ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for ATR

Gene summary

Gene information	Gene symbol	ATR
	Gene ID	545
	Gene name	ATR serine/threonine kinase
	Synonyms	FCTCS\|FRP1\|MEC1\|SCKL\|SCKL1
	Cytomap	3q23
	Type of gene	protein-coding
	Description	serine/threonine-protein kinase ATRFRAP-related protein-1MEC1, mitosis entry checkpoint 1, homologataxia telangiectasia and Rad3-related protein
	Modification date	20180523
	UniProtAcc	Q13535
	Context	PubMed: ATR [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
ATR	GO:0000077	DNA damage checkpoint	14657349
ATR	GO:0006974	cellular response to DNA damage stimulus	27723717\|27723720
ATR	GO:0018105	peptidyl-serine phosphorylation	9733515
ATR	GO:0046777	protein autophosphorylation	9733515
ATR	GO:0071480	cellular response to gamma radiation	9925639

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Exon skipping events across known transcript of Ensembl for ATR 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 ATR

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 ATR

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_389119	3	142168159:142168444:142169307:142169444:142171958:142172008	142169307:142169444	ENSG00000175054.10	ENST00000515810.1
exon_skip_389120	3	142168159:142168444:142169307:142169444:142171969:142172075	142169307:142169444	ENSG00000175054.10	ENST00000504521.1
exon_skip_389122	3	142168159:142168444:142171969:142172075:142176445:142176552	142171969:142172075	ENSG00000175054.10	ENST00000350721.4,ENST00000383101.3,ENST00000515107.1
exon_skip_389124	3	142176445:142176597:142177799:142177953:142178068:142178225	142177799:142177953	ENSG00000175054.10	ENST00000350721.4,ENST00000383101.3,ENST00000513291.1
exon_skip_389126	3	142178068:142178225:142180781:142180932:142183938:142184082	142180781:142180932	ENSG00000175054.10	ENST00000350721.4,ENST00000383101.3,ENST00000513291.1
exon_skip_389127	3	142180781:142180932:142183938:142184082:142185165:142185375	142183938:142184082	ENSG00000175054.10	ENST00000350721.4,ENST00000383101.3,ENST00000513291.1
exon_skip_389132	3	142183938:142184082:142185165:142185375:142186775:142186910	142185165:142185375	ENSG00000175054.10	ENST00000350721.4,ENST00000383101.3,ENST00000513291.1
exon_skip_389135	3	142188927:142189025:142203981:142204124:142211973:142212153	142203981:142204124	ENSG00000175054.10	ENST00000350721.4,ENST00000383101.3
exon_skip_389140	3	142211973:142212153:142215202:142215362:142215854:142216034	142215202:142215362	ENSG00000175054.10	ENST00000350721.4,ENST00000383101.3
exon_skip_389142	3	142215238:142215362:142215854:142216034:142217438:142217616	142215854:142216034	ENSG00000175054.10	ENST00000350721.4,ENST00000514393.1,ENST00000383101.3
exon_skip_389143	3	142215238:142215362:142215975:142216034:142217438:142217616	142215975:142216034	ENSG00000175054.10	ENST00000507620.1
exon_skip_389144	3	142215975:142216034:142217438:142217616:142218468:142218560	142217438:142217616	ENSG00000175054.10	ENST00000350721.4,ENST00000383101.3,ENST00000507620.1
exon_skip_389145	3	142218468:142218560:142222203:142222295:142223980:142224145	142222203:142222295	ENSG00000175054.10	ENST00000350721.4,ENST00000383101.3
exon_skip_389150	3	142222203:142222295:142223980:142224145:142226772:142226951	142223980:142224145	ENSG00000175054.10	ENST00000350721.4,ENST00000383101.3
exon_skip_389152	3	142223980:142224145:142226772:142226951:142231101:142231312	142226772:142226951	ENSG00000175054.10	ENST00000350721.4,ENST00000383101.3
exon_skip_389154	3	142226772:142226951:142231101:142231312:142232342:142232480	142231101:142231312	ENSG00000175054.10	ENST00000350721.4,ENST00000383101.3
exon_skip_389156	3	142232342:142232480:142234236:142234357:142238510:142238626	142234236:142234357	ENSG00000175054.10	ENST00000350721.4,ENST00000383101.3
exon_skip_389157	3	142241569:142241683:142242834:142243041:142253921:142254047	142242834:142243041	ENSG00000175054.10	ENST00000350721.4,ENST00000383101.3
exon_skip_389159	3	142257323:142257467:142259745:142259876:142261506:142261599	142259745:142259876	ENSG00000175054.10	ENST00000350721.4,ENST00000383101.3
exon_skip_389160	3	142274911:142274981:142275224:142275417:142277465:142277618	142275224:142275417	ENSG00000175054.10	ENST00000350721.4,ENST00000515863.1,ENST00000383101.3
exon_skip_389164	3	142278092:142278283:142279104:142279296:142280084:142280238	142279104:142279296	ENSG00000175054.10	ENST00000350721.4
exon_skip_389165	3	142280084:142280263:142281073:142281190:142284962:142285103	142281073:142281190	ENSG00000175054.10	ENST00000507148.1
exon_skip_389166	3	142280084:142280263:142281073:142281951:142284962:142285103	142281073:142281951	ENSG00000175054.10	ENST00000350721.4,ENST00000383101.3
exon_skip_389167	3	142284962:142285103:142286904:142286996:142297487:142297566	142286904:142286996	ENSG00000175054.10	ENST00000507148.1,ENST00000350721.4,ENST00000383101.3

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for ATR

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_389119	3	142168159:142168444:142169307:142169444:142171958:142172008	142169307:142169444	ENSG00000175054.10	ENST00000515810.1
exon_skip_389120	3	142168159:142168444:142169307:142169444:142171969:142172075	142169307:142169444	ENSG00000175054.10	ENST00000504521.1
exon_skip_389122	3	142168159:142168444:142171969:142172075:142176445:142176552	142171969:142172075	ENSG00000175054.10	ENST00000350721.4,ENST00000383101.3,ENST00000515107.1
exon_skip_389124	3	142176445:142176597:142177799:142177953:142178068:142178225	142177799:142177953	ENSG00000175054.10	ENST00000350721.4,ENST00000513291.1,ENST00000383101.3
exon_skip_389126	3	142178068:142178225:142180781:142180932:142183938:142184082	142180781:142180932	ENSG00000175054.10	ENST00000350721.4,ENST00000513291.1,ENST00000383101.3
exon_skip_389127	3	142180781:142180932:142183938:142184082:142185165:142185375	142183938:142184082	ENSG00000175054.10	ENST00000350721.4,ENST00000513291.1,ENST00000383101.3
exon_skip_389132	3	142183938:142184082:142185165:142185375:142186775:142186910	142185165:142185375	ENSG00000175054.10	ENST00000350721.4,ENST00000513291.1,ENST00000383101.3
exon_skip_389135	3	142188927:142189025:142203981:142204124:142211973:142212153	142203981:142204124	ENSG00000175054.10	ENST00000350721.4,ENST00000383101.3
exon_skip_389140	3	142211973:142212153:142215202:142215362:142215854:142216034	142215202:142215362	ENSG00000175054.10	ENST00000350721.4,ENST00000383101.3
exon_skip_389142	3	142215238:142215362:142215854:142216034:142217438:142217616	142215854:142216034	ENSG00000175054.10	ENST00000350721.4,ENST00000383101.3,ENST00000514393.1
exon_skip_389143	3	142215238:142215362:142215975:142216034:142217438:142217616	142215975:142216034	ENSG00000175054.10	ENST00000507620.1
exon_skip_389144	3	142215975:142216034:142217438:142217616:142218468:142218560	142217438:142217616	ENSG00000175054.10	ENST00000350721.4,ENST00000383101.3,ENST00000507620.1
exon_skip_389145	3	142218468:142218560:142222203:142222295:142223980:142224145	142222203:142222295	ENSG00000175054.10	ENST00000350721.4,ENST00000383101.3
exon_skip_389150	3	142222203:142222295:142223980:142224145:142226772:142226951	142223980:142224145	ENSG00000175054.10	ENST00000350721.4,ENST00000383101.3
exon_skip_389152	3	142223980:142224145:142226772:142226951:142231101:142231312	142226772:142226951	ENSG00000175054.10	ENST00000350721.4,ENST00000383101.3
exon_skip_389154	3	142226772:142226951:142231101:142231312:142232342:142232480	142231101:142231312	ENSG00000175054.10	ENST00000350721.4,ENST00000383101.3
exon_skip_389156	3	142232342:142232480:142234236:142234357:142238510:142238626	142234236:142234357	ENSG00000175054.10	ENST00000350721.4,ENST00000383101.3
exon_skip_389157	3	142241569:142241683:142242834:142243041:142253921:142254047	142242834:142243041	ENSG00000175054.10	ENST00000350721.4,ENST00000383101.3
exon_skip_389159	3	142257323:142257467:142259745:142259876:142261506:142261599	142259745:142259876	ENSG00000175054.10	ENST00000350721.4,ENST00000383101.3
exon_skip_389160	3	142274911:142274981:142275224:142275417:142277465:142277618	142275224:142275417	ENSG00000175054.10	ENST00000350721.4,ENST00000383101.3,ENST00000515863.1
exon_skip_389164	3	142278092:142278283:142279104:142279296:142280084:142280238	142279104:142279296	ENSG00000175054.10	ENST00000350721.4
exon_skip_389165	3	142280084:142280263:142281073:142281190:142284962:142285103	142281073:142281190	ENSG00000175054.10	ENST00000507148.1
exon_skip_389166	3	142280084:142280263:142281073:142281951:142284962:142285103	142281073:142281951	ENSG00000175054.10	ENST00000350721.4,ENST00000383101.3

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 ATR

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
ENST00000350721	142171969	142172075	Frame-shift
ENST00000350721	142177799	142177953	Frame-shift
ENST00000350721	142180781	142180932	Frame-shift
ENST00000350721	142203981	142204124	Frame-shift
ENST00000350721	142215202	142215362	Frame-shift
ENST00000350721	142217438	142217616	Frame-shift
ENST00000350721	142222203	142222295	Frame-shift
ENST00000350721	142226772	142226951	Frame-shift
ENST00000350721	142231101	142231312	Frame-shift
ENST00000350721	142234236	142234357	Frame-shift
ENST00000350721	142259745	142259876	Frame-shift
ENST00000350721	142275224	142275417	Frame-shift
ENST00000350721	142281073	142281951	Frame-shift
ENST00000350721	142286904	142286996	Frame-shift
ENST00000350721	142183938	142184082	In-frame
ENST00000350721	142185165	142185375	In-frame
ENST00000350721	142215854	142216034	In-frame
ENST00000350721	142223980	142224145	In-frame
ENST00000350721	142242834	142243041	In-frame
ENST00000350721	142279104	142279296	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
ENST00000350721	142171969	142172075	Frame-shift
ENST00000350721	142177799	142177953	Frame-shift
ENST00000350721	142180781	142180932	Frame-shift
ENST00000350721	142203981	142204124	Frame-shift
ENST00000350721	142215202	142215362	Frame-shift
ENST00000350721	142217438	142217616	Frame-shift
ENST00000350721	142222203	142222295	Frame-shift
ENST00000350721	142226772	142226951	Frame-shift
ENST00000350721	142231101	142231312	Frame-shift
ENST00000350721	142234236	142234357	Frame-shift
ENST00000350721	142259745	142259876	Frame-shift
ENST00000350721	142275224	142275417	Frame-shift
ENST00000350721	142281073	142281951	Frame-shift
ENST00000350721	142183938	142184082	In-frame
ENST00000350721	142185165	142185375	In-frame
ENST00000350721	142215854	142216034	In-frame
ENST00000350721	142223980	142224145	In-frame
ENST00000350721	142242834	142243041	In-frame
ENST00000350721	142279104	142279296	In-frame

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

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
ENST00000350721	8266	2644	142279104	142279296	1472	1663	450	513
ENST00000350721	8266	2644	142242834	142243041	4068	4274	1315	1384
ENST00000350721	8266	2644	142223980	142224145	5154	5318	1677	1732
ENST00000350721	8266	2644	142215854	142216034	5681	5860	1853	1912
ENST00000350721	8266	2644	142185165	142185375	6810	7019	2229	2299
ENST00000350721	8266	2644	142183938	142184082	7020	7163	2299	2347

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
ENST00000350721	8266	2644	142279104	142279296	1472	1663	450	513
ENST00000350721	8266	2644	142242834	142243041	4068	4274	1315	1384
ENST00000350721	8266	2644	142223980	142224145	5154	5318	1677	1732
ENST00000350721	8266	2644	142215854	142216034	5681	5860	1853	1912
ENST00000350721	8266	2644	142185165	142185375	6810	7019	2229	2299
ENST00000350721	8266	2644	142183938	142184082	7020	7163	2299	2347

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
Q13535	450	513	450	450	Alternative sequence	ID=VSP_013305;Note=In isoform 2. E->D;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11470508;Dbxref=PMID:11470508
Q13535	450	513	451	514	Alternative sequence	ID=VSP_013304;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11470508;Dbxref=PMID:11470508
Q13535	450	513	1	2644	Chain	ID=PRO_0000088844;Note=Serine/threonine-protein kinase ATR
Q13535	1315	1384	1	2644	Chain	ID=PRO_0000088844;Note=Serine/threonine-protein kinase ATR
Q13535	1315	1384	1329	1365	Repeat	Note=HEAT 2
Q13535	1677	1732	1	2644	Chain	ID=PRO_0000088844;Note=Serine/threonine-protein kinase ATR
Q13535	1677	1732	1640	2185	Domain	Note=FAT;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00534
Q13535	1853	1912	1	2644	Chain	ID=PRO_0000088844;Note=Serine/threonine-protein kinase ATR
Q13535	1853	1912	1640	2185	Domain	Note=FAT;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00534
Q13535	2229	2299	1	2644	Chain	ID=PRO_0000088844;Note=Serine/threonine-protein kinase ATR
Q13535	2229	2299	2233	2233	Natural variant	ID=VAR_041597;Note=In a lung large cell carcinoma sample%3B somatic mutation. S->I;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17344846;Dbxref=PMID:17344846
Q13535	2299	2347	1	2644	Chain	ID=PRO_0000088844;Note=Serine/threonine-protein kinase ATR
Q13535	2299	2347	2322	2567	Domain	Note=PI3K/PI4K;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00269
Q13535	2299	2347	2327	2327	Mutagenesis	Note=Abolishes kinase activity. K->R;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:11114888,ECO:0000269\|PubMed:12011431,ECO:0000269\|PubMed:9925639;Dbxref=PMID:11114888,PMID:12011431,PMID:9925639

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
Q13535	450	513	450	450	Alternative sequence	ID=VSP_013305;Note=In isoform 2. E->D;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11470508;Dbxref=PMID:11470508
Q13535	450	513	451	514	Alternative sequence	ID=VSP_013304;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11470508;Dbxref=PMID:11470508
Q13535	450	513	1	2644	Chain	ID=PRO_0000088844;Note=Serine/threonine-protein kinase ATR
Q13535	1315	1384	1	2644	Chain	ID=PRO_0000088844;Note=Serine/threonine-protein kinase ATR
Q13535	1315	1384	1329	1365	Repeat	Note=HEAT 2
Q13535	1677	1732	1	2644	Chain	ID=PRO_0000088844;Note=Serine/threonine-protein kinase ATR
Q13535	1677	1732	1640	2185	Domain	Note=FAT;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00534
Q13535	1853	1912	1	2644	Chain	ID=PRO_0000088844;Note=Serine/threonine-protein kinase ATR
Q13535	1853	1912	1640	2185	Domain	Note=FAT;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00534
Q13535	2229	2299	1	2644	Chain	ID=PRO_0000088844;Note=Serine/threonine-protein kinase ATR
Q13535	2229	2299	2233	2233	Natural variant	ID=VAR_041597;Note=In a lung large cell carcinoma sample%3B somatic mutation. S->I;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:17344846;Dbxref=PMID:17344846
Q13535	2299	2347	1	2644	Chain	ID=PRO_0000088844;Note=Serine/threonine-protein kinase ATR
Q13535	2299	2347	2322	2567	Domain	Note=PI3K/PI4K;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00269
Q13535	2299	2347	2327	2327	Mutagenesis	Note=Abolishes kinase activity. K->R;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:11114888,ECO:0000269\|PubMed:12011431,ECO:0000269\|PubMed:9925639;Dbxref=PMID:11114888,PMID:12011431,PMID:9925639

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SNVs in the skipped exons for ATR

- 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-G3-A3CJ-01		142177800	142177953	142177807	142177807	Frame_Shift_Del	A	-	p.F2499fs
LIHC	TCGA-DD-A3A0-01		142177800	142177953	142177900	142177900	Frame_Shift_Del	C	-	p.G2468fs
STAD	TCGA-B7-A5TI-01	exon_skip_389126	142180782	142180932	142180784	142180784	Frame_Shift_Del	T	-	p.K2397fs
LIHC	TCGA-DD-A39Y-01	exon_skip_389126	142180782	142180932	142180829	142180829	Frame_Shift_Del	T	-	p.N2382fs
LIHC	TCGA-BC-A3KG-01	exon_skip_389126	142180782	142180932	142180843	142180843	Frame_Shift_Del	A	-	p.I2377fs
LIHC	TCGA-DD-A3A0-01	exon_skip_389126	142180782	142180932	142180855	142180855	Frame_Shift_Del	T	-	p.E2373fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_389132	142185166	142185375	142185234	142185234	Frame_Shift_Del	G	-	p.H2277fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_389140	142215203	142215362	142215223	142215223	Frame_Shift_Del	C	-	p.A1960fs
LIHC	TCGA-DD-A1EG-01	exon_skip_389140	142215203	142215362	142215226	142215226	Frame_Shift_Del	T	-	p.R1959fs
LIHC	TCGA-DD-A39Y-01	exon_skip_389144	142217439	142217616	142217557	142217557	Frame_Shift_Del	T	-	p.R1814fs
STAD	TCGA-BR-8361-01	exon_skip_389144	142217439	142217616	142217557	142217557	Frame_Shift_Del	T	-	p.R1814fs
STAD	TCGA-CG-4442-01	exon_skip_389144	142217439	142217616	142217557	142217557	Frame_Shift_Del	T	-	p.R1814fs
UCEC	TCGA-A5-A0VQ-01	exon_skip_389144	142217439	142217616	142217557	142217557	Frame_Shift_Del	T	-	p.R1814fs
UCEC	TCGA-B5-A0JV-01	exon_skip_389144	142217439	142217616	142217557	142217557	Frame_Shift_Del	T	-	p.R1814fs
UCEC	TCGA-DI-A0WH-01	exon_skip_389144	142217439	142217616	142217557	142217557	Frame_Shift_Del	T	-	p.R1814fs
LIHC	TCGA-DD-A39Y-01	exon_skip_389154	142231102	142231312	142231130	142231130	Frame_Shift_Del	T	-	p.K1608fs
LIHC	TCGA-DD-A3A0-01	exon_skip_389157	142242835	142243041	142243008	142243008	Frame_Shift_Del	T	-	p.T1327fs
LIHC	TCGA-DD-A1EG-01	exon_skip_389160	142275225	142275417	142275275	142275275	Frame_Shift_Del	A	-	p.F676fs
SARC	TCGA-DX-A1KY-01	exon_skip_389164	142279105	142279296	142279108	142279108	Frame_Shift_Del	T	-	p.N513fs
LUAD	TCGA-75-6214-01	exon_skip_389164	142279105	142279296	142279124	142279124	Frame_Shift_Del	A	-	p.S508fs
LIHC	TCGA-DD-A1EG-01	exon_skip_389165	142281074	142281190	142281118	142281118	Frame_Shift_Del	A	-	p.C376fs
LIHC	TCGA-DD-A1EG-01	exon_skip_389166	142281074	142281951	142281118	142281118	Frame_Shift_Del	A	-	p.C376fs
UCEC	TCGA-D1-A0ZS-01	exon_skip_389166	142281074	142281951	142281435	142281435	Frame_Shift_Del	A	-	p.F270fs
LIHC	TCGA-DD-A1EG-01	exon_skip_389166	142281074	142281951	142281476	142281476	Frame_Shift_Del	A	-	p.F256fs
LIHC	TCGA-DD-A1EG-01	exon_skip_389166	142281074	142281951	142281476	142281476	Frame_Shift_Del	A	-	p.Q257fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_389166	142281074	142281951	142281476	142281476	Frame_Shift_Del	A	-	p.F256fs
UCEC	TCGA-AX-A0J1-01	exon_skip_389166	142281074	142281951	142281578	142281578	Frame_Shift_Del	A	-	p.F222fs
STAD	TCGA-CD-A4MI-01	exon_skip_389157	142242835	142243041	142242920	142242921	Frame_Shift_Ins	-	C	p.E1356fs
STAD	TCGA-HF-A5NB-01	exon_skip_389157	142242835	142243041	142242920	142242921	Frame_Shift_Ins	-	C	p.E1356fs
STAD	TCGA-HF-A5NB-01	exon_skip_389157	142242835	142243041	142242920	142242921	Frame_Shift_Ins	-	C	p.M1356fs
STAD	TCGA-CD-A4MI-01	exon_skip_389157	142242835	142243041	142242921	142242922	Frame_Shift_Ins	-	C	p.E1356fs
UCEC	TCGA-AP-A0LH-01	exon_skip_389157	142242835	142243041	142243035	142243036	Frame_Shift_Ins	-	A	p.L1317fs
UCEC	TCGA-BS-A0UV-01	exon_skip_389142	142215855	142216034	142215937	142215937	Nonsense_Mutation	G	A	p.R1886*
SKCM	TCGA-EE-A29V-06	exon_skip_389144	142217439	142217616	142217461	142217461	Nonsense_Mutation	G	A	p.R1846*
SKCM	TCGA-W3-AA1Q-06	exon_skip_389152	142226773	142226951	142226892	142226892	Nonsense_Mutation	G	A	p.Q1638*
STAD	TCGA-IN-A6RP-01	exon_skip_389160	142275225	142275417	142275400	142275400	Nonsense_Mutation	G	A	p.R635*
STAD	TCGA-IN-A6RP-01	exon_skip_389160	142275225	142275417	142275400	142275400	Nonsense_Mutation	G	A	p.R635X
UCEC	TCGA-AP-A051-01	exon_skip_389166	142281074	142281951	142281203	142281203	Nonsense_Mutation	G	T	p.C347*
LUAD	TCGA-50-8457-01	exon_skip_389166	142281074	142281951	142281217	142281217	Nonsense_Mutation	T	A	p.K343*
LIHC	TCGA-MI-A75G-01	exon_skip_389144	142217439	142217616	142217617	142217617	Splice_Site	C	A	.
UCEC	TCGA-AP-A05N-01	exon_skip_389150	142223981	142224145	142224146	142224146	Splice_Site	C	T	e29-1
UCEC	TCGA-AP-A05N-01	exon_skip_389150	142223981	142224145	142224146	142224146	Splice_Site	C	T	p.K1678_splice
BRCA	TCGA-A2-A25D-01	exon_skip_389156	142234237	142234357	142234359	142234359	Splice_Site	T	C	e25-2
STAD	TCGA-BR-8680-01	exon_skip_389166	142281074	142281951	142281952	142281952	Splice_Site	C	A	.
STAD	TCGA-BR-8680-01	exon_skip_389166	142281074	142281951	142281952	142281952	Splice_Site	C	A	p.E98_splice

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

Depth of coverage in three exons	Mutation description
	Sample: TCGA-BR-8680-01
	Cancer type: STAD
	ESID: exon_skip_389166
	Skipped exon start: 142281074
	Skipped exon end: 142281951
	Mutation start: 142281952
	Mutation end: 142281952
	Mutation type: Splice_Site
	Reference seq: C
	Mutation seq: A
	AAchange: .
	Sample: TCGA-BR-8680-01
	Cancer type: STAD
	ESID: exon_skip_389166
	Skipped exon start: 142281074
	Skipped exon end: 142281951
	Mutation start: 142281952
	Mutation end: 142281952
	Mutation type: Splice_Site
	Reference seq: C
	Mutation seq: A
	AAchange: p.E98_splice
exon_skip_106946_STAD_TCGA-BR-8680-01.png
exon_skip_107215_STAD_TCGA-BR-8680-01.png
exon_skip_122567_STAD_TCGA-BR-8680-01.png
exon_skip_122573_STAD_TCGA-BR-8680-01.png
exon_skip_144294_STAD_TCGA-BR-8680-01.png
exon_skip_26878_STAD_TCGA-BR-8680-01.png
exon_skip_30156_STAD_TCGA-BR-8680-01.png
exon_skip_324648_STAD_TCGA-BR-8680-01.png
exon_skip_326437_STAD_TCGA-BR-8680-01.png
exon_skip_326558_STAD_TCGA-BR-8680-01.png
exon_skip_326569_STAD_TCGA-BR-8680-01.png
exon_skip_328488_STAD_TCGA-BR-8680-01.png
exon_skip_335090_STAD_TCGA-BR-8680-01.png
exon_skip_389166_STAD_TCGA-BR-8680-01.png
exon_skip_40432_STAD_TCGA-BR-8680-01.png
exon_skip_40460_STAD_TCGA-BR-8680-01.png
exon_skip_40461_STAD_TCGA-BR-8680-01.png
exon_skip_436498_STAD_TCGA-BR-8680-01.png
exon_skip_466512_STAD_TCGA-BR-8680-01.png
exon_skip_478774_STAD_TCGA-BR-8680-01.png
exon_skip_484956_STAD_TCGA-BR-8680-01.png
exon_skip_64135_STAD_TCGA-BR-8680-01.png
exon_skip_64136_STAD_TCGA-BR-8680-01.png
exon_skip_64137_STAD_TCGA-BR-8680-01.png
exon_skip_69365_STAD_TCGA-BR-8680-01.png
exon_skip_69375_STAD_TCGA-BR-8680-01.png
exon_skip_75101_STAD_TCGA-BR-8680-01.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
HGC27_STOMACH	142183939	142184082	142184033	142184033	Frame_Shift_Del	C	-	p.G2316fs
HEC151_ENDOMETRIUM	142217439	142217616	142217557	142217557	Frame_Shift_Del	T	-	p.R1814fs
CW2_LARGE_INTESTINE	142217439	142217616	142217557	142217557	Frame_Shift_Del	T	-	p.R1814fs
CTV1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	142281074	142281951	142281435	142281435	Frame_Shift_Del	A	-	p.F270fs
AMO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	142281074	142281951	142281434	142281435	Frame_Shift_Ins	-	A	p.F270fs
HS766T_PANCREAS	142281074	142281951	142281434	142281435	Frame_Shift_Ins	-	A	p.F270fs
KARPAS299_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	142281074	142281951	142281434	142281435	Frame_Shift_Ins	-	A	p.F270fs
KE39_STOMACH	142281074	142281951	142281434	142281435	Frame_Shift_Ins	-	A	p.F270fs
KPNSI9S_AUTONOMIC_GANGLIA	142281074	142281951	142281434	142281435	Frame_Shift_Ins	-	A	p.F270fs
MOLP2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	142281074	142281951	142281434	142281435	Frame_Shift_Ins	-	A	p.F270fs
NCIH2171_LUNG	142281074	142281951	142281434	142281435	Frame_Shift_Ins	-	A	p.F270fs
OVK18_OVARY	142281074	142281951	142281434	142281435	Frame_Shift_Ins	-	A	p.F270fs
SNU475_LIVER	142281074	142281951	142281434	142281435	Frame_Shift_Ins	-	A	p.F270fs
SNU1040_LARGE_INTESTINE	142177800	142177953	142177948	142177948	Missense_Mutation	C	T	p.S2452N
SW48_LARGE_INTESTINE	142180782	142180932	142180848	142180848	Missense_Mutation	T	C	p.I2376V
NCIH1944_LUNG	142180782	142180932	142180878	142180878	Missense_Mutation	C	T	p.A2366T
MCC13_SKIN	142180782	142180932	142180893	142180893	Missense_Mutation	G	A	p.H2361Y
GSU_STOMACH	142180782	142180932	142180907	142180907	Missense_Mutation	C	T	p.R2356H
SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	142203982	142204124	142204001	142204001	Missense_Mutation	T	C	p.I2068V
A3KAW_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	142203982	142204124	142204006	142204006	Missense_Mutation	C	T	p.R2066Q
SUPT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	142203982	142204124	142204006	142204006	Missense_Mutation	C	T	p.R2066Q
T84_LARGE_INTESTINE	142203982	142204124	142204093	142204093	Missense_Mutation	T	C	p.D2037G
KYSE510_OESOPHAGUS	142203982	142204124	142204103	142204103	Missense_Mutation	C	T	p.E2034K
OVK18_OVARY	142215203	142215362	142215225	142215225	Missense_Mutation	C	A	p.R1959M
HEC59_ENDOMETRIUM	142215203	142215362	142215261	142215261	Missense_Mutation	G	A	p.A1947V
NCIH1184_LUNG	142215203	142215362	142215310	142215310	Missense_Mutation	C	G	p.A1931P
ZR7530_BREAST	142215203	142215362	142215323	142215323	Missense_Mutation	C	G	p.Q1926H
PL18_PANCREAS	142215203	142215362	142215357	142215357	Missense_Mutation	T	C	p.D1915G
NCIH1693_LUNG	142215855	142216034	142215895	142215895	Missense_Mutation	T	C	p.I1900V
NCIH1819_LUNG	142215855	142216034	142215895	142215895	Missense_Mutation	T	C	p.I1900V
SW684_SOFT_TISSUE	142215855	142216034	142215906	142215906	Missense_Mutation	G	A	p.A1896V
DMS454_LUNG	142215855	142216034	142215909	142215909	Missense_Mutation	C	G	p.R1895T
NCIH524_LUNG	142215855	142216034	142215952	142215952	Missense_Mutation	G	T	p.L1881I
K5_THYROID	142215855	142216034	142215976	142215976	Missense_Mutation	C	A	p.G1873C
K5_THYROID	142215976	142216034	142215976	142215976	Missense_Mutation	C	A	p.G1873C
D425_CENTRAL_NERVOUS_SYSTEM	142215855	142216034	142215989	142215989	Missense_Mutation	G	T	p.F1868L
D425_CENTRAL_NERVOUS_SYSTEM	142215976	142216034	142215989	142215989	Missense_Mutation	G	T	p.F1868L
D458_CENTRAL_NERVOUS_SYSTEM	142215855	142216034	142215989	142215989	Missense_Mutation	G	T	p.F1868L
D458_CENTRAL_NERVOUS_SYSTEM	142215976	142216034	142215989	142215989	Missense_Mutation	G	T	p.F1868L
WSUNHL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	142215855	142216034	142216005	142216005	Missense_Mutation	C	T	p.S1863N
WSUNHL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	142215976	142216034	142216005	142216005	Missense_Mutation	C	T	p.S1863N
HCT15_LARGE_INTESTINE	142217439	142217616	142217446	142217446	Missense_Mutation	T	C	p.I1851V
HRT18_LARGE_INTESTINE	142217439	142217616	142217446	142217446	Missense_Mutation	T	C	p.I1851V
PCI38_UPPER_AERODIGESTIVE_TRACT	142217439	142217616	142217499	142217499	Missense_Mutation	G	A	p.P1833L
SNU1079_BILIARY_TRACT	142217439	142217616	142217601	142217601	Missense_Mutation	G	T	p.T1799K
HCT15_LARGE_INTESTINE	142217439	142217616	142217605	142217605	Missense_Mutation	T	C	p.T1798A
JEKO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	142222204	142222295	142222241	142222241	Missense_Mutation	T	C	p.T1751A
NCIH661_LUNG	142223981	142224145	142224091	142224091	Missense_Mutation	T	C	p.R1696G
NCIH1048_LUNG	142223981	142224145	142224100	142224100	Missense_Mutation	T	C	p.S1693G
CHSA0011_BONE	142223981	142224145	142224112	142224112	Missense_Mutation	C	A	p.V1689L
OVK18_OVARY	142226773	142226951	142226817	142226817	Missense_Mutation	T	C	p.T1663A
KASUMI2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	142226773	142226951	142226852	142226852	Missense_Mutation	T	C	p.Y1651C
NCIH2286_LUNG	142226773	142226951	142226904	142226904	Missense_Mutation	C	A	p.D1634Y
GP2D_LARGE_INTESTINE	142231102	142231312	142231140	142231140	Missense_Mutation	G	A	p.P1605L
GP5D_LARGE_INTESTINE	142231102	142231312	142231140	142231140	Missense_Mutation	G	A	p.P1605L
EN_ENDOMETRIUM	142231102	142231312	142231158	142231158	Missense_Mutation	A	G	p.L1599P
RERFLCKJ_LUNG	142231102	142231312	142231198	142231198	Missense_Mutation	C	A	p.D1586Y
SJSA1_BONE	142234237	142234357	142234291	142234291	Missense_Mutation	C	G	p.L1483F
HEC251_ENDOMETRIUM	142242835	142243041	142242849	142242849	Missense_Mutation	C	A	p.D1380Y
LNCAPCLONEFGC_PROSTATE	142242835	142243041	142242850	142242850	Missense_Mutation	T	A	p.K1379N
CORL88_LUNG	142242835	142243041	142242935	142242935	Missense_Mutation	C	A	p.R1351L
MSTO211H_PLEURA	142242835	142243041	142242975	142242975	Missense_Mutation	C	G	p.V1338L
HEC251_ENDOMETRIUM	142275225	142275417	142275252	142275252	Missense_Mutation	G	T	p.S684Y
MEWO_SKIN	142275225	142275417	142275306	142275306	Missense_Mutation	A	T	p.V666E
MEWO_SKIN	142275225	142275417	142275306	142275307	Missense_Mutation	AC	TT	p.V666K
MEWO_SKIN	142275225	142275417	142275307	142275307	Missense_Mutation	C	T	p.V666I
HEC108_ENDOMETRIUM	142279105	142279296	142279186	142279186	Missense_Mutation	A	G	p.I487T
CMLT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	142279105	142279296	142279222	142279222	Missense_Mutation	A	C	p.I475S
SNU1040_LARGE_INTESTINE	142279105	142279296	142279261	142279261	Missense_Mutation	A	G	p.L462S
NCIH2081_LUNG	142279105	142279296	142279288	142279288	Missense_Mutation	T	G	p.H453P
CW2_LARGE_INTESTINE	142281074	142281951	142281256	142281256	Missense_Mutation	C	G	p.E330Q
NCIH716_LARGE_INTESTINE	142281074	142281951	142281262	142281262	Missense_Mutation	T	C	p.M328V
SNU1040_LARGE_INTESTINE	142281074	142281951	142281613	142281613	Missense_Mutation	T	C	p.M211V
HEC251_ENDOMETRIUM	142281074	142281951	142281759	142281759	Missense_Mutation	C	A	p.R162I
SNU81_LARGE_INTESTINE	142281074	142281951	142281831	142281831	Missense_Mutation	C	A	p.S138I
HEC108_ENDOMETRIUM	142286905	142286996	142286977	142286977	Missense_Mutation	T	C	p.N27D
NCIH1944_LUNG	142180782	142180932	142180887	142180887	Nonsense_Mutation	G	A	p.R2363*
SF126_CENTRAL_NERVOUS_SYSTEM	142226773	142226951	142226847	142226847	Nonsense_Mutation	G	A	p.R1653*
SARC9371_BONE	142234237	142234357	142234344	142234344	Nonsense_Mutation	G	A	p.Q1466*
NB17_AUTONOMIC_GANGLIA	142281074	142281951	142281542	142281542	Nonsense_Mutation	A	T	p.C234*

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

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_389145	3	142218468:142218560:142222203:142222295:142223980:142224145	142222203:142222295	ENST00000350721.4,ENST00000383101.3	STAD	rs2227931	chr3:142222284	A/G	1.14e-03

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

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

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RelatedDrugs for ATR

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 ATR

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
ATR	C0032273	Pneumoconiosis	1	CTD_human
ATR	C0033578	Prostatic Neoplasms	1	CTD_human
ATR	C0042076	Urologic Neoplasms	1	CTD_human
ATR	C3281203	CUTANEOUS TELANGIECTASIA AND CANCER SYNDROME, FAMILIAL	1	ORPHANET;UNIPROT

	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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