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Center for Computational Systems Medicine
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Gene summary

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Gene structures and expression levels

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Exon skipping events with PSIs in RPSMAP, MSBB, and Mayo

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Open reading frame (ORF) annotation in the exon skipping event

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Exon skipping events in the canonical protein sequence

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3'-UTR located exon skipping events lost miRNA binding sites

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SNVs in the skipped exons with depth of coverage

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AD stage-associated exon skipping events

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Splicing Quantitative Trait Loci (sQTLs) in the skipped exons

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Correlation with RNA binding proteins (RBPs)

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Related drugs with this gene

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Related diseases with this gene

Gene summary for PPP6R3

check button Gene summary
Gene informationGene symbol

PPP6R3

Gene ID

55291

Gene nameprotein phosphatase 6 regulatory subunit 3
SynonymsC11orf23|PP6R3|SAP190|SAPL|SAPLa|SAPS3
Cytomap

11q13.2

Type of geneprotein-coding
Descriptionserine/threonine-protein phosphatase 6 regulatory subunit 3SAPS domain family, member 3sporulation-induced transcript 4-associated protein SAPL
Modification date20200313
UniProtAcc

A0A1D5RMU2,

E9PJD8,

E9PK08,

E9PKF6,

E9PKG4,

E9PNN8,

E9PQP7,

H0YDK9,

H0YDW1,

H0YEN2,

H0YEV0,

H7BXH2,

Q5H9R7,

Context

check button Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez
GeneGO IDGO termPubMed ID
PPP6R3

GO:0043666

regulation of phosphoprotein phosphatase activity

16716191


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Gene structures and expression levels for PPP6R3

check buttonSkipped exons in the ROSMAP, MSBB, and Mayo based on Ensembl gene isoform structure.
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

ENSG00000110075
check button Differentially expressed gene analysis across multiple brain tissues between AD and control.
Tissue typeDEG directionBase mean exp.log2FC(AD/control)P-valueAdj. p-value

check button Differentially expressed isoform analysis across multiple brain tissues between AD and control.
gencode gene structure
Tissue typeDEG directionENSTTranscript info.Base mean exp.log2FC(AD/control)P-valueAdjc. p-value
PCCUPENST00000265637.8PPP6R3-202:protein_coding:PPP6R37.271076e+019.826604e-012.224265e-034.172121e-02
PGUPENST00000524904.5PPP6R3-206:protein_coding:PPP6R32.829152e+011.780286e+004.938042e-034.528226e-02
CBUPENST00000530734.1PPP6R3-221:protein_coding:PPP6R32.286092e+018.332766e-011.789934e-084.950600e-07
CBDOWNENST00000265637.8PPP6R3-202:protein_coding:PPP6R31.126256e+03-1.205778e+002.496832e-074.600361e-06
CBUPENST00000525421.5PPP6R3-209:nonsense_mediated_decay:PPP6R31.223747e+018.445786e-012.311151e-052.139862e-04
CBUPENST00000534534.5PPP6R3-226:protein_coding:PPP6R35.543067e+001.000691e+007.459083e-032.734097e-02

check button Landscape of isoform expressions across multiple brain tissues between AD and control.
gencode gene structure

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Exon skipping events with PSIs in ROSMAP, MSBB, and Mayo for PPP6R3

check button Landscape of individual exon skipping event across AD tissues and controls (PSI heatmap).
boxplot

check button All exon skipping events in AD cohorts.
Exon skip IDchrExons involved in exon skippingSkipped exon
exon_skip_100730chr1168460813:68460827:68505145:68505249:68519501:6851965168505145:68505249
exon_skip_100929chr1168460752:68460827:68519501:68519651:68537659:6853789168519501:68519651
exon_skip_109289chr1168558642:68558679:68564303:68564432:68567014:6856716668564303:68564432
exon_skip_112385chr1168575973:68576043:68583043:68583129:68587945:6858802468583043:68583129
exon_skip_126638chr1168574109:68574224:68575958:68576043:68587978:6858802468575958:68576043
exon_skip_140704chr1168603342:68603492:68609473:68609628:68609904:6861002368609473:68609628
exon_skip_141018chr1168583043:68583129:68587945:68588024:68590660:6859071468587945:68588024
exon_skip_141203chr1168575958:68576043:68587945:68588024:68590660:6859071468587945:68588024
exon_skip_147387chr1168505145:68505271:68515028:68515166:68519501:6851965168515028:68515166
exon_skip_148971chr1168603348:68603492:68609611:68609628:68609904:6861002368609611:68609628
exon_skip_173569chr1168603348:68603492:68609473:68609628:68609904:6861002368609473:68609628
exon_skip_17874chr1168575958:68576043:68583043:68583129:68587945:6858802468583043:68583129
exon_skip_185482chr1168574109:68574224:68575958:68576043:68587927:6858802468575958:68576043
exon_skip_196815chr1168460813:68460827:68519501:68519651:68544838:6854502468519501:68519651
exon_skip_219021chr1168519635:68519651:68537659:68537891:68544838:6854502468537659:68537891
exon_skip_23223chr1168575958:68576043:68587927:68588024:68590660:6859071468587927:68588024
exon_skip_232278chr1168583043:68583129:68587798:68588024:68590660:6859071468587798:68588024
exon_skip_23902chr1168574109:68574224:68575958:68576043:68583043:6858312968575958:68576043
exon_skip_241676chr1168583043:68583129:68587927:68588024:68590660:6859071468587927:68588024
exon_skip_254009chr1168460813:68460827:68519501:68519651:68537659:6853766968519501:68519651
exon_skip_256699chr1168564303:68564432:68566999:68567166:68569748:6856989768566999:68567166
exon_skip_259942chr1168564424:68564432:68567014:68567166:68569748:6856989768567014:68567166
exon_skip_272291chr1168575958:68576043:68583043:68583129:68587798:6858802468583043:68583129
exon_skip_280143chr1168575973:68576043:68583043:68583129:68587798:6858802468583043:68583129
exon_skip_289799chr1168460813:68460827:68505145:68505271:68519501:6851965168505145:68505271
exon_skip_38109chr1168609611:68609628:68609904:68610023:68613066:6861311768609904:68610023
exon_skip_40441chr1168603342:68603492:68609611:68609628:68609904:6861002368609611:68609628
exon_skip_64370chr1168460813:68460827:68515028:68515166:68519501:6851965168515028:68515166
exon_skip_65307chr1168548067:68548204:68551121:68551186:68554145:6855422068551121:68551186
exon_skip_66142chr1168575973:68576043:68583043:68583129:68587927:6858802468583043:68583129
exon_skip_67741chr1168460752:68460827:68537659:68537891:68544838:6854502468537659:68537891
exon_skip_7157chr1168603342:68603492:68609904:68610023:68613066:6861311768609904:68610023
exon_skip_74249chr1168519635:68519651:68522494:68522689:68537659:6853766968522494:68522689
exon_skip_7998chr1168575958:68576043:68587978:68588024:68590660:6859071468587978:68588024
exon_skip_86204chr1168590660:68590714:68591576:68591706:68596097:6859621868591576:68591706
exon_skip_86362chr1168519635:68519651:68544838:68545024:68548067:6854820468544838:68545024
exon_skip_87175chr1168575958:68576043:68583043:68583129:68587927:6858802468583043:68583129
exon_skip_89426chr1168460813:68460827:68505145:68505271:68515028:6851516668505145:68505271
exon_skip_89612chr1168548067:68548204:68567014:68567166:68569748:6856989768567014:68567166
exon_skip_95613chr1168551121:68551186:68554145:68554257:68558566:6855867968554145:68554257

check button Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control.
psi tcga
Exon skipping informationTissue typeAvg(PSIs) in ADAvg(PSIs) in controlDifference (PSI)Adj. p-value
exon_skip_40441MSBB_STG3.869355e-015.479167e-01-1.609812e-012.409942e-02


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Open reading frame (ORF) annotation in the exon skipping event for PPP6R3

check button Open reading frame (ORF) of individual exon skipping events in ROSMAP based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST0000039380068537659685378915CDS-5UTR
ENST0000039380068519501685196515UTR-5UTR
ENST000003938006855414568554257Frame-shift
ENST000003938006857595868576043Frame-shift
ENST000003938006858792768588024Frame-shift
ENST000003938006856701468567166In-frame
ENST000003938006858304368583129In-frame
ENST000003938006860990468610023In-frame

check button Open reading frame (ORF) of individual exon skipping events in MSBB based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST0000039380068537659685378915CDS-5UTR
ENST0000039380068519501685196515UTR-5UTR
ENST000003938006855414568554257Frame-shift
ENST000003938006857595868576043Frame-shift
ENST000003938006858792768588024Frame-shift
ENST000003938006859157668591706Frame-shift
ENST000003938006856701468567166In-frame
ENST000003938006858304368583129In-frame

check button Open reading frame (ORF) of individual exon skipping events in Mayo based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST0000039380068537659685378915CDS-5UTR
ENST0000039380068519501685196515UTR-5UTR
ENST000003938006855414568554257Frame-shift
ENST000003938006856430368564432Frame-shift
ENST000003938006857595868576043Frame-shift
ENST000003938006858792768588024Frame-shift
ENST000003938006859157668591706Frame-shift
ENST000003938006855112168551186In-frame
ENST000003938006856701468567166In-frame
ENST000003938006858304368583129In-frame
ENST000003938006860990468610023In-frame

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Infer the effects of exon skipping event on protein functional features for PPP6R3

p-ENSG00000110075_img4.png
boxplot

check button Loci of skipped exons in ROSMAP across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end
ENST000003938005110873685670146856716612311382325376
ENST000003938005110873685830436858312918011886515544
ENST000003938005110873686099046861002327062824817856

check button Loci of skipped exons in MSBB across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end
ENST000003938005110873685670146856716612311382325376
ENST000003938005110873685830436858312918011886515544

check button Loci of skipped exons in Mayo across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end
ENST0000039380051108736855112168551186808872184206
ENST000003938005110873685670146856716612311382325376
ENST000003938005110873685830436858312918011886515544
ENST000003938005110873686099046861002327062824817856

check button Lost protein functional features of individual exon skipping events in ROSMAP.
UniProt acc.Start of exon skipping (AA)End of exon skipping (AA)Protein feature start (AA)Protein feature end (AA)Category of protein featureDescription of feature
Q5H9R7325376326376Alternative sequenceID=VSP_017140;Note=In isoform 3 and isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:11401438;Dbxref=PMID:11401438
Q5H9R73253761873ChainID=PRO_0000046100;Note=Serine/threonine-protein phosphatase 6 regulatory subunit 3
Q5H9R7515544516544Alternative sequenceID=VSP_017141;Note=In isoform 3%2C isoform 4 and isoform 6. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:11401438,ECO:0000303|PubMed:15489334;Dbxref=PMID:11401438,PMID:15489334
Q5H9R7515544544549Alternative sequenceID=VSP_017142;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:17974005;Dbxref=PMID:17974005
Q5H9R75155441873ChainID=PRO_0000046100;Note=Serine/threonine-protein phosphatase 6 regulatory subunit 3
Q5H9R7817856817817Alternative sequenceID=VSP_017143;Note=In isoform 5. S->RVLKSYR;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:10997877;Dbxref=PMID:10997877
Q5H9R78178561873ChainID=PRO_0000046100;Note=Serine/threonine-protein phosphatase 6 regulatory subunit 3
Q5H9R7817856853853Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163
Q5H9R7817856842842Natural variantID=VAR_057720;Note=A->V;Dbxref=dbSNP:rs34009811

check button Lost protein functional features of individual exon skipping events in MSBB.
UniProt acc.Start of exon skipping (AA)End of exon skipping (AA)Protein feature start (AA)Protein feature end (AA)Category of protein featureDescription of feature
Q5H9R7325376326376Alternative sequenceID=VSP_017140;Note=In isoform 3 and isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:11401438;Dbxref=PMID:11401438
Q5H9R73253761873ChainID=PRO_0000046100;Note=Serine/threonine-protein phosphatase 6 regulatory subunit 3
Q5H9R7515544516544Alternative sequenceID=VSP_017141;Note=In isoform 3%2C isoform 4 and isoform 6. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:11401438,ECO:0000303|PubMed:15489334;Dbxref=PMID:11401438,PMID:15489334
Q5H9R7515544544549Alternative sequenceID=VSP_017142;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:17974005;Dbxref=PMID:17974005
Q5H9R75155441873ChainID=PRO_0000046100;Note=Serine/threonine-protein phosphatase 6 regulatory subunit 3

check button Lost protein functional features of individual exon skipping events in Mayo.
UniProt acc.Start of exon skipping (AA)End of exon skipping (AA)Protein feature start (AA)Protein feature end (AA)Category of protein featureDescription of feature
Q5H9R71842061873ChainID=PRO_0000046100;Note=Serine/threonine-protein phosphatase 6 regulatory subunit 3
Q5H9R7325376326376Alternative sequenceID=VSP_017140;Note=In isoform 3 and isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:11401438;Dbxref=PMID:11401438
Q5H9R73253761873ChainID=PRO_0000046100;Note=Serine/threonine-protein phosphatase 6 regulatory subunit 3
Q5H9R7515544516544Alternative sequenceID=VSP_017141;Note=In isoform 3%2C isoform 4 and isoform 6. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303|PubMed:11401438,ECO:0000303|PubMed:15489334;Dbxref=PMID:11401438,PMID:15489334
Q5H9R7515544544549Alternative sequenceID=VSP_017142;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:17974005;Dbxref=PMID:17974005
Q5H9R75155441873ChainID=PRO_0000046100;Note=Serine/threonine-protein phosphatase 6 regulatory subunit 3
Q5H9R7817856817817Alternative sequenceID=VSP_017143;Note=In isoform 5. S->RVLKSYR;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:10997877;Dbxref=PMID:10997877
Q5H9R78178561873ChainID=PRO_0000046100;Note=Serine/threonine-protein phosphatase 6 regulatory subunit 3
Q5H9R7817856853853Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163
Q5H9R7817856842842Natural variantID=VAR_057720;Note=A->V;Dbxref=dbSNP:rs34009811


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3'-UTR located exon skipping events that lost miRNA binding sites in PPP6R3

check button 3'-UTR exon skipping evnets lost miRNA binding.
Tissue typeENSTExon skip startExon skip endmicroRNABinding site by TargetScanBinding type by TargetScanBdinding site by miRandaScore of miRandaEnergy by miRanda

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SNVs in the skipped exons for PPP6R3

check button - Differential PSIs between mutated versus non-mutated samples.

check button - Depth of Coverage in the skipped exon of the mutated samples.

check button - Sashimi plot in the skipped exon of the mutated samples.

check button - Non-synonymous mutations located in the skipped exons.
Cancer typeSampleESIDSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange

check button - Non-synonymous mutations located in the skipped exons in CCLE.
SampleSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange

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AD stage-associated exon skippint events for PPP6R3

check button Associated exon skipping events with Braak staging or Clinical Dementia Rating (CDR).
AD stage infoCohortTissueSE idCoefficient P-valueChromosomeStrandE1 startE1 endSkipped startSkipped endE2 startE2 end

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PPP6R3

check button sQTL information located at the skipped exons.
Tissue typeExon skip IDSNP idLocationP-valueFDR

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Correlation with RNA binding proteins (RBPs) for PPP6R3

check button Correlated RBP and related information.
Tissue typeRBP nameExon skip IDCorrelation coeifficientP-value
CBTARDBPexon_skip_194782-5.254736e-011.889832e-11
CBCNOT4exon_skip_194782-5.187210e-013.771041e-11
CBTRA2Aexon_skip_194782-5.209153e-013.017759e-11
CBNUP42exon_skip_1947824.238540e-011.471444e-07
CBSRSF1exon_skip_194782-4.421500e-013.611514e-08
CBPCBP4exon_skip_239025.278546e-015.429147e-12
CBFUBP1exon_skip_23902-4.784909e-017.702734e-10
CBRBM45exon_skip_239026.486162e-014.953054e-19
CBTRA2Aexon_skip_87175-5.270051e-015.042825e-12
CBRC3H1exon_skip_241676-4.026840e-014.273707e-07
CBFUBP1exon_skip_241676-5.097884e-014.258904e-11
CBPTBP1exon_skip_241676-4.654493e-012.848459e-09
CBPCBP2exon_skip_1735694.350346e-013.290532e-08
CBPUM1exon_skip_1735694.251518e-017.199441e-08
CBRALYLexon_skip_1735694.250696e-017.245753e-08
CBNOVA1exon_skip_1735694.185120e-011.201496e-07
HCCTARDBPexon_skip_40441-4.012278e-016.074434e-12
HCCRBM6exon_skip_40441-6.348735e-014.276122e-32
HCCPCBP4exon_skip_40441-5.483605e-019.392834e-23
IFGTRA2Aexon_skip_100730-4.060977e-013.953965e-02
IFGNUP42exon_skip_2897995.720417e-011.823502e-03
IFGIGF2BP3exon_skip_87175-4.073452e-013.495182e-02
IFGKHDRBS2exon_skip_87175-5.343724e-014.087612e-03
IFGHNRNPA0exon_skip_87175-4.227593e-012.802365e-02
IFGRALYLexon_skip_87175-5.025972e-017.544917e-03
IFGNOVA1exon_skip_87175-5.702064e-011.900863e-03
PCCELAVL4exon_skip_1735694.155199e-014.788425e-10
PCCRBM6exon_skip_148971-4.490429e-011.025132e-11
PCCPCBP4exon_skip_148971-4.831777e-011.448152e-13

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RelatedDrugs for PPP6R3

check button Approved drugs targeting this gene.
(DrugBank Version 5.1.0 2018-04-02)
UniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for PPP6R3

check button Diseases associated with this gene.
(DisGeNet 4.0)
GeneDisease IDDisease name# pubmedsSource