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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 TCGA

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Exon skipping events with PSIs in GTEx

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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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SNVs in the skipped exons with depth of coverage

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Splicing Quantitative Trait Loci (sQTLs) in the skipped exons

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon

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Related drugs with this gene

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Related diseases with this gene

Gene summary for RAPGEF3

check button Gene summary
Gene informationGene symbol

RAPGEF3

Gene ID

10411

Gene nameRap guanine nucleotide exchange factor 3
SynonymsCAMP-GEFI|EPAC|EPAC1|HSU79275|bcm910
Cytomap

12q13.11

Type of geneprotein-coding
Descriptionrap guanine nucleotide exchange factor 39330170P05RikEPAC 1Rap guanine nucleotide exchange factor (GEF) 3Rap1 guanine-nucleotide-exchange factor directly activated by cAMPcAMP-regulated guanine nucleotide exchange factor Iexchange factor directly ac
Modification date20180527
UniProtAcc

O95398

ContextPubMed: RAPGEF3 [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract]
- Title (PMID)

check button Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez
GeneGO IDGO termPubMed ID
RAPGEF3

GO:0033138

positive regulation of peptidyl-serine phosphorylation

23867755

RAPGEF3

GO:0046827

positive regulation of protein export from nucleus

23867755

RAPGEF3

GO:0071320

cellular response to cAMP

21840392


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Exon skipping events across known transcript of Ensembl for RAPGEF3 from UCSC genome browser

check buttonSkipped exons in TCGA and GTEx 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

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Gene isoform structures and expression levels for RAPGEF3

check button Expression levels of gene isoforms across TCGA.
gencode gene structure

check button Expression levels of gene isoforms across GTEx.
gencode gene structure


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Exon skipping events with PSIs in TCGA for RAPGEF3

check button Information of exkip skipping event in TCGA.
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_914061248132949:48133013:48133153:48133201:48133923:4813397448133153:48133201ENSG00000079337.11ENST00000548434.1
exon_skip_914081248134087:48134178:48134424:48134606:48134697:4813482348134424:48134606ENSG00000079337.11ENST00000171000.4,ENST00000548434.1,ENST00000395360.2,ENST00000547856.1,ENST00000405493.2,ENST00000389212.3,ENST00000549151.1,ENST00000449771.2,ENST00000488250.1
exon_skip_914101248134697:48134823:48135287:48135385:48137312:4813745948135287:48135385ENSG00000079337.11ENST00000171000.4,ENST00000479866.1,ENST00000395360.2,ENST00000547856.1,ENST00000405493.2,ENST00000389212.3,ENST00000482843.1,ENST00000549151.1,ENST00000449771.2
exon_skip_914151248135287:48135385:48137312:48137459:48137769:4813785148137312:48137459ENSG00000079337.11ENST00000171000.4,ENST00000479866.1,ENST00000395360.2,ENST00000547856.1,ENST00000405493.2,ENST00000389212.3,ENST00000482843.1,ENST00000549151.1,ENST00000449771.2
exon_skip_914231248137769:48137851:48140642:48140682:48141326:4814140948140642:48140682ENSG00000079337.11ENST00000171000.4,ENST00000548919.1,ENST00000479866.1,ENST00000547856.1,ENST00000405493.2,ENST00000389212.3,ENST00000482843.1,ENST00000549151.1,ENST00000449771.2
exon_skip_914271248140642:48140682:48141326:48141409:48141494:4814164548141326:48141409ENSG00000079337.11ENST00000171000.4,ENST00000548919.1,ENST00000479866.1,ENST00000547856.1,ENST00000405493.2,ENST00000389212.3,ENST00000395358.3,ENST00000482843.1,ENST00000549151.1,ENST00000449771.2,ENST00000494764.1
exon_skip_914471248145505:48145612:48145698:48145752:48151648:4815186148145698:48145752ENSG00000079337.11ENST00000171000.4,ENST00000548919.1,ENST00000479866.1,ENST00000405493.2,ENST00000389212.3,ENST00000495953.2,ENST00000395358.3,ENST00000466322.1,ENST00000482843.1,ENST00000549151.1,ENST00000449771.2
exon_skip_914481248145698:48145752:48151648:48151861:48164639:4816481748151648:48151861ENSG00000079337.11ENST00000548919.1,ENST00000549151.1

check button PSI values of skipped exons in TCGA.
psi tcga

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Exon skipping events with PSIs in GTEx for RAPGEF3

check button Information of exkip skipping event in GTEx
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_914061248132949:48133013:48133153:48133201:48133923:4813397448133153:48133201ENSG00000079337.11ENST00000548434.1
exon_skip_914081248134087:48134178:48134424:48134606:48134697:4813482348134424:48134606ENSG00000079337.11ENST00000405493.2,ENST00000449771.2,ENST00000547856.1,ENST00000549151.1,ENST00000395360.2,ENST00000488250.1,ENST00000389212.3,ENST00000171000.4,ENST00000548434.1
exon_skip_914101248134697:48134823:48135287:48135385:48137312:4813745948135287:48135385ENSG00000079337.11ENST00000405493.2,ENST00000449771.2,ENST00000547856.1,ENST00000549151.1,ENST00000395360.2,ENST00000482843.1,ENST00000479866.1,ENST00000389212.3,ENST00000171000.4
exon_skip_914151248135287:48135385:48137312:48137459:48137769:4813785148137312:48137459ENSG00000079337.11ENST00000405493.2,ENST00000449771.2,ENST00000547856.1,ENST00000549151.1,ENST00000395360.2,ENST00000482843.1,ENST00000479866.1,ENST00000389212.3,ENST00000171000.4
exon_skip_914231248137769:48137851:48140642:48140682:48141326:4814140948140642:48140682ENSG00000079337.11ENST00000405493.2,ENST00000449771.2,ENST00000547856.1,ENST00000549151.1,ENST00000482843.1,ENST00000479866.1,ENST00000389212.3,ENST00000171000.4,ENST00000548919.1
exon_skip_914271248140642:48140682:48141326:48141409:48141494:4814164548141326:48141409ENSG00000079337.11ENST00000405493.2,ENST00000449771.2,ENST00000547856.1,ENST00000549151.1,ENST00000482843.1,ENST00000479866.1,ENST00000389212.3,ENST00000171000.4,ENST00000548919.1,ENST00000395358.3,ENST00000494764.1
exon_skip_914471248145505:48145612:48145698:48145752:48151648:4815186148145698:48145752ENSG00000079337.11ENST00000405493.2,ENST00000449771.2,ENST00000549151.1,ENST00000482843.1,ENST00000479866.1,ENST00000389212.3,ENST00000171000.4,ENST00000548919.1,ENST00000395358.3,ENST00000466322.1,ENST00000495953.2
exon_skip_914481248145698:48145752:48151648:48151861:48164639:4816481748151648:48151861ENSG00000079337.11ENST00000549151.1,ENST00000548919.1

check button PSI values of skipped exons in GTEx.
psi gtex

* Skipped exon sequences.

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Open reading frame (ORF) annotation in the exon skipping event for RAPGEF3

check button Open reading frame (ORF) of individual exon skipping events in TCGA based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST000003892124813442448134606Frame-shift
ENST000004497714813442448134606Frame-shift
ENST000003892124813528748135385Frame-shift
ENST000004497714813528748135385Frame-shift
ENST000003892124814064248140682Frame-shift
ENST000004497714814064248140682Frame-shift
ENST000003892124814132648141409Frame-shift
ENST000004497714814132648141409Frame-shift
ENST000003892124813731248137459In-frame
ENST000004497714813731248137459In-frame
ENST000003892124814569848145752In-frame
ENST000004497714814569848145752In-frame

check button Open reading frame (ORF) of individual exon skipping events in GTEx based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST000003892124813442448134606Frame-shift
ENST000004497714813442448134606Frame-shift
ENST000003892124813528748135385Frame-shift
ENST000004497714813528748135385Frame-shift
ENST000003892124814064248140682Frame-shift
ENST000004497714814064248140682Frame-shift
ENST000003892124814132648141409Frame-shift
ENST000004497714814132648141409Frame-shift
ENST000003892124813731248137459In-frame
ENST000004497714813731248137459In-frame
ENST000003892124814569848145752In-frame
ENST000004497714814569848145752In-frame

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Infer the effects of exon skipping event on protein functional features for RAPGEF3

check button Exon skipping at the protein sequence level and followed lost functional features.
* Click on the image to enlarge it in a new window.
prot feature distribution

check button Loci of skipped exons in TCGA across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end
ENST00000389212331192348145698481457524324857391
ENST00000449771338792348145698481457523093627391
ENST000003892123311923481373124813745918912037559608
ENST000004497713387923481373124813745917681914559608

check button Loci of skipped exons in GTEx across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end
ENST00000389212331192348145698481457524324857391
ENST00000449771338792348145698481457523093627391
ENST000003892123311923481373124813745918912037559608
ENST000004497713387923481373124813745917681914559608

check button Lost protein functional features of individual exon skipping events in TCGA.
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
O9539873911923ChainID=PRO_0000068867;Note=Rap guanine nucleotide exchange factor 3
O9539873911923ChainID=PRO_0000068867;Note=Rap guanine nucleotide exchange factor 3
O9539873917979Modified residueNote=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q8VCC8
O9539873917979Modified residueNote=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q8VCC8
O95398559608533598Alternative sequenceID=VSP_007608;Note=In isoform 2. ARNLPVWLPNQDEPLPGSSCAIQVGDKVPYDICRPDHSVLTLQLPVTASVREVMAALAQEDGWTKG->VSAWPQFLSSAPPGLQAPPSPPDPEGLCGRGKLSSHRHTLGSLIGVHGALAACGALGQAVPGGAEA;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:9856955;Dbxref=PMID:9856955
O95398559608533598Alternative sequenceID=VSP_007608;Note=In isoform 2. ARNLPVWLPNQDEPLPGSSCAIQVGDKVPYDICRPDHSVLTLQLPVTASVREVMAALAQEDGWTKG->VSAWPQFLSSAPPGLQAPPSPPDPEGLCGRGKLSSHRHTLGSLIGVHGALAACGALGQAVPGGAEA;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:9856955;Dbxref=PMID:9856955
O95398559608599923Alternative sequenceID=VSP_007609;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:9856955;Dbxref=PMID:9856955
O95398559608599923Alternative sequenceID=VSP_007609;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:9856955;Dbxref=PMID:9856955
O953985596081923ChainID=PRO_0000068867;Note=Rap guanine nucleotide exchange factor 3
O953985596081923ChainID=PRO_0000068867;Note=Rap guanine nucleotide exchange factor 3


check button Lost protein functional features of individual exon skipping events in GTEx.
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
O9539873911923ChainID=PRO_0000068867;Note=Rap guanine nucleotide exchange factor 3
O9539873911923ChainID=PRO_0000068867;Note=Rap guanine nucleotide exchange factor 3
O9539873917979Modified residueNote=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q8VCC8
O9539873917979Modified residueNote=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250|UniProtKB:Q8VCC8
O95398559608533598Alternative sequenceID=VSP_007608;Note=In isoform 2. ARNLPVWLPNQDEPLPGSSCAIQVGDKVPYDICRPDHSVLTLQLPVTASVREVMAALAQEDGWTKG->VSAWPQFLSSAPPGLQAPPSPPDPEGLCGRGKLSSHRHTLGSLIGVHGALAACGALGQAVPGGAEA;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:9856955;Dbxref=PMID:9856955
O95398559608533598Alternative sequenceID=VSP_007608;Note=In isoform 2. ARNLPVWLPNQDEPLPGSSCAIQVGDKVPYDICRPDHSVLTLQLPVTASVREVMAALAQEDGWTKG->VSAWPQFLSSAPPGLQAPPSPPDPEGLCGRGKLSSHRHTLGSLIGVHGALAACGALGQAVPGGAEA;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:9856955;Dbxref=PMID:9856955
O95398559608599923Alternative sequenceID=VSP_007609;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:9856955;Dbxref=PMID:9856955
O95398559608599923Alternative sequenceID=VSP_007609;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:9856955;Dbxref=PMID:9856955
O953985596081923ChainID=PRO_0000068867;Note=Rap guanine nucleotide exchange factor 3
O953985596081923ChainID=PRO_0000068867;Note=Rap guanine nucleotide exchange factor 3


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SNVs in the skipped exons for RAPGEF3

check button - Lollipop plot for presenting exon skipping associated SNVs.
* Click on the image to enlarge it in a new window.
lollipop

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

check button - Non-synonymous mutations located in the skipped exons in TCGA.
Cancer typeSampleESIDSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
SKCMTCGA-EE-A2ME-06exon_skip_91408
48134425481346064813446548134465Frame_Shift_DelG-p.R689fs
LIHCTCGA-DD-A39Y-01exon_skip_91408
48134425481346064813447848134478Frame_Shift_DelG-p.P684fs
LIHCTCGA-G3-A3CJ-01exon_skip_91408
48134425481346064813458148134581Frame_Shift_DelC-p.G650fs
LIHCTCGA-DD-A1EG-01exon_skip_91410
48135288481353854813530748135307Frame_Shift_DelG-p.P593fs
LIHCTCGA-DD-A1EG-01exon_skip_91410
48135288481353854813533648135336Frame_Shift_DelC-p.G583fs
LIHCTCGA-DD-A1EG-01exon_skip_91415
48137313481374594813734448137344Frame_Shift_DelC-p.G556fs
PRADTCGA-M7-A720-01exon_skip_91448
48151649481518614815171448151714Frame_Shift_DelG-p.R10fs
HNSCTCGA-QK-A64Z-01exon_skip_91448
48151649481518614815182748151830Frame_Shift_DelCCCA-p.VG13fs
KIRCTCGA-CJ-4903-01exon_skip_91448
48151649481518614815182748151830Frame_Shift_DelCCCA-p.VG13fs
LUADTCGA-78-7539-01exon_skip_91448
48151649481518614815182748151830Frame_Shift_DelCCCA-p.VG13fs
BLCATCGA-UY-A78N-01exon_skip_91410
48135288481353854813532948135330Frame_Shift_Ins-Ap.E586fs
PAADTCGA-YB-A89D-01exon_skip_91410
48135288481353854813532948135329Nonsense_MutationCAp.E628X
READTCGA-F5-6814-01exon_skip_91415
48137313481374594813738848137388Nonsense_MutationCAp.E542X
BRCATCGA-A2-A0CS-01exon_skip_91427
48141327481414094814133748141337Nonsense_MutationGAp.R516*
PAADTCGA-IB-7651-01exon_skip_91427
48141327481414094814133748141337Nonsense_MutationGAp.R474*
PAADTCGA-IB-7651-01exon_skip_91427
48141327481414094814133748141337Nonsense_MutationGAp.R516*
PAADTCGA-IB-7651-01exon_skip_91427
48141327481414094814133748141337Nonsense_MutationGAp.R516X

check button - Depth of coverage in the three exons composing exon skipping event
Depth of coverage in three exonsMutation description

check button - Non-synonymous mutations located in the skipped exons in CCLE.
SampleSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
BE2M17_AUTONOMIC_GANGLIA48134425481346064813443148134431Missense_MutationGAp.A742V
HS688AT_FIBROBLAST48134425481346064813443148134431Missense_MutationGAp.A742V
SKNBE2_AUTONOMIC_GANGLIA48134425481346064813443148134431Missense_MutationGAp.A742V
JURKAT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE48134425481346064813446548134465Missense_MutationGCp.R731G
KARPAS45_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE48134425481346064813453148134531Missense_MutationGAp.R709C
JVM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE48134425481346064813454048134540Missense_MutationGCp.R706G
SNU1040_LARGE_INTESTINE48134425481346064813456648134566Missense_MutationCTp.R697Q
NCIH211_LUNG48134425481346064813459048134590Missense_MutationTCp.Y689C
EN_ENDOMETRIUM48137313481374594813739948137399Missense_MutationGAp.A580V
NCIH630_LARGE_INTESTINE48141327481414094814133648141336Missense_MutationCTp.R516Q
NUGC2_STOMACH48145699481457524814573448145734Missense_MutationCTp.E80K
HUH7_LIVER48151649481518614815165448151654Missense_MutationGAp.R72C
KYM1_SOFT_TISSUE48151649481518614815179748151797Missense_MutationCTp.G24E
MDAPCA2B_PROSTATE48141327481414094814133748141337Nonsense_MutationGAp.R516*
JHOS2_OVARY48137313481374594813731348137313Splice_SiteCTp.D609N
SNU387_LIVER48140643481406824814064348140643Splice_SiteCGp.K532N

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for RAPGEF3

check button sQTL information located at the skipped exons.
Exon skip IDChromosomeThree exonsSkippped exonENSTCancer typeSNP idLocationDNA change (ref/var)P-value

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for RAPGEF3


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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for RAPGEF3


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RelatedDrugs for RAPGEF3

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

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RelatedDiseases for RAPGEF3

check button Diseases associated with this gene.
(DisGeNet 4.0)
GeneDisease IDDisease name# pubmedsSource
RAPGEF3C0024117Chronic Obstructive Airway Disease1CTD_human
RAPGEF3C0035585Rickettsia Infections1CTD_human
RAPGEF3C0162700Tick-Borne Diseases1CTD_human
RAPGEF3C2609414Acute kidney injury1CTD_human