ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for PTPN6

Gene summary

Gene information	Gene symbol	PTPN6
	Gene ID	5777
	Gene name	protein tyrosine phosphatase, non-receptor type 6
	Synonyms	HCP\|HCPH\|HPTP1C\|PTP-1C\|SH-PTP1\|SHP-1\|SHP-1L\|SHP1
	Cytomap	12p13.31
	Type of gene	protein-coding
	Description	tyrosine-protein phosphatase non-receptor type 6hematopoietic cell phosphatasehematopoietic cell protein-tyrosine phosphataseprotein-tyrosine phosphatase 1Cprotein-tyrosine phosphatase SHP-1
	Modification date	20180527
	UniProtAcc	P29350
	Context	PubMed: PTPN6 [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
PTPN6	GO:0006470	protein dephosphorylation	11266449
PTPN6	GO:0008283	cell proliferation	11266449
PTPN6	GO:0018108	peptidyl-tyrosine phosphorylation	9285411\|18802077
PTPN6	GO:0030154	cell differentiation	11266449
PTPN6	GO:0070372	regulation of ERK1 and ERK2 cascade	11266449

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Exon skipping events across known transcript of Ensembl for PTPN6 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 PTPN6

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 PTPN6

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_79835	12	7055872:7055902:7060667:7060894:7061145:7061340	7060667:7060894	ENSG00000111679.12	ENST00000538318.1
exon_skip_79840	12	7055872:7055902:7060771:7060894:7061145:7061340	7060771:7060894	ENSG00000111679.12	ENST00000399448.1
exon_skip_79841	12	7055872:7055902:7060771:7060894:7061275:7061340	7060771:7060894	ENSG00000111679.12	ENST00000542848.1
exon_skip_79844	12	7055872:7055902:7061074:7061340:7063967:7064010	7061074:7061340	ENSG00000111679.12	ENST00000543120.1
exon_skip_79845	12	7055872:7055902:7061145:7061340:7063967:7064010	7061145:7061340	ENSG00000111679.12	ENST00000447931.2,ENST00000534900.1
exon_skip_79847	12	7060537:7060683:7060771:7060894:7061145:7061340	7060771:7060894	ENSG00000111679.12	ENST00000542277.1,ENST00000543115.1,ENST00000536521.1,ENST00000541698.1,ENST00000318974.9,ENST00000538715.1,ENST00000456013.1
exon_skip_79848	12	7060771:7060894:7061074:7061340:7063967:7064010	7061074:7061340	ENSG00000111679.12	ENST00000540740.1,ENST00000545153.1
exon_skip_79849	12	7060771:7060894:7061145:7061340:7063967:7064010	7061145:7061340	ENSG00000111679.12	ENST00000399448.1,ENST00000541698.1,ENST00000538318.1,ENST00000318974.9,ENST00000538715.1,ENST00000456013.1,ENST00000539365.1
exon_skip_79850	12	7060771:7060894:7061179:7061340:7063967:7064010	7061179:7061340	ENSG00000111679.12	ENST00000535462.1
exon_skip_79852	12	7060771:7060894:7061275:7061340:7063967:7064010	7061275:7061340	ENSG00000111679.12	ENST00000542848.1,ENST00000536013.1
exon_skip_79853	12	7064116:7064157:7064313:7064430:7064534:7064557	7064313:7064430	ENSG00000111679.12	ENST00000447931.2,ENST00000416215.2,ENST00000536013.1,ENST00000399448.1,ENST00000545153.1,ENST00000318974.9,ENST00000456013.1,ENST00000539365.1
exon_skip_79856	12	7066816:7066948:7067081:7067236:7069089:7069157	7067081:7067236	ENSG00000111679.12	ENST00000447931.2,ENST00000416215.2,ENST00000399448.1,ENST00000318974.9,ENST00000456013.1
exon_skip_79858	12	7069250:7069402:7069506:7069598:7069968:7070108	7069506:7069598	ENSG00000111679.12	ENST00000539029.1,ENST00000447931.2,ENST00000416215.2,ENST00000399448.1,ENST00000318974.9,ENST00000537533.1

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for PTPN6

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_79835	12	7055872:7055902:7060667:7060894:7061145:7061340	7060667:7060894	ENSG00000111679.12	ENST00000538318.1
exon_skip_79840	12	7055872:7055902:7060771:7060894:7061145:7061340	7060771:7060894	ENSG00000111679.12	ENST00000399448.1
exon_skip_79844	12	7055872:7055902:7061074:7061340:7063967:7064010	7061074:7061340	ENSG00000111679.12	ENST00000543120.1
exon_skip_79845	12	7055872:7055902:7061145:7061340:7063967:7064010	7061145:7061340	ENSG00000111679.12	ENST00000534900.1,ENST00000447931.2
exon_skip_79847	12	7060537:7060683:7060771:7060894:7061145:7061340	7060771:7060894	ENSG00000111679.12	ENST00000543115.1,ENST00000538715.1,ENST00000318974.9,ENST00000456013.1,ENST00000536521.1,ENST00000541698.1,ENST00000542277.1
exon_skip_79848	12	7060771:7060894:7061074:7061340:7063967:7064010	7061074:7061340	ENSG00000111679.12	ENST00000540740.1,ENST00000545153.1
exon_skip_79849	12	7060771:7060894:7061145:7061340:7063967:7064010	7061145:7061340	ENSG00000111679.12	ENST00000399448.1,ENST00000538318.1,ENST00000538715.1,ENST00000318974.9,ENST00000456013.1,ENST00000541698.1,ENST00000539365.1
exon_skip_79850	12	7060771:7060894:7061179:7061340:7063967:7064010	7061179:7061340	ENSG00000111679.12	ENST00000535462.1
exon_skip_79852	12	7060771:7060894:7061275:7061340:7063967:7064010	7061275:7061340	ENSG00000111679.12	ENST00000542848.1,ENST00000536013.1
exon_skip_79853	12	7064116:7064157:7064313:7064430:7064534:7064557	7064313:7064430	ENSG00000111679.12	ENST00000399448.1,ENST00000447931.2,ENST00000318974.9,ENST00000456013.1,ENST00000416215.2,ENST00000545153.1,ENST00000536013.1,ENST00000539365.1
exon_skip_79856	12	7066816:7066948:7067081:7067236:7069089:7069157	7067081:7067236	ENSG00000111679.12	ENST00000399448.1,ENST00000447931.2,ENST00000318974.9,ENST00000456013.1,ENST00000416215.2
exon_skip_79858	12	7069250:7069402:7069506:7069598:7069968:7070108	7069506:7069598	ENSG00000111679.12	ENST00000399448.1,ENST00000447931.2,ENST00000318974.9,ENST00000416215.2,ENST00000539029.1,ENST00000537533.1

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 PTPN6

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
ENST00000318974	7067081	7067236	Frame-shift
ENST00000318974	7069506	7069598	Frame-shift
ENST00000318974	7060771	7060894	In-frame
ENST00000318974	7061145	7061340	In-frame
ENST00000318974	7064313	7064430	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
ENST00000318974	7067081	7067236	Frame-shift
ENST00000318974	7069506	7069598	Frame-shift
ENST00000318974	7060771	7060894	In-frame
ENST00000318974	7061145	7061340	In-frame
ENST00000318974	7064313	7064430	In-frame

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Infer the effects of exon skipping event on protein functional features for PTPN6

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
ENST00000318974	2262	595	7060771	7060894	253	375	3	43
ENST00000318974	2262	595	7061145	7061340	376	570	44	108
ENST00000318974	2262	595	7064313	7064430	761	877	172	211

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
ENST00000318974	2262	595	7060771	7060894	253	375	3	43
ENST00000318974	2262	595	7061145	7061340	376	570	44	108
ENST00000318974	2262	595	7064313	7064430	761	877	172	211

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
P29350	3	43	1	39	Alternative sequence	ID=VSP_005129;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:1652101;Dbxref=PMID:1652101
P29350	3	43	1	3	Alternative sequence	ID=VSP_007775;Note=In isoform 2. MVR->MLSRG;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
P29350	3	43	40	44	Alternative sequence	ID=VSP_005130;Note=In isoform 3. SLSVR->MLSRG;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:1652101;Dbxref=PMID:1652101
P29350	3	43	26	31	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2B3O
P29350	3	43	33	45	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2B3O
P29350	3	43	1	595	Chain	ID=PRO_0000094758;Note=Tyrosine-protein phosphatase non-receptor type 6
P29350	3	43	4	100	Domain	Note=SH2 1;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00191
P29350	3	43	11	21	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2B3O
P29350	3	43	10	10	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P81718
P29350	3	43	6	6	Sequence conflict	Note=H->L;Ontology_term=ECO:0000305;evidence=ECO:0000305
P29350	44	108	40	44	Alternative sequence	ID=VSP_005130;Note=In isoform 3. SLSVR->MLSRG;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:1652101;Dbxref=PMID:1652101
P29350	44	108	33	45	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2B3O
P29350	44	108	48	55	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2B3O
P29350	44	108	57	59	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2B3O
P29350	44	108	61	63	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2B3O
P29350	44	108	68	70	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2B3O
P29350	44	108	89	91	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2B3O
P29350	44	108	1	595	Chain	ID=PRO_0000094758;Note=Tyrosine-protein phosphatase non-receptor type 6
P29350	44	108	4	100	Domain	Note=SH2 1;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00191
P29350	44	108	72	80	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2B3O
P29350	44	108	105	107	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2B3O
P29350	44	108	57	57	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P29351
P29350	44	108	64	64	Modified residue	Note=Phosphotyrosine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:19690332;Dbxref=PMID:19690332
P29350	44	108	86	86	Sequence conflict	Note=L->V;Ontology_term=ECO:0000305;evidence=ECO:0000305
P29350	44	108	86	86	Sequence conflict	Note=L->V;Ontology_term=ECO:0000305;evidence=ECO:0000305
P29350	172	211	175	181	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2B3O
P29350	172	211	184	186	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2B3O
P29350	172	211	199	201	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2RMX
P29350	172	211	202	204	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2B3O
P29350	172	211	205	207	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2RMX
P29350	172	211	1	595	Chain	ID=PRO_0000094758;Note=Tyrosine-protein phosphatase non-receptor type 6
P29350	172	211	110	213	Domain	Note=SH2 2;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00191
P29350	172	211	172	174	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3PS5
P29350	172	211	187	197	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2B3O

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
P29350	3	43	1	39	Alternative sequence	ID=VSP_005129;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:1652101;Dbxref=PMID:1652101
P29350	3	43	1	3	Alternative sequence	ID=VSP_007775;Note=In isoform 2. MVR->MLSRG;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
P29350	3	43	40	44	Alternative sequence	ID=VSP_005130;Note=In isoform 3. SLSVR->MLSRG;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:1652101;Dbxref=PMID:1652101
P29350	3	43	26	31	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2B3O
P29350	3	43	33	45	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2B3O
P29350	3	43	1	595	Chain	ID=PRO_0000094758;Note=Tyrosine-protein phosphatase non-receptor type 6
P29350	3	43	4	100	Domain	Note=SH2 1;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00191
P29350	3	43	11	21	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2B3O
P29350	3	43	10	10	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P81718
P29350	3	43	6	6	Sequence conflict	Note=H->L;Ontology_term=ECO:0000305;evidence=ECO:0000305
P29350	44	108	40	44	Alternative sequence	ID=VSP_005130;Note=In isoform 3. SLSVR->MLSRG;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:1652101;Dbxref=PMID:1652101
P29350	44	108	33	45	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2B3O
P29350	44	108	48	55	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2B3O
P29350	44	108	57	59	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2B3O
P29350	44	108	61	63	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2B3O
P29350	44	108	68	70	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2B3O
P29350	44	108	89	91	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2B3O
P29350	44	108	1	595	Chain	ID=PRO_0000094758;Note=Tyrosine-protein phosphatase non-receptor type 6
P29350	44	108	4	100	Domain	Note=SH2 1;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00191
P29350	44	108	72	80	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2B3O
P29350	44	108	105	107	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2B3O
P29350	44	108	57	57	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:P29351
P29350	44	108	64	64	Modified residue	Note=Phosphotyrosine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:19690332;Dbxref=PMID:19690332
P29350	44	108	86	86	Sequence conflict	Note=L->V;Ontology_term=ECO:0000305;evidence=ECO:0000305
P29350	44	108	86	86	Sequence conflict	Note=L->V;Ontology_term=ECO:0000305;evidence=ECO:0000305
P29350	172	211	175	181	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2B3O
P29350	172	211	184	186	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2B3O
P29350	172	211	199	201	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2RMX
P29350	172	211	202	204	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2B3O
P29350	172	211	205	207	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2RMX
P29350	172	211	1	595	Chain	ID=PRO_0000094758;Note=Tyrosine-protein phosphatase non-receptor type 6
P29350	172	211	110	213	Domain	Note=SH2 2;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00191
P29350	172	211	172	174	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3PS5
P29350	172	211	187	197	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:2B3O

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SNVs in the skipped exons for PTPN6

- 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.

PTPN6_LUAD_exon_skip_79853_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
LIHC	TCGA-DD-A3A0-01	exon_skip_79844 exon_skip_79848	7061075	7061340	7061308	7061308	Frame_Shift_Del	C	-	p.Y98fs
LIHC	TCGA-DD-A3A0-01	exon_skip_79845 exon_skip_79849 exon_skip_79850	7061146	7061340	7061308	7061308	Frame_Shift_Del	C	-	p.Y98fs
LIHC	TCGA-DD-A3A0-01	exon_skip_79845 exon_skip_79849 exon_skip_79850	7061180	7061340	7061308	7061308	Frame_Shift_Del	C	-	p.Y98fs
LIHC	TCGA-DD-A3A0-01	exon_skip_79852	7061276	7061340	7061308	7061308	Frame_Shift_Del	C	-	p.Y98fs
LUAD	TCGA-69-A59K-01	exon_skip_79853	7064314	7064430	7064388	7064388	Frame_Shift_Del	G	-	p.T197fs
UCEC	TCGA-D1-A101-01	exon_skip_79858	7069507	7069598	7069549	7069549	Frame_Shift_Del	C	-	p.P542fs
ACC	TCGA-OR-A5L2-01	exon_skip_79835	7060668	7060894	7060782	7060782	Nonsense_Mutation	C	T	p.R7*
ACC	TCGA-OR-A5L2-01	exon_skip_79835	7060668	7060894	7060782	7060782	Nonsense_Mutation	C	T	p.R7X
ACC	TCGA-OR-A5L2-01	exon_skip_79835	7060668	7060894	7060782	7060782	Nonsense_Mutation	C	T	p.R9X
ACC	TCGA-OR-A5L2-01	exon_skip_79840 exon_skip_79841 exon_skip_79847	7060772	7060894	7060782	7060782	Nonsense_Mutation	C	T	p.R7*
ACC	TCGA-OR-A5L2-01	exon_skip_79840 exon_skip_79841 exon_skip_79847	7060772	7060894	7060782	7060782	Nonsense_Mutation	C	T	p.R7X
ACC	TCGA-OR-A5L2-01	exon_skip_79840 exon_skip_79841 exon_skip_79847	7060772	7060894	7060782	7060782	Nonsense_Mutation	C	T	p.R9X
BLCA	TCGA-ZF-AA51-01	exon_skip_79835	7060668	7060894	7060782	7060782	Nonsense_Mutation	C	T	p.R7*
BLCA	TCGA-ZF-AA51-01	exon_skip_79840 exon_skip_79841 exon_skip_79847	7060772	7060894	7060782	7060782	Nonsense_Mutation	C	T	p.R7*
DLBC	TCGA-VB-A8QN-01	exon_skip_79844 exon_skip_79848	7061075	7061340	7061261	7061261	Nonsense_Mutation	C	T	p.Q85X
DLBC	TCGA-VB-A8QN-01	exon_skip_79845 exon_skip_79849 exon_skip_79850	7061146	7061340	7061261	7061261	Nonsense_Mutation	C	T	p.Q85X
DLBC	TCGA-VB-A8QN-01	exon_skip_79845 exon_skip_79849 exon_skip_79850	7061180	7061340	7061261	7061261	Nonsense_Mutation	C	T	p.Q85X

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

Depth of coverage in three exons	Mutation description
	Sample: TCGA-69-A59K-01
	Cancer type: LUAD
	ESID: exon_skip_79853
	Skipped exon start: 7064314
	Skipped exon end: 7064430
	Mutation start: 7064388
	Mutation end: 7064388
	Mutation type: Frame_Shift_Del
	Reference seq: G
	Mutation seq: -
	AAchange: p.T197fs
exon_skip_79853_LUAD_TCGA-69-A59K-01.png
	Sample: TCGA-VB-A8QN-01
	Cancer type: DLBC
	ESID: exon_skip_79848
	Skipped exon start: 7061075
	Skipped exon end: 7061340
	Mutation start: 7061261
	Mutation end: 7061261
	Mutation type: Nonsense_Mutation
	Reference seq: C
	Mutation seq: T
	AAchange: p.Q85X
	Sample: TCGA-VB-A8QN-01
	Cancer type: DLBC
	ESID: exon_skip_79850
	Skipped exon start: 7061146
	Skipped exon end: 7061340
	Mutation start: 7061261
	Mutation end: 7061261
	Mutation type: Nonsense_Mutation
	Reference seq: C
	Mutation seq: T
	AAchange: p.Q85X
	Sample: TCGA-VB-A8QN-01
	Cancer type: DLBC
	ESID: exon_skip_79850
	Skipped exon start: 7061180
	Skipped exon end: 7061340
	Mutation start: 7061261
	Mutation end: 7061261
	Mutation type: Nonsense_Mutation
	Reference seq: C
	Mutation seq: T
	AAchange: p.Q85X
exon_skip_150039_DLBC_TCGA-VB-A8QN-01.png
exon_skip_457585_DLBC_TCGA-VB-A8QN-01.png
exon_skip_79848_DLBC_TCGA-VB-A8QN-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
SW48_LARGE_INTESTINE	7061075	7061340	7061149	7061149	Frame_Shift_Del	G	-	p.V45fs
SW48_LARGE_INTESTINE	7061146	7061340	7061149	7061149	Frame_Shift_Del	G	-	p.V45fs
HCC1143_BREAST	7060772	7060894	7060785	7060785	Missense_Mutation	G	T	p.D8Y
HCC1143_BREAST	7060668	7060894	7060785	7060785	Missense_Mutation	G	T	p.D8Y
2313287_STOMACH	7060772	7060894	7060822	7060822	Missense_Mutation	G	A	p.G20D
2313287_STOMACH	7060668	7060894	7060822	7060822	Missense_Mutation	G	A	p.G20D
ST486_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	7060772	7060894	7060839	7060839	Missense_Mutation	A	C	p.S26R
ST486_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	7060668	7060894	7060839	7060839	Missense_Mutation	A	C	p.S26R
CW2_LARGE_INTESTINE	7060772	7060894	7060877	7060877	Missense_Mutation	C	A	p.D38E
CW2_LARGE_INTESTINE	7060668	7060894	7060877	7060877	Missense_Mutation	C	A	p.D38E
SW900_LUNG	7060772	7060894	7060878	7060878	Missense_Mutation	T	G	p.F39V
SW900_LUNG	7060668	7060894	7060878	7060878	Missense_Mutation	T	G	p.F39V
LNZTA3WT4_CENTRAL_NERVOUS_SYSTEM	7060772	7060894	7060888	7060888	Missense_Mutation	C	T	p.S42F
LNZTA3WT4_CENTRAL_NERVOUS_SYSTEM	7060668	7060894	7060888	7060888	Missense_Mutation	C	T	p.S42F
HEC6_ENDOMETRIUM	7061075	7061340	7061172	7061172	Missense_Mutation	G	A	p.R53Q
HEC6_ENDOMETRIUM	7061146	7061340	7061172	7061172	Missense_Mutation	G	A	p.R53Q
647V_URINARY_TRACT	7061075	7061340	7061205	7061205	Missense_Mutation	A	G	p.Y64C
647V_URINARY_TRACT	7061146	7061340	7061205	7061205	Missense_Mutation	A	G	p.Y64C
647V_URINARY_TRACT	7061180	7061340	7061205	7061205	Missense_Mutation	A	G	p.Y64C
HEC6_ENDOMETRIUM	7061075	7061340	7061240	7061240	Missense_Mutation	G	A	p.V76M
HEC6_ENDOMETRIUM	7061146	7061340	7061240	7061240	Missense_Mutation	G	A	p.V76M
HEC6_ENDOMETRIUM	7061180	7061340	7061240	7061240	Missense_Mutation	G	A	p.V76M
NCIH2141_LUNG	7061075	7061340	7061267	7061267	Missense_Mutation	G	T	p.V85F
NCIH2141_LUNG	7061146	7061340	7061267	7061267	Missense_Mutation	G	T	p.V85F
NCIH2141_LUNG	7061180	7061340	7061267	7061267	Missense_Mutation	G	T	p.V85F
SNU1040_LARGE_INTESTINE	7061075	7061340	7061285	7061285	Missense_Mutation	G	A	p.G91S
SNU1040_LARGE_INTESTINE	7061146	7061340	7061285	7061285	Missense_Mutation	G	A	p.G91S
SNU1040_LARGE_INTESTINE	7061276	7061340	7061285	7061285	Missense_Mutation	G	A	p.G91S
SNU1040_LARGE_INTESTINE	7061180	7061340	7061285	7061285	Missense_Mutation	G	A	p.G91S
A3KAW_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	7061075	7061340	7061328	7061328	Missense_Mutation	C	T	p.P105L
A3KAW_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	7061146	7061340	7061328	7061328	Missense_Mutation	C	T	p.P105L
A3KAW_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	7061276	7061340	7061328	7061328	Missense_Mutation	C	T	p.P105L
A3KAW_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	7061180	7061340	7061328	7061328	Missense_Mutation	C	T	p.P105L
SNGM_ENDOMETRIUM	7064314	7064430	7064425	7064425	Missense_Mutation	C	T	p.R210W
A3KAW_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	7067082	7067236	7067131	7067131	Missense_Mutation	A	G	p.D419G
BFTC909_KIDNEY	7067082	7067236	7067212	7067212	Missense_Mutation	C	A	p.A446E
JURKAT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	7069507	7069598	7069550	7069550	Missense_Mutation	C	T	p.P542L
CW2_LARGE_INTESTINE	7060772	7060894	7060782	7060782	Nonsense_Mutation	C	T	p.R7*
CW2_LARGE_INTESTINE	7060668	7060894	7060782	7060782	Nonsense_Mutation	C	T	p.R7*
NCIH513_PLEURA	7064314	7064430	7064421	7064421	Nonsense_Mutation	C	A	p.Y208*

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for PTPN6

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 PTPN6

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for PTPN6

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RelatedDrugs for PTPN6

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 PTPN6

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
PTPN6	C0006663	Calcinosis	1	CTD_human
PTPN6	C0018824	Heart valve disease	1	CTD_human
PTPN6	C0035228	Respiratory Hypersensitivity	1	CTD_human
PTPN6	C0036341	Schizophrenia	1	PSYGENET

	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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