteins for RPAP3 (Q9H6T32, 3 ENSP000000053864) via UniProtKB, MINT, STRING, and/or I2D (see all 47)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    MAP3K3Q997592, 3MINT-48370 I2D: score=2 
    WDR92Q96MX62, 3, ENSP000002951214MINT-6551118 MINT-6551132 MINT-6551090 MINT-6551101 I2D: score=1 STRING: ENSP00000295121
    ITCHQ96J023, ENSP000003639984I2D: score=2 STRING: ENSP00000363998
    STK11Q158313, ENSP000003248564I2D: score=2 STRING: ENSP00000324856
    ANAPC1Q9H1A43, ENSP000003391094I2D: score=1 STRING: ENSP00000339109
    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 RPAP3
    Search CenterWatch for drugs/clinical trials and news about RPAP3 

    (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 RPAP3 gene (3 alternative transcripts): 
    NM_001146075.1  NM_001146076.1  NM_024604.2  

    Unigene Cluster for RPAP3:

    RNA polymerase II associated protein 3
    Hs.437855  [show with all ESTs]
    Unigene Representative Sequence: NM_024604
    7 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000005386(uc001rpr.3 uc010slk.2 uc001rps.3) ENST00000548211
    ENST00000432584 ENST00000380650 ENST00000548296 ENST00000547706 ENST00000551293


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    8/19 QIAGEN miScript miRNA Assays for microRNAs that regulate RPAP3 (see all 19):
    hsa-miR-3146 hsa-miR-199b-3p hsa-miR-199a-3p hsa-miR-3129-5p hsa-miR-548x hsa-miR-3143 hsa-miR-3148 hsa-miR-548c-3p
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    Inhib. RNA
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    Additional cDNA sequence: 

    AK025561.1 AK299465.1 BC003680.1 BC056415.1 

    8 DOTS entries:

    DT.313903  DT.91714060  DT.92424072  DT.101982708  DT.92025804  DT.40110545  DT.95174301  DT.99949739 

    24/171 AceView cDNA sequences (see all 171):

    BE550565 AK025561 BQ005466 BQ045110 AI382905 AI089506 CB120468 AI690479 
    BC056415 AW168178 AA286884 AA594583 F12403 CF528698 AA837273 AA314382 
    BQ431287 BE501605 BM788781 BP363461 BM759526 BU675027 AA829294 BX490334 

    GeneLoc Exon Structure

    4 Alternative Splicing Database (ASD) splice patterns (SP) for RPAP3    About this scheme

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


    ECgene alternative splicing isoforms for RPAP3

    (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

    RPAP3 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS
    CGAP TAG: ACTTTTACAT

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

    About this image
    See RPAP3 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for RPAP3

    SOURCE GeneReport for Unigene cluster: Hs.437855
        SABiosciences Custom PCR Arrays for RPAP3
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for RPAP3

    (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 RPAP3 gene from 7/23 species (see all 23)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chicken
    (Gallus gallus)
    Aves RPAP31 RNA polymerase II associated protein 3 72.09(n)
    65.95(a)
      417811  NM_001006231.1  NP_001006231.1 
    lizard
    (Anolis carolinensis)
    Reptilia RPAP36
    --
    61(a)
    1 ↔ 1
    5(52940893-52962953)
    African clawed frog
    (Xenopus laevis)
    Amphibia Xl.48282 Xenopus laevis transcribed sequence with weak similarity more 75.9(n)    BX844157.1 
    zebrafish
    (Danio rerio)
    Actinopterygii zgc561782 hypothetical protein MGC56178 74.44(n)   393173  BC045972.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta spag1 spaghetti 41.03(n)
    29.6(a)
      43958  NM_079925.2  NP_524664.1 
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT1G564401 tetratricopeptide repeat domain-containing protein 45.95(n)
    32.66(a)
      842097  NM_104522.3  NP_176039.2 
    rice
    (Oryza sativa)
    Liliopsida Os05g01299001 hypothetical protein 46.99(n)
    35.81(a)
      4337703  NM_001061083.1  NP_001054548.1 


    ENSEMBL Gene Tree for RPAP3 (if available)
    TreeFam Gene Tree for RPAP3 (if available) 

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for RPAP3 gene
    TOMM342  STIP12  TTC12  SPAG12  

    RPAP3 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

    10/718 NCBI SNPs in RPAP3 are shown (see all 718    About this table
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 12 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1819762181,2
    --48055218(+) ATTCAC/TTCAAT 3 -- ds50010--------
    rs9483941,2
    C,F,A,H,--48055232(-) TGGGTA/GTAAGT 3 -- ds500119Minor allele frequency- G:0.16NS EA NA WA 2342
    rs1852096551,2
    --48055404(+) TTTTTA/TAAAAT 3 -- ds50010--------
    rs1467340211,2
    --48055422(+) CTATAC/GTAAAT 3 -- ds50010--------
    rs1403250111,2
    --48055434(+) TTGTGA/TTCTGT 3 -- ds50010--------
    rs1504328501,2
    --48055449(+) CTTCAA/GTTAAC 3 -- ds50010--------
    rs1174773801,2
    C,F,--48055620(+) AGAATG/AACAAT 3 -- ds50011Minor allele frequency- A:0.03EA 120
    rs1452252371,2
    --48055685(+) CCATTC/TGGGTT 3 -- ds50010--------
    rs123153561,2
    C,F,H,--48055686(+) CATTCG/AGGTTG 3 -- ds500112Minor allele frequency- A:0.01NS EA NA WA 1730
    rs12330421,2
    C,F,H,--48055705(-) GTTTGA/TTATTT 3 -- ds500111Minor allele frequency- T:0.25MN NS EA NA 848

    HapMap Linkage Disequilibrium report for RPAP3 (48055715 - 48099844 bp)
    Structural Variations (Copy Number Variations, Insertions/Deletions, Inversions)
    Database of Genomic Variants (DGV): 2 variations for RPAP3
         2 CNVs: 8728 86366

    SABiosciences Cancer Mutation PCR Assays
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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

    RPAP3 for disorders           About GeneDecksing

    OMIM gene information: 611477    OMIM disorders: --

    1 disease for RPAP3:    About MalaCards
    malaria

    1 disease from the University of Copenhagen DISEASES database for RPAP3:
    Malaria

    Export disorders for RPAP3 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 RPAP3 gene, integrated from 9 sources (see all 30):
    (articles sorted by number of sources associating them with RPAP3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Systematic analysis of the protein interaction network for the human transcription machinery reveals the identity of the 7SK capping enzyme. (PubMed id 17643375)1, 2, 3 Jeronimo C.... Coulombe B. (2007)
    2. A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (2012)
    3. Charting the landscape of tandem BRCT domain-mediated protein interactions. (PubMed id 22990118)1 Woods N.T....Monteiro A.N. (2012)
    4. Initial characterization of the human central proteome. (PubMed id 21269460)2 Burkard T.R.... Colinge J. (2011)
    5. PIDD orchestrates translesion DNA synthesis in respon se to UV irradiation. (PubMed id 21415862)1 Logette E....Tschopp J. (2011)
    6. RPAP3 enhances cytotoxicity of doxorubicin by impairi ng NF-kappa B pathway. (PubMed id 21184742)1 Shimada K....Kamisaki Y. (2011)
    7. System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation. (PubMed id 21406692)2 Rigbolt K.T....Blagoev B. (2011)
    8. Interactions of pathological hallmark proteins: tubul in polymerization promoting protein/p25, beta-amyloid, and alpha-synuclein. (PubMed id 21832049)1 OlA!h J....OvA!di J. (2011)
    9. Mass spectrometric analysis of lysine ubiquitylation r eveals promiscuity at site level. (PubMed id 21139048)1 Danielsen J.M....Nielsen M.L. (2011)
    10. Genome-wide YFP fluorescence complementation screen id entifies new regulators for telomere signaling in human cells. (PubMed id 21044950)1 Lee O.H....Songyang Z. (2011)

    (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: 79657 HGNC: 26151 AceView: FLJ21908 Ensembl:ENSG00000005175 euGenes: HUgn79657
    ECgene: RPAP3 H-InvDB: RPAP3

    (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 RPAP3 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 RPAP3 gene:
    Search GeneIP for patents involving RPAP3

    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, SABiosciences, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Uscn, Thermo Fisher Scientific, Gene Editing from DNA2.0, Clones from EMD Millipore, OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript and LifeMap BioReagents, PCR Arrays from SABiosciences, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, and/or Enzo Life Sciences),
    In Situ Hybridization Assays from
    Advanced Cell Diagnostics
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    GeneCards Homepage - Last full update: 18 Mar 2013 - Incrementals: 21 Mar 2013 , 15 Apr 2013 , 27 Apr 2013

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