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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 RAP1GAP2

check button Gene summary
Gene informationGene symbol

RAP1GAP2

Gene ID

23108

Gene nameRAP1 GTPase activating protein 2
SynonymsGARNL4|RAP1GA3
Cytomap

17p13.3

Type of geneprotein-coding
Descriptionrap1 GTPase-activating protein 2GTPase activating RANGAP domain-like 4GTPase activating Rap/RanGAP domain-like 4GTPase-activating Rap/Ran-GAP domain-like protein 4
Modification date20200313
UniProtAcc

A0A1B0GV05,

Q684P5,

Context

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

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Gene structures and expression levels for RAP1GAP2

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

ENSG00000132359
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
CBUPENST00000575979.1RAP1GAP2-208:retained_intron:RAP1GAP27.314387e+018.581395e-018.833376e-165.231068e-13
CBUPENST00000366401.8RAP1GAP2-202:protein_coding:RAP1GAP21.840962e+031.139963e+003.814930e-151.647870e-12

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 RAP1GAP2

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_121274chr172998221:2998376:3005341:3005440:3005955:30060413005341:3005440
exon_skip_125229chr172984983:2985066:2991297:2991397:2995337:29954662991297:2991397
exon_skip_167900chr173020477:3020595:3026008:3026121:3026350:30264643026008:3026121
exon_skip_172734chr172981195:2981248:2984983:2985066:2991297:29913972984983:2985066
exon_skip_201482chr172998221:2998376:3005369:3005440:3005955:30060403005369:3005440
exon_skip_218827chr172957759:2957794:2962670:2962714:2963430:29634622962670:2962714
exon_skip_265663chr173018061:3018198:3020477:3020595:3026008:30261213020477:3020595
exon_skip_276190chr173030922:3030998:3032411:3032449:3033392:30342073032411:3032449
exon_skip_27668chr172998221:2998376:3005341:3005440:3005955:30060403005341:3005440
exon_skip_281057chr173005955:3006041:3008011:3008145:3018061:30181983008011:3008145
exon_skip_283957chr172905284:2905368:2957759:2957794:2963430:29634622957759:2957794
exon_skip_295157chr172800515:2800550:2905284:2905368:2957759:29577942905284:2905368
exon_skip_42069chr172998221:2998376:3005369:3005440:3005955:30060413005369:3005440
exon_skip_51892chr172980287:2980365:2981195:2981248:2984983:29850662981195:2981248
exon_skip_71398chr172905284:2905368:2957759:2957794:2962670:29627142957759:2957794
exon_skip_75605chr173008101:3008145:3018061:3018198:3020477:30205953018061:3018198
exon_skip_93388chr173026944:3027070:3030922:3030998:3032411:30324493030922:3030998

check button Differentially expressed PSI values of individual exon skipping events in multiple brain tissues between AD and control.
Exon skipping informationTissue typeAvg(PSIs) in ADAvg(PSIs) in controlDifference (PSI)Adj. p-value


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Open reading frame (ORF) annotation in the exon skipping event for RAP1GAP2

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
ENST00000254695303241130324493UTR-3CDS
ENST00000542807303241130324493UTR-3CDS
ENST0000025469529052842905368Frame-shift
ENST0000054280729052842905368Frame-shift
ENST0000025469529577592957794In-frame
ENST0000054280729577592957794In-frame
ENST0000025469529626702962714In-frame
ENST0000054280729626702962714In-frame
ENST0000025469530053693005440In-frame
ENST0000054280730053693005440In-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
ENST0000025469529052842905368Frame-shift
ENST0000054280729052842905368Frame-shift
ENST0000025469529626702962714In-frame
ENST0000054280729626702962714In-frame
ENST0000025469530053693005440In-frame
ENST0000054280730053693005440In-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
ENST00000254695303241130324493UTR-3CDS
ENST00000542807303241130324493UTR-3CDS
ENST0000025469529052842905368Frame-shift
ENST0000054280729052842905368Frame-shift
ENST0000025469529912972991397Frame-shift
ENST0000054280729912972991397Frame-shift
ENST0000025469530204773020595Frame-shift
ENST0000054280730204773020595Frame-shift
ENST0000025469530309223030998Frame-shift
ENST0000054280730309223030998Frame-shift
ENST0000025469529577592957794In-frame
ENST0000054280729577592957794In-frame
ENST0000025469529626702962714In-frame
ENST0000054280729626702962714In-frame
ENST0000025469529811952981248In-frame
ENST0000054280729811952981248In-frame
ENST0000025469529849832985066In-frame
ENST0000054280729849832985066In-frame
ENST0000025469530053693005440In-frame
ENST0000054280730053693005440In-frame
ENST0000025469530080113008145In-frame
ENST0000054280730080113008145In-frame
ENST0000025469530180613018198In-frame
ENST0000054280730180613018198In-frame
ENST0000025469530260083026121In-frame
ENST0000054280730260083026121In-frame

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Infer the effects of exon skipping event on protein functional features for RAP1GAP2

p-ENSG00000132359_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
ENST000002546956678730295775929577942572915567
ENST000005428073127730295775929577942132475567
ENST000002546956678730296267029627142933366782
ENST000005428073127730296267029627142492926782
ENST0000025469566787303005369300544012921362400424
ENST0000054280731277303005369300544012481318400424

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
ENST000002546956678730296267029627142933366782
ENST000005428073127730296267029627142492926782
ENST0000025469566787303005369300544012921362400424
ENST0000054280731277303005369300544012481318400424

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
ENST000002546956678730295775929577942572915567
ENST000005428073127730295775929577942132475567
ENST000002546956678730296267029627142933366782
ENST000005428073127730296267029627142492926782
ENST00000254695667873029811952981248767819225243
ENST00000542807312773029811952981248723775225243
ENST00000254695667873029849832985066821903243271
ENST00000542807312773029849832985066777859243271
ENST0000025469566787303005369300544012921362400424
ENST0000054280731277303005369300544012481318400424
ENST0000025469566787303008011300814514511584453498
ENST0000054280731277303008011300814514071540453498
ENST0000025469566787303018061301819815861722498544
ENST0000054280731277303018061301819815421678498544
ENST0000025469566787303026008302612118431955584621
ENST0000054280731277303026008302612117991911584621

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
Q684P555671730ChainID=PRO_0000312716;Note=Rap1 GTPase-activating protein 2
Q684P555671730ChainID=PRO_0000312716;Note=Rap1 GTPase-activating protein 2
Q684P567826882Alternative sequenceID=VSP_029889;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15632203;Dbxref=PMID:15632203
Q684P567826882Alternative sequenceID=VSP_029889;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15632203;Dbxref=PMID:15632203
Q684P567821730ChainID=PRO_0000312716;Note=Rap1 GTPase-activating protein 2
Q684P567821730ChainID=PRO_0000312716;Note=Rap1 GTPase-activating protein 2
Q684P54004241730ChainID=PRO_0000312716;Note=Rap1 GTPase-activating protein 2
Q684P54004241730ChainID=PRO_0000312716;Note=Rap1 GTPase-activating protein 2
Q684P5400424248464DomainNote=Rap-GAP;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00165
Q684P5400424248464DomainNote=Rap-GAP;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00165

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
Q684P567826882Alternative sequenceID=VSP_029889;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15632203;Dbxref=PMID:15632203
Q684P567826882Alternative sequenceID=VSP_029889;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15632203;Dbxref=PMID:15632203
Q684P567821730ChainID=PRO_0000312716;Note=Rap1 GTPase-activating protein 2
Q684P567821730ChainID=PRO_0000312716;Note=Rap1 GTPase-activating protein 2
Q684P54004241730ChainID=PRO_0000312716;Note=Rap1 GTPase-activating protein 2
Q684P54004241730ChainID=PRO_0000312716;Note=Rap1 GTPase-activating protein 2
Q684P5400424248464DomainNote=Rap-GAP;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00165
Q684P5400424248464DomainNote=Rap-GAP;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00165

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
Q684P555671730ChainID=PRO_0000312716;Note=Rap1 GTPase-activating protein 2
Q684P555671730ChainID=PRO_0000312716;Note=Rap1 GTPase-activating protein 2
Q684P567826882Alternative sequenceID=VSP_029889;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15632203;Dbxref=PMID:15632203
Q684P567826882Alternative sequenceID=VSP_029889;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:15632203;Dbxref=PMID:15632203
Q684P567821730ChainID=PRO_0000312716;Note=Rap1 GTPase-activating protein 2
Q684P567821730ChainID=PRO_0000312716;Note=Rap1 GTPase-activating protein 2
Q684P52252431730ChainID=PRO_0000312716;Note=Rap1 GTPase-activating protein 2
Q684P52252431730ChainID=PRO_0000312716;Note=Rap1 GTPase-activating protein 2
Q684P52432711730ChainID=PRO_0000312716;Note=Rap1 GTPase-activating protein 2
Q684P52432711730ChainID=PRO_0000312716;Note=Rap1 GTPase-activating protein 2
Q684P5243271248464DomainNote=Rap-GAP;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00165
Q684P5243271248464DomainNote=Rap-GAP;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00165
Q684P54004241730ChainID=PRO_0000312716;Note=Rap1 GTPase-activating protein 2
Q684P54004241730ChainID=PRO_0000312716;Note=Rap1 GTPase-activating protein 2
Q684P5400424248464DomainNote=Rap-GAP;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00165
Q684P5400424248464DomainNote=Rap-GAP;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00165
Q684P54534981730ChainID=PRO_0000312716;Note=Rap1 GTPase-activating protein 2
Q684P54534981730ChainID=PRO_0000312716;Note=Rap1 GTPase-activating protein 2
Q684P5453498248464DomainNote=Rap-GAP;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00165
Q684P5453498248464DomainNote=Rap-GAP;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00165
Q684P54985441730ChainID=PRO_0000312716;Note=Rap1 GTPase-activating protein 2
Q684P54985441730ChainID=PRO_0000312716;Note=Rap1 GTPase-activating protein 2
Q684P5498544507507Modified residueNote=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q5SVL6
Q684P5498544507507Modified residueNote=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q5SVL6
Q684P5498544544544Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:16964243,ECO:0000244|PubMed:19690332;Dbxref=PMID:16964243,PMID:19690332
Q684P5498544544544Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:16964243,ECO:0000244|PubMed:19690332;Dbxref=PMID:16964243,PMID:19690332
Q684P55846211730ChainID=PRO_0000312716;Note=Rap1 GTPase-activating protein 2
Q684P55846211730ChainID=PRO_0000312716;Note=Rap1 GTPase-activating protein 2
Q684P5584621586726Compositional biasNote=Ser-rich
Q684P5584621586726Compositional biasNote=Ser-rich
Q684P5584621612612Modified residueNote=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q5SVL6
Q684P5584621612612Modified residueNote=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q5SVL6
Q684P5584621613613Modified residueNote=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q5SVL6
Q684P5584621613613Modified residueNote=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q5SVL6


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3'-UTR located exon skipping events that lost miRNA binding sites in RAP1GAP2

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 RAP1GAP2

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 RAP1GAP2

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 RAP1GAP2

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 RAP1GAP2

check button Correlated RBP and related information.
Tissue typeRBP nameExon skip IDCorrelation coeifficientP-value
CBPABPN1exon_skip_218827-4.216342e-013.444264e-08
CBZNF638exon_skip_218827-5.454743e-011.253199e-13
CBTRA2Aexon_skip_218827-5.650742e-011.039942e-14
CBSNRPAexon_skip_218827-4.518904e-012.523580e-09
CBRBM4exon_skip_201482-5.245725e-011.499810e-12
CBRBM4Bexon_skip_201482-4.262584e-012.348188e-08

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RelatedDrugs for RAP1GAP2

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 RAP1GAP2

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