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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 ARHGAP39

check button Gene summary
Gene informationGene symbol

ARHGAP39

Gene ID

80728

Gene nameRho GTPase activating protein 39
SynonymsCrGAP|Vilse
Cytomap

8q24.3

Type of geneprotein-coding
Descriptionrho GTPase-activating protein 39RhoGAP93B homologcrossGAP homolog
Modification date20180523
UniProtAcc

Q9C0H5

ContextPubMed: ARHGAP39 [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

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Exon skipping events across known transcript of Ensembl for ARHGAP39 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 ARHGAP39

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 ARHGAP39

check button Information of exkip skipping event in TCGA.
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_4944608145755794:145756000:145756085:145756255:145757688:145757780145756085:145756255ENSG00000147799.7ENST00000377307.2,ENST00000276826.5,ENST00000540274.1
exon_skip_4944618145759512:145759586:145763104:145763197:145770632:145771048145763104:145763197ENSG00000147799.7ENST00000377307.2
exon_skip_4944648145763141:145763197:145769256:145769354:145770632:145771048145769256:145769354ENSG00000147799.7ENST00000528810.1
exon_skip_4944668145770632:145771194:145772510:145773873:145780943:145781027145772510:145773873ENSG00000147799.7ENST00000377307.2,ENST00000276826.5,ENST00000540274.1
exon_skip_4944688145780943:145781027:145806229:145806661:145830919:145831080145806229:145806661ENSG00000147799.7ENST00000276826.5,ENST00000540274.1
exon_skip_4944698145806229:145806661:145830919:145831080:145911070:145911194145830919:145831080ENSG00000147799.7ENST00000540274.1

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

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Exon skipping events with PSIs in GTEx for ARHGAP39

check button Information of exkip skipping event in GTEx
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_4944608145755794:145756000:145756085:145756255:145757688:145757780145756085:145756255ENSG00000147799.7ENST00000377307.2,ENST00000276826.5,ENST00000540274.1
exon_skip_4944618145759512:145759586:145763104:145763197:145770632:145771048145763104:145763197ENSG00000147799.7ENST00000377307.2
exon_skip_4944648145763141:145763197:145769256:145769354:145770632:145771048145769256:145769354ENSG00000147799.7ENST00000528810.1
exon_skip_4944668145770632:145771194:145772510:145773873:145780943:145781027145772510:145773873ENSG00000147799.7ENST00000377307.2,ENST00000276826.5,ENST00000540274.1
exon_skip_4944688145780943:145781027:145806229:145806661:145830919:145831080145806229:145806661ENSG00000147799.7ENST00000276826.5,ENST00000540274.1
exon_skip_4944698145806229:145806661:145830919:145831080:145911070:145911194145830919:145831080ENSG00000147799.7ENST00000540274.1

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 ARHGAP39

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
ENST00000276826145756085145756255Frame-shift
ENST00000276826145772510145773873Frame-shift
ENST00000276826145806229145806661In-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
ENST00000276826145756085145756255Frame-shift
ENST00000276826145772510145773873Frame-shift
ENST00000276826145806229145806661In-frame

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Infer the effects of exon skipping event on protein functional features for ARHGAP39

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
ENST000002768264714108314580622914580666128371427170

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
ENST000002768264714108314580622914580666128371427170

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
Q9C0H52717021083ChainID=PRO_0000076092;Note=Rho GTPase-activating protein 39
Q9C0H5271702558DomainNote=WW 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00224
Q9C0H5271706397DomainNote=WW 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00224
Q9C0H527170169169Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163


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
Q9C0H52717021083ChainID=PRO_0000076092;Note=Rho GTPase-activating protein 39
Q9C0H5271702558DomainNote=WW 1;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00224
Q9C0H5271706397DomainNote=WW 2;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00224
Q9C0H527170169169Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163


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SNVs in the skipped exons for ARHGAP39

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.
ARHGAP39_ESCA_exon_skip_494466_psi_boxplot.png
boxplot
ARHGAP39_STAD_exon_skip_494466_psi_boxplot.png
boxplot

check button - Non-synonymous mutations located in the skipped exons in TCGA.
Cancer typeSampleESIDSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
LIHCTCGA-DD-A39Y-01exon_skip_494460
145756086145756255145756093145756093Frame_Shift_DelA-p.F1017fs
ESCATCGA-JY-A938-01exon_skip_494466
145772511145773873145772875145772875Frame_Shift_DelC-p.S532fs
LIHCTCGA-DD-A39Y-01exon_skip_494466
145772511145773873145773004145773004Frame_Shift_DelG-p.P489fs
COADTCGA-D5-6927-01exon_skip_494466
145772511145773873145773375145773375Frame_Shift_DelG-p.S366fs
COADTCGA-G4-6586-01exon_skip_494466
145772511145773873145773375145773375Frame_Shift_DelG-p.S366fs
UCSTCGA-N7-A4Y0-01exon_skip_494466
145772511145773873145773375145773375Frame_Shift_DelG-p.P365fs
UCSTCGA-N7-A4Y0-01exon_skip_494466
145772511145773873145773375145773375Frame_Shift_DelG-p.S366fs
STADTCGA-HU-A4GT-01exon_skip_494466
145772511145773873145773476145773476Frame_Shift_DelC-p.V332fs
UVMTCGA-VD-AA8M-01exon_skip_494466
145772511145773873145773633145773634Frame_Shift_DelGG-p.A279fs
LIHCTCGA-G3-A3CJ-01exon_skip_494466
145772511145773873145773714145773714Frame_Shift_DelG-p.P252fs
HNSCTCGA-F7-A624-01exon_skip_494468
145806230145806661145806259145806277Frame_Shift_DelCGCCGCGGGCCGCCCGGCC-p.RAGRPAA155fs
LIHCTCGA-G3-A3CJ-01exon_skip_494468
145806230145806661145806436145806436Frame_Shift_DelC-p.P102fs
TGCTTCGA-2G-AAFZ-01exon_skip_494468
145806230145806661145806589145806590Frame_Shift_Ins-CACTCACCp.C51fs

check button - Depth of coverage in the three exons composing exon skipping event
Depth of coverage in three exonsMutation description
ARHGAP39_145770632_145771194_145772510_145773873_145780943_145781027_TCGA-JY-A938-01Sample: TCGA-JY-A938-01
Cancer type: ESCA
ESID: exon_skip_494466
Skipped exon start: 145772511
Skipped exon end: 145773873
Mutation start: 145772875
Mutation end: 145772875
Mutation type: Frame_Shift_Del
Reference seq: C
Mutation seq: -
AAchange: p.S532fs
exon_skip_112879_ESCA_TCGA-JY-A938-01.png
boxplot
exon_skip_489575_ESCA_TCGA-JY-A938-01.png
boxplot
exon_skip_494466_ESCA_TCGA-JY-A938-01.png
boxplot

check button - Non-synonymous mutations located in the skipped exons in CCLE.
SampleSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
MFE319_ENDOMETRIUM145772511145773873145772931145772931Frame_Shift_DelG-p.P513fs
SNUC2A_LARGE_INTESTINE145772511145773873145773375145773375Frame_Shift_DelG-p.P365fs
EFO27_OVARY145772511145773873145773375145773375Frame_Shift_DelG-p.P365fs
RKO_LARGE_INTESTINE145772511145773873145773375145773375Frame_Shift_DelG-p.P365fs
IGROV1_OVARY145772511145773873145773375145773375Frame_Shift_DelG-p.P365fs
SW48_LARGE_INTESTINE145772511145773873145773375145773375Frame_Shift_DelG-p.P365fs
C33A_CERVIX145772511145773873145773476145773476Frame_Shift_DelC-p.V332fs
PC9_LUNG145806230145806661145806266145806273Frame_Shift_DelGGCCGCCC-p.GRP157fs
BT12_SOFT_TISSUE145772511145773873145773374145773375Frame_Shift_Ins-Gp.S366fs
KU812_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE145772511145773873145773374145773375Frame_Shift_Ins-Gp.S366fs
KYSE270_OESOPHAGUS145772511145773873145773374145773375Frame_Shift_Ins-Gp.S366fs
LC1F_LUNG145772511145773873145773374145773375Frame_Shift_Ins-Gp.S366fs
HEKTE_KIDNEY145772511145773873145773669145773671In_Frame_DelGAA-p.F267del
HCC1569_BREAST145756086145756255145756105145756105Missense_MutationTCp.Y1013C
GSS_STOMACH145772511145773873145772589145772589Missense_MutationGTp.F627L
CA922_UPPER_AERODIGESTIVE_TRACT145772511145773873145772589145772589Missense_MutationGTp.F627L
P31FUJ_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE145772511145773873145772589145772589Missense_MutationGTp.F627L
SNU1040_LARGE_INTESTINE145772511145773873145772782145772782Missense_MutationGAp.A563V
ISHIKAWAHERAKLIO02ER_ENDOMETRIUM145772511145773873145772785145772785Missense_MutationTCp.E562G
MEWO_SKIN145772511145773873145772815145772815Missense_MutationGAp.P552L
SUPM2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE145772511145773873145772817145772817Missense_MutationCAp.E551D
EFM192A_BREAST145772511145773873145772822145772822Missense_MutationCTp.A550T
SNU1040_LARGE_INTESTINE145772511145773873145772857145772857Missense_MutationCTp.R538Q
NCIH441_LUNG145772511145773873145772881145772881Missense_MutationCAp.G530V
COLO201_LARGE_INTESTINE145772511145773873145772947145772947Missense_MutationGAp.T508I
NCIH2087_LUNG145772511145773873145773037145773037Missense_MutationTAp.Q478L
CCK81_LARGE_INTESTINE145772511145773873145773055145773055Missense_MutationGAp.A472V
KMS34_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE145772511145773873145773061145773061Missense_MutationTCp.E470G
MEG01_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE145772511145773873145773061145773061Missense_MutationTCp.E470G
SNU685_ENDOMETRIUM145772511145773873145773082145773082Missense_MutationGAp.T463M
KINGS1_CENTRAL_NERVOUS_SYSTEM145772511145773873145773085145773085Missense_MutationGCp.P462R
SCC3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE145772511145773873145773085145773085Missense_MutationGCp.P462R
SNU1040_LARGE_INTESTINE145772511145773873145773101145773101Missense_MutationGAp.R457W
NCIH1651_LUNG145772511145773873145773175145773175Missense_MutationCTp.S432N
KARPAS45_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE145772511145773873145773200145773200Missense_MutationCTp.G424S
SNU175_LARGE_INTESTINE145772511145773873145773203145773203Missense_MutationCTp.G423S
EN_ENDOMETRIUM145772511145773873145773217145773217Missense_MutationTCp.Y418C
COLO678_LARGE_INTESTINE145772511145773873145773302145773302Missense_MutationCTp.A390T
HEC59_ENDOMETRIUM145772511145773873145773424145773424Missense_MutationGAp.P349L
HEC108_ENDOMETRIUM145772511145773873145773431145773431Missense_MutationGAp.R347W
HT144_SKIN145772511145773873145773529145773529Missense_MutationTGp.E314A
NCIH1930_LUNG145772511145773873145773538145773538Missense_MutationGAp.P311L
RS411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE145772511145773873145773557145773557Missense_MutationGAp.R305C
SNU1040_LARGE_INTESTINE145772511145773873145773557145773557Missense_MutationGAp.R305C
EW7_BONE145772511145773873145773581145773581Missense_MutationCTp.G297R
COV362_OVARY145772511145773873145773730145773730Missense_MutationCTp.G247D
MZ2MEL_SKIN145772511145773873145773812145773812Missense_MutationGAp.R220W
OVK18_OVARY145772511145773873145773818145773818Missense_MutationCTp.A218T
KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE145772511145773873145773824145773824Missense_MutationTCp.K216E
RS411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE145772511145773873145773835145773835Missense_MutationCTp.R212H
AML193_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE145806230145806661145806284145806284Missense_MutationGAp.P153L
G361_SKIN145806230145806661145806329145806329Missense_MutationGAp.S138F
HEC108_ENDOMETRIUM145806230145806661145806473145806473Missense_MutationGAp.T90M
TE8_OESOPHAGUS145806230145806661145806542145806542Missense_MutationTGp.N67T
HEC265_ENDOMETRIUM145806230145806661145806620145806620Missense_MutationCTp.R41H
HEC151_ENDOMETRIUM145806230145806661145806626145806626Missense_MutationCTp.R39H
RPMI8866_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE145830920145831080145830926145830926Missense_MutationTAp.N25I
KMS11_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE145830920145831080145830984145830984Missense_MutationCAp.D6Y
HEC1A_ENDOMETRIUM145830920145831080145830985145830985Missense_MutationCAp.Q5H
HUH6_LIVER145830920145831080145830989145830989Missense_MutationGAp.T4M
HUH6CLONE5_LIVER145830920145831080145830989145830989Missense_MutationGAp.T4M
SNUC5_LARGE_INTESTINE145830920145831080145830989145830989Missense_MutationGAp.T4M
EPLC272H_LUNG145756086145756255145756202145756202Nonsense_MutationCAp.E981*
NCIH1435_LUNG145772511145773873145773873145773873Splice_SiteCAp.R199S
NCIH630_LARGE_INTESTINE145830920145831080145830921145830921Splice_SiteGAp.R27W

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for ARHGAP39

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 ARHGAP39


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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for ARHGAP39


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RelatedDrugs for ARHGAP39

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 ARHGAP39

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