ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for TSG101

Gene summary

Gene information	Gene symbol	TSG101
	Gene ID	7251
	Gene name	tumor susceptibility 101
	Synonyms	TSG10\|VPS23
	Cytomap	11p15.1
	Type of gene	protein-coding
	Description	tumor susceptibility gene 101 proteinESCRT-I complex subunit TSG101tumor susceptibility gene 10tumor susceptibility gene 101tumor susceptibility protein
	Modification date	20180522
	UniProtAcc	Q99816
	Context	PubMed: TSG101 [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
TSG101	GO:0043162	ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway	15611048

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Exon skipping events across known transcript of Ensembl for TSG101 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 TSG101

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 TSG101

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_69833	11	18490577:18490765:18502031:18502182:18503176:18503278	18502031:18502182	ENSG00000074319.8	ENST00000580814.1
exon_skip_69837	11	18501449:18501593:18502054:18502182:18503176:18503278	18502054:18502182	ENSG00000074319.8	ENST00000584526.1
exon_skip_69841	11	18524089:18524124:18528403:18528470:18531088:18531212	18528403:18528470	ENSG00000074319.8	ENST00000543087.1,ENST00000438874.2,ENST00000543054.1,ENST00000357193.3,ENST00000544804.1,ENST00000536719.1,ENST00000251968.3
exon_skip_69847	11	18528412:18528470:18531088:18531212:18536224:18536388	18531088:18531212	ENSG00000074319.8	ENST00000543087.1,ENST00000438874.2,ENST00000543054.1,ENST00000536719.1,ENST00000251968.3,ENST00000535077.1
exon_skip_69848	11	18528412:18528470:18531088:18531212:18537645:18537711	18531088:18531212	ENSG00000074319.8	ENST00000542488.1
exon_skip_69854	11	18531088:18531212:18536224:18536388:18537645:18537710	18536224:18536388	ENSG00000074319.8	ENST00000438874.2,ENST00000536719.1,ENST00000251968.3,ENST00000535077.1
exon_skip_69859	11	18531088:18531212:18537645:18537711:18548321:18548368	18537645:18537711	ENSG00000074319.8	ENST00000542488.1
exon_skip_69862	11	18536224:18536388:18537645:18537711:18541065:18541150	18537645:18537711	ENSG00000074319.8	ENST00000545247.2,ENST00000536719.1,ENST00000251968.3,ENST00000535077.1
exon_skip_69865	11	18537645:18537711:18541065:18541150:18548321:18548368	18541065:18541150	ENSG00000074319.8	ENST00000545247.2,ENST00000251968.3
exon_skip_69868	11	18541065:18541150:18547207:18547249:18548321:18548368	18547207:18547249	ENSG00000074319.8	ENST00000535077.1

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for TSG101

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_69833	11	18490577:18490765:18502031:18502182:18503176:18503278	18502031:18502182	ENSG00000074319.8	ENST00000580814.1
exon_skip_69837	11	18501449:18501593:18502054:18502182:18503176:18503278	18502054:18502182	ENSG00000074319.8	ENST00000584526.1
exon_skip_69841	11	18524089:18524124:18528403:18528470:18531088:18531212	18528403:18528470	ENSG00000074319.8	ENST00000536719.1,ENST00000251968.3,ENST00000357193.3,ENST00000543054.1,ENST00000543087.1,ENST00000544804.1,ENST00000438874.2
exon_skip_69847	11	18528412:18528470:18531088:18531212:18536224:18536388	18531088:18531212	ENSG00000074319.8	ENST00000536719.1,ENST00000251968.3,ENST00000543054.1,ENST00000543087.1,ENST00000438874.2,ENST00000535077.1
exon_skip_69848	11	18528412:18528470:18531088:18531212:18537645:18537711	18531088:18531212	ENSG00000074319.8	ENST00000542488.1
exon_skip_69854	11	18531088:18531212:18536224:18536388:18537645:18537710	18536224:18536388	ENSG00000074319.8	ENST00000536719.1,ENST00000251968.3,ENST00000438874.2,ENST00000535077.1
exon_skip_69859	11	18531088:18531212:18537645:18537711:18548321:18548368	18537645:18537711	ENSG00000074319.8	ENST00000542488.1
exon_skip_69862	11	18536224:18536388:18537645:18537711:18541065:18541150	18537645:18537711	ENSG00000074319.8	ENST00000536719.1,ENST00000251968.3,ENST00000545247.2,ENST00000535077.1
exon_skip_69865	11	18537645:18537711:18541065:18541150:18548321:18548368	18541065:18541150	ENSG00000074319.8	ENST00000251968.3,ENST00000545247.2
exon_skip_69868	11	18541065:18541150:18547207:18547249:18548321:18548368	18547207:18547249	ENSG00000074319.8	ENST00000535077.1

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 TSG101

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
ENST00000251968	18528403	18528470	Frame-shift
ENST00000251968	18531088	18531212	Frame-shift
ENST00000251968	18536224	18536388	Frame-shift
ENST00000251968	18541065	18541150	Frame-shift
ENST00000251968	18537645	18537711	In-frame

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
ENST00000251968	18528403	18528470	Frame-shift
ENST00000251968	18531088	18531212	Frame-shift
ENST00000251968	18536224	18536388	Frame-shift
ENST00000251968	18541065	18541150	Frame-shift
ENST00000251968	18537645	18537711	In-frame

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Infer the effects of exon skipping event on protein functional features for TSG101

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
ENST00000251968	1841	390	18537645	18537711	544	609	42	64

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
ENST00000251968	1841	390	18537645	18537711	544	609	42	64

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
Q99816	42	64	15	119	Alternative sequence	ID=VSP_004440;Note=In isoform 2. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q99816	42	64	35	42	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3OBQ
Q99816	42	64	51	62	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3OBQ
Q99816	42	64	2	390	Chain	ID=PRO_0000082606;Note=Tumor susceptibility gene 101 protein
Q99816	42	64	2	145	Domain	Note=UEV;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00652
Q99816	42	64	43	43	Mutagenesis	Note=Reduces interaction with ubiquitin%3B inhibits down-regulation of EGFR. V->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12006492;Dbxref=PMID:12006492
Q99816	42	64	45	45	Mutagenesis	Note=Reduces interaction with ubiquitin. No effect on MGRN1-binding. N->A;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:12006492,ECO:0000269\|PubMed:12802020,ECO:0000269\|PubMed:17229889;Dbxref=PMID:12006492,PMID:12802020,PMI
Q99816	42	64	46	46	Mutagenesis	Note=Reduces interaction with ubiquitin. D->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12006492;Dbxref=PMID:12006492
Q99816	42	64	63	63	Mutagenesis	Note=Reduces interaction with HIV-1 p6%3B impairs HIV-1 budding. Y->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12006492;Dbxref=PMID:12006492
Q99816	42	64	47	49	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3P9G

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
Q99816	42	64	15	119	Alternative sequence	ID=VSP_004440;Note=In isoform 2. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q99816	42	64	35	42	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3OBQ
Q99816	42	64	51	62	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3OBQ
Q99816	42	64	2	390	Chain	ID=PRO_0000082606;Note=Tumor susceptibility gene 101 protein
Q99816	42	64	2	145	Domain	Note=UEV;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00652
Q99816	42	64	43	43	Mutagenesis	Note=Reduces interaction with ubiquitin%3B inhibits down-regulation of EGFR. V->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12006492;Dbxref=PMID:12006492
Q99816	42	64	45	45	Mutagenesis	Note=Reduces interaction with ubiquitin. No effect on MGRN1-binding. N->A;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:12006492,ECO:0000269\|PubMed:12802020,ECO:0000269\|PubMed:17229889;Dbxref=PMID:12006492,PMID:12802020,PMI
Q99816	42	64	46	46	Mutagenesis	Note=Reduces interaction with ubiquitin. D->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12006492;Dbxref=PMID:12006492
Q99816	42	64	63	63	Mutagenesis	Note=Reduces interaction with HIV-1 p6%3B impairs HIV-1 budding. Y->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:12006492;Dbxref=PMID:12006492
Q99816	42	64	47	49	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3P9G

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SNVs in the skipped exons for TSG101

- 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.

TSG101_KIRP_exon_skip_69865_psi_boxplot.png
boxplot

- 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
KIRP	TCGA-J7-8537-01	exon_skip_69865	18541066	18541150	18541141	18541142	Frame_Shift_Del	TG	-	p.18_18del
KIRP	TCGA-J7-8537-01	exon_skip_69865	18541066	18541150	18541141	18541142	Frame_Shift_Del	TG	-	p.Y17fs
KIRP	TCGA-J7-8537-01	exon_skip_69865	18541066	18541150	18541141	18541142	Frame_Shift_Del	TG	-	p.YR17fs
CHOL	TCGA-4G-AAZT-01	exon_skip_69854	18536225	18536388	18536390	18536390	Splice_Site	T	A	.
LUSC	TCGA-18-3421-01	exon_skip_69854	18536225	18536388	18536390	18536390	Splice_Site	T	G	p.G65_splice

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

Depth of coverage in three exons	Mutation description
	Sample: TCGA-J7-8537-01
	Cancer type: KIRP
	ESID: exon_skip_69865
	Skipped exon start: 18541066
	Skipped exon end: 18541150
	Mutation start: 18541141
	Mutation end: 18541142
	Mutation type: Frame_Shift_Del
	Reference seq: TG
	Mutation seq: -
	AAchange: p.18_18del
	Sample: TCGA-J7-8537-01
	Cancer type: KIRP
	ESID: exon_skip_69865
	Skipped exon start: 18541066
	Skipped exon end: 18541150
	Mutation start: 18541141
	Mutation end: 18541142
	Mutation type: Frame_Shift_Del
	Reference seq: TG
	Mutation seq: -
	AAchange: p.YR17fs
	Sample: TCGA-J7-8537-01
	Cancer type: KIRP
	ESID: exon_skip_69865
	Skipped exon start: 18541066
	Skipped exon end: 18541150
	Mutation start: 18541141
	Mutation end: 18541142
	Mutation type: Frame_Shift_Del
	Reference seq: TG
	Mutation seq: -
	AAchange: p.Y17fs
exon_skip_69865_KIRP_TCGA-J7-8537-01.png

- 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
CMLT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	18502055	18502182	18502163	18502163	Missense_Mutation	C	T	p.R368H
CMLT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	18502032	18502182	18502163	18502163	Missense_Mutation	C	T	p.R368H
DV90_LUNG	18531089	18531212	18531139	18531139	Missense_Mutation	C	T	p.R144H
A2058_SKIN	18536225	18536388	18536233	18536233	Missense_Mutation	A	G	p.W117R
SNUC2A_LARGE_INTESTINE	18541066	18541150	18541140	18541140	Missense_Mutation	C	A	p.R18I
HCC95_LUNG	18541066	18541150	18541097	18541097	Nonsense_Mutation	G	T	p.Y32*

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for TSG101

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

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for TSG101

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for TSG101

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RelatedDrugs for TSG101

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 TSG101

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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