ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for VPS8

Gene summary

Gene information	Gene symbol	VPS8
	Gene ID	23355
	Gene name	VPS8, CORVET complex subunit
	Synonyms	KIAA0804
	Cytomap	3q27.2
	Type of gene	protein-coding
	Description	vacuolar protein sorting-associated protein 8 homologvacuolar protein sorting 8 homolog
	Modification date	20180519
	UniProtAcc	Q8N3P4
	Context	PubMed: VPS8 [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract] - Title (PMID)

Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Gene

GO ID

GO term

PubMed ID

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Exon skipping events across known transcript of Ensembl for VPS8 from UCSC genome browser

Skipped 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.

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Gene isoform structures and expression levels for VPS8

Expression levels of gene isoforms across TCGA.

Expression levels of gene isoforms across GTEx.

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Exon skipping events with PSIs in TCGA for VPS8

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_379922	3	184529983:184530013:184541934:184542020:184542332:184542573	184541934:184542020	ENSG00000156931.11	ENST00000422105.1
exon_skip_379925	3	184529983:184530013:184542332:184542573:184543950:184544019	184542332:184542573	ENSG00000156931.11	ENST00000436792.2,ENST00000446204.2,ENST00000437079.3
exon_skip_379930	3	184530303:184530577:184531532:184531655:184533571:184533608	184531532:184531655	ENSG00000156931.11	ENST00000471655.1
exon_skip_379931	3	184542346:184542573:184542718:184542836:184543950:184544019	184542718:184542836	ENSG00000156931.11	ENST00000424721.1
exon_skip_379933	3	184543950:184544019:184550476:184550607:184552436:184552448	184550476:184550607	ENSG00000156931.11	ENST00000422105.1,ENST00000436792.2,ENST00000441141.1,ENST00000287546.4,ENST00000446204.2,ENST00000424463.2,ENST00000445089.1,ENST00000437079.3,ENST00000452666.1,ENST00000424721.1
exon_skip_379934	3	184552462:184552530:184554034:184554118:184556501:184556534	184554034:184554118	ENSG00000156931.11	ENST00000426319.1
exon_skip_379935	3	184552462:184552530:184556501:184556534:184557485:184557540	184556501:184556534	ENSG00000156931.11	ENST00000422105.1,ENST00000436792.2,ENST00000287546.4,ENST00000446204.2,ENST00000437079.3,ENST00000469479.1
exon_skip_379943	3	184556501:184556534:184557485:184557540:184566858:184566983	184557485:184557540	ENSG00000156931.11	ENST00000422105.1,ENST00000436792.2,ENST00000446204.2,ENST00000469479.1
exon_skip_379947	3	184557485:184557540:184561027:184561033:184566858:184566983	184561027:184561033	ENSG00000156931.11	ENST00000437079.3
exon_skip_379949	3	184567723:184567810:184570287:184570355:184571644:184571674	184570287:184570355	ENSG00000156931.11	ENST00000436792.2,ENST00000465818.1,ENST00000469713.1,ENST00000287546.4,ENST00000446204.2,ENST00000437079.3
exon_skip_379951	3	184580684:184580855:184584663:184584738:184585811:184585847	184584663:184584738	ENSG00000156931.11	ENST00000465213.1,ENST00000436792.2,ENST00000287546.4,ENST00000446204.2,ENST00000437079.3
exon_skip_379953	3	184587310:184587316:184588503:184588593:184603897:184603944	184588503:184588593	ENSG00000156931.11	ENST00000436792.2,ENST00000458721.1,ENST00000287546.4,ENST00000437079.3
exon_skip_379956	3	184588531:184588593:184600136:184600221:184603897:184603944	184600136:184600221	ENSG00000156931.11	ENST00000421069.1
exon_skip_379958	3	184588503:184588593:184603897:184603944:184612490:184612713	184603897:184603944	ENSG00000156931.11	ENST00000436792.2,ENST00000287546.4,ENST00000437079.3
exon_skip_379966	3	184603897:184603944:184611021:184611200:184612490:184612713	184611021:184611200	ENSG00000156931.11	ENST00000458721.1
exon_skip_379968	3	184603897:184603944:184612490:184612713:184616352:184616442	184612490:184612713	ENSG00000156931.11	ENST00000421069.1,ENST00000436792.2,ENST00000492449.1,ENST00000287546.4,ENST00000437079.3
exon_skip_379971	3	184616352:184616442:184618708:184618760:184631306:184631349	184618708:184618760	ENSG00000156931.11	ENST00000436792.2,ENST00000458721.1,ENST00000492449.1,ENST00000287546.4,ENST00000446204.2,ENST00000437079.3
exon_skip_379972	3	184637914:184637986:184640216:184640271:184642649:184642769	184640216:184640271	ENSG00000156931.11	ENST00000452140.1
exon_skip_379977	3	184700799:184700882:184711770:184711851:184714119:184714289	184711770:184711851	ENSG00000156931.11	ENST00000436792.2,ENST00000488255.1,ENST00000492449.1,ENST00000287546.4,ENST00000446204.2,ENST00000437079.3
exon_skip_379978	3	184717483:184717649:184742123:184742177:184766266:184766347	184742123:184742177	ENSG00000156931.11	ENST00000436792.2,ENST00000492449.1,ENST00000287546.4,ENST00000446204.2,ENST00000437079.3

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for VPS8

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_379922	3	184529983:184530013:184541934:184542020:184542332:184542573	184541934:184542020	ENSG00000156931.11	ENST00000422105.1
exon_skip_379925	3	184529983:184530013:184542332:184542573:184543950:184544019	184542332:184542573	ENSG00000156931.11	ENST00000437079.3,ENST00000436792.2,ENST00000446204.2
exon_skip_379930	3	184530303:184530577:184531532:184531655:184533571:184533608	184531532:184531655	ENSG00000156931.11	ENST00000471655.1
exon_skip_379931	3	184542346:184542573:184542718:184542836:184543950:184544019	184542718:184542836	ENSG00000156931.11	ENST00000424721.1
exon_skip_379933	3	184543950:184544019:184550476:184550607:184552436:184552448	184550476:184550607	ENSG00000156931.11	ENST00000287546.4,ENST00000437079.3,ENST00000436792.2,ENST00000446204.2,ENST00000422105.1,ENST00000441141.1,ENST00000445089.1,ENST00000424721.1,ENST00000424463.2,ENST00000452666.1
exon_skip_379934	3	184552462:184552530:184554034:184554118:184556501:184556534	184554034:184554118	ENSG00000156931.11	ENST00000426319.1
exon_skip_379935	3	184552462:184552530:184556501:184556534:184557485:184557540	184556501:184556534	ENSG00000156931.11	ENST00000287546.4,ENST00000437079.3,ENST00000436792.2,ENST00000446204.2,ENST00000422105.1,ENST00000469479.1
exon_skip_379936	3	184552462:184552530:184556501:184556534:184566858:184566983	184556501:184556534	ENSG00000156931.11	ENST00000452666.1
exon_skip_379943	3	184556501:184556534:184557485:184557540:184566858:184566983	184557485:184557540	ENSG00000156931.11	ENST00000436792.2,ENST00000446204.2,ENST00000422105.1,ENST00000469479.1
exon_skip_379947	3	184557485:184557540:184561027:184561033:184566858:184566983	184561027:184561033	ENSG00000156931.11	ENST00000437079.3
exon_skip_379949	3	184567723:184567810:184570287:184570355:184571644:184571674	184570287:184570355	ENSG00000156931.11	ENST00000287546.4,ENST00000437079.3,ENST00000436792.2,ENST00000446204.2,ENST00000465818.1,ENST00000469713.1
exon_skip_379951	3	184580684:184580855:184584663:184584738:184585811:184585847	184584663:184584738	ENSG00000156931.11	ENST00000287546.4,ENST00000437079.3,ENST00000436792.2,ENST00000446204.2,ENST00000465213.1
exon_skip_379953	3	184587310:184587316:184588503:184588593:184603897:184603944	184588503:184588593	ENSG00000156931.11	ENST00000287546.4,ENST00000437079.3,ENST00000436792.2,ENST00000458721.1
exon_skip_379956	3	184588531:184588593:184600136:184600221:184603897:184603944	184600136:184600221	ENSG00000156931.11	ENST00000421069.1
exon_skip_379958	3	184588503:184588593:184603897:184603944:184612490:184612713	184603897:184603944	ENSG00000156931.11	ENST00000287546.4,ENST00000437079.3,ENST00000436792.2
exon_skip_379966	3	184603897:184603944:184611021:184611200:184612490:184612713	184611021:184611200	ENSG00000156931.11	ENST00000458721.1
exon_skip_379968	3	184603897:184603944:184612490:184612713:184616352:184616442	184612490:184612713	ENSG00000156931.11	ENST00000287546.4,ENST00000437079.3,ENST00000436792.2,ENST00000421069.1,ENST00000492449.1
exon_skip_379971	3	184616352:184616442:184618708:184618760:184631306:184631349	184618708:184618760	ENSG00000156931.11	ENST00000287546.4,ENST00000437079.3,ENST00000436792.2,ENST00000446204.2,ENST00000458721.1,ENST00000492449.1
exon_skip_379972	3	184637914:184637986:184640216:184640271:184642649:184642769	184640216:184640271	ENSG00000156931.11	ENST00000452140.1
exon_skip_379977	3	184700799:184700882:184711770:184711851:184714119:184714289	184711770:184711851	ENSG00000156931.11	ENST00000287546.4,ENST00000437079.3,ENST00000436792.2,ENST00000446204.2,ENST00000492449.1,ENST00000488255.1
exon_skip_379978	3	184717483:184717649:184742123:184742177:184766266:184766347	184742123:184742177	ENSG00000156931.11	ENST00000287546.4,ENST00000437079.3,ENST00000436792.2,ENST00000446204.2,ENST00000492449.1

PSI values of skipped exons in GTEx.

* Skipped exon sequences.

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Open reading frame (ORF) annotation in the exon skipping event for VPS8

Open reading frame (ORF) of individual exon skipping events in TCGA based on the Ensembl gene structure combined from isoforms.

ENST

Start of skipped exon

End of skipped exon

ORF

Open reading frame (ORF) of individual exon skipping events in GTEx based on the Ensembl gene structure combined from isoforms.

ENST

Start of skipped exon

End of skipped exon

ORF

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Infer the effects of exon skipping event on protein functional features for VPS8

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

Loci of skipped exons in TCGA across genomic, transcript, and protein sequence levels of In-frame cases.

ENST

Length of mRNA

Length of AA seq.

Genomic start

Genomic end

mRNA start

mRNA end

AA start

AA end

Loci of skipped exons in GTEx across genomic, transcript, and protein sequence levels of In-frame cases.

ENST

Length of mRNA

Length of AA seq.

Genomic start

Genomic end

mRNA start

mRNA end

AA start

AA end

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 feature

Description of feature

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 feature

Description of feature

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SNVs in the skipped exons for VPS8

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

- Differential PSIs between mutated versus non-mutated samples.

- Non-synonymous mutations located in the skipped exons in TCGA.

Cancer type	Sample	ESID	Skipped exon start	Skipped exon end	Mutation start	Mutation end	Mutation type	Reference seq	Mutation seq	AAchange
LIHC	TCGA-DD-A3A0-01	exon_skip_379925	184542333	184542573	184542562	184542562	Frame_Shift_Del	A	-	p.K48fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_379953	184588504	184588593	184588563	184588563	Frame_Shift_Del	A	-	p.G568fs
LIHC	TCGA-DD-A39Y-01	exon_skip_379968	184612491	184612713	184612519	184612519	Frame_Shift_Del	A	-	p.K604fs
LIHC	TCGA-DD-A1EG-01	exon_skip_379968	184612491	184612713	184612645	184612645	Frame_Shift_Del	A	-	p.K647fs
LIHC	TCGA-DD-A39Y-01	exon_skip_379968	184612491	184612713	184612645	184612645	Frame_Shift_Del	A	-	p.K647fs
LIHC	TCGA-DD-A1EG-01	exon_skip_379971	184618709	184618760	184618713	184618713	Frame_Shift_Del	T	-	p.L700fs
COAD	TCGA-AZ-4315-01	exon_skip_379925	184542333	184542573	184542484	184542484	Nonsense_Mutation	G	T	p.E22X
UCEC	TCGA-AP-A054-01	exon_skip_379951	184584664	184584738	184584687	184584687	Nonsense_Mutation	T	A	p.C473*
SKCM	TCGA-W3-A824-06	exon_skip_379953	184588504	184588593	184588534	184588534	Nonsense_Mutation	C	T	p.R559*
SKCM	TCGA-Z2-A8RT-06	exon_skip_379953	184588504	184588593	184588534	184588534	Nonsense_Mutation	C	T	p.R559*
UCEC	TCGA-B5-A11Q-01	exon_skip_379953	184588504	184588593	184588534	184588534	Nonsense_Mutation	C	T	p.R559*
COAD	TCGA-AD-6964-01	exon_skip_379978	184742124	184742177	184742172	184742172	Nonsense_Mutation	A	T	p.K1351X
BLCA	TCGA-BT-A20Q-01	exon_skip_379943	184557486	184557540	184557485	184557485	Splice_Site	G	A	p.A161_splice
KIRP	TCGA-PJ-A5Z8-01	exon_skip_379968	184612491	184612713	184612489	184612503	Splice_Site	AGGGATCTTTTATTT	-	p.K594_splice

- Depth of coverage in the three exons composing exon skipping event

Depth of coverage in three exons

Mutation description

- Non-synonymous mutations located in the skipped exons in CCLE.

Sample	Skipped exon start	Skipped exon end	Mutation start	Mutation end	Mutation type	Reference seq	Mutation seq	AAchange
SNU324_PANCREAS	184618709	184618760	184618747	184618747	Frame_Shift_Del	A	-	p.G711fs
H9_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	184542333	184542573	184542515	184542515	Missense_Mutation	C	T	p.S32L
HUT78_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	184542333	184542573	184542515	184542515	Missense_Mutation	C	T	p.S32L
AU565_BREAST	184542333	184542573	184542528	184542528	Missense_Mutation	C	G	p.F36L
HCC2450_LUNG	184542333	184542573	184542538	184542538	Missense_Mutation	G	C	p.D40H
JHUEM7_ENDOMETRIUM	184550477	184550607	184550495	184550495	Missense_Mutation	T	C	p.S81P
SNU520_STOMACH	184550477	184550607	184550588	184550588	Missense_Mutation	G	A	p.D112N
OSC20_UPPER_AERODIGESTIVE_TRACT	184612491	184612713	184612564	184612564	Missense_Mutation	C	G	p.L619V
COLO794_SKIN	184612491	184612713	184612600	184612600	Missense_Mutation	A	C	p.I631L
COLO800_SKIN	184612491	184612713	184612600	184612600	Missense_Mutation	A	C	p.I631L
NCIH1693_LUNG	184711771	184711851	184711798	184711798	Missense_Mutation	G	C	p.G1205R
HOS_BONE	184742124	184742177	184742149	184742149	Missense_Mutation	A	G	p.Q1343R
NCIH1436_LUNG	184742124	184742177	184742154	184742154	Missense_Mutation	A	G	p.K1345E
MDAPCA2B_PROSTATE	184557486	184557540	184557539	184557539	Splice_Site	T	C	p.F178F
MFE319_ENDOMETRIUM	184742124	184742177	184742176	184742176	Splice_Site	A	G	p.K1352R

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for VPS8

sQTL information located at the skipped exons.

Exon skip ID	Chromosome	Three exons	Skippped exon	ENST	Cancer type	SNP id	Location	DNA change (ref/var)	P-value
exon_skip_379933	3	184543950:184544019:184550476:184550607:184552436:184552448	184550476:184550607	ENST00000422105.1,ENST00000436792.2,ENST00000441141.1,ENST00000287546.4,ENST00000446204.2,ENST00000424463.2,ENST00000445089.1,ENST00000437079.3,ENST00000452666.1,ENST00000424721.1	LGG	rs9830734	chr3:184550501	C/T	6.15e-04
exon_skip_379933	3	184543950:184544019:184550476:184550607:184552436:184552448	184550476:184550607	ENST00000422105.1,ENST00000436792.2,ENST00000441141.1,ENST00000287546.4,ENST00000446204.2,ENST00000424463.2,ENST00000445089.1,ENST00000437079.3,ENST00000452666.1,ENST00000424721.1	KIRC	rs9830734	chr3:184550501	C/T	3.41e-04
exon_skip_379933	3	184543950:184544019:184550476:184550607:184552436:184552448	184550476:184550607	ENST00000422105.1,ENST00000436792.2,ENST00000441141.1,ENST00000287546.4,ENST00000446204.2,ENST00000424463.2,ENST00000445089.1,ENST00000437079.3,ENST00000452666.1,ENST00000424721.1	OV	rs9830734	chr3:184550501	C/T	1.00e-03

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for VPS8

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for VPS8

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RelatedDrugs for VPS8

Approved drugs targeting this gene.
(DrugBank Version 5.1.0 2018-04-02)

Gene

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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RelatedDiseases for VPS8

Diseases associated with this gene.
(DisGeNet 4.0)

Gene

Disease ID

Disease name

# pubmeds

Source

	Gene summary
	Gene structures and expression levels
	Exon skipping events with PSIs in TCGA
	Exon skipping events with PSIs in GTEx
	Open reading frame (ORF) annotation in the exon skipping event
	Exon skipping events in the canonical protein sequence
	SNVs in the skipped exons with depth of coverage
	Splicing Quantitative Trait Loci (sQTLs) in the skipped exons
	Splicing Quantitative Trait Methylation (sQTM) in the skipped exon
	Related drugs with this gene
	Related diseases with this gene

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Gene summary for VPS8

Exon skipping events across known transcript of Ensembl for VPS8 from UCSC genome browser

Gene isoform structures and expression levels for VPS8

Exon skipping events with PSIs in TCGA for VPS8

Exon skipping events with PSIs in GTEx for VPS8

Open reading frame (ORF) annotation in the exon skipping event for VPS8

Infer the effects of exon skipping event on protein functional features for VPS8

SNVs in the skipped exons for VPS8

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for VPS8

Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for VPS8

Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for VPS8

RelatedDrugs for VPS8

RelatedDiseases for VPS8