ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for COL1A1

Gene summary

Gene information	Gene symbol	COL1A1
	Gene ID	1277
	Gene name	collagen type I alpha 1 chain
	Synonyms	EDSARTH1\|EDSC\|OI1\|OI2\|OI3\|OI4
	Cytomap	17q21.33
	Type of gene	protein-coding
	Description	collagen alpha-1(I) chainalpha-1 type I collagenalpha1(I) procollagencollagen alpha 1 chain type Icollagen alpha-1(I) chain preproproteincollagen of skin, tendon and bone, alpha-1 chaincollagen, type I, alpha 1pro-alpha-1 collagen type 1type I pro
	Modification date	20180527
	UniProtAcc	P02452
	Context	PubMed: COL1A1 [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
COL1A1	GO:0010718	positive regulation of epithelial to mesenchymal transition	20018240
COL1A1	GO:0030335	positive regulation of cell migration	20018240
COL1A1	GO:0034504	protein localization to nucleus	20018240
COL1A1	GO:0045893	positive regulation of transcription, DNA-templated	20018240
COL1A1	GO:0090263	positive regulation of canonical Wnt signaling pathway	20018240

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Exon skipping events across known transcript of Ensembl for COL1A1 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 COL1A1

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 COL1A1

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_291308	17	48264193:48264283:48264375:48264483:48264844:48264879	48264375:48264483	ENSG00000108821.9	ENST00000225964.5
exon_skip_291318	17	48264375:48264483:48264844:48264898:48265236:48265254	48264844:48264898	ENSG00000108821.9	ENST00000225964.5
exon_skip_291339	17	48265236:48265344:48265456:48265510:48265890:48265998	48265456:48265510	ENSG00000108821.9	ENST00000225964.5
exon_skip_291346	17	48266263:48266371:48266528:48266636:48266737:48266763	48266528:48266636	ENSG00000108821.9	ENST00000225964.5
exon_skip_291361	17	48266528:48266636:48266737:48266899:48267039:48267093	48266737:48266899	ENSG00000108821.9	ENST00000225964.5
exon_skip_291380	17	48266737:48266899:48267039:48267093:48267219:48267273	48267039:48267093	ENSG00000108821.9	ENST00000225964.5
exon_skip_291390	17	48267039:48267093:48267219:48267273:48267361:48267469	48267219:48267273	ENSG00000108821.9	ENST00000225964.5
exon_skip_291397	17	48267219:48267273:48267361:48267469:48267687:48267741	48267361:48267469	ENSG00000108821.9	ENST00000225964.5
exon_skip_291398	17	48267687:48267741:48267903:48267957:48268177:48268285	48267903:48267957	ENSG00000108821.9	ENST00000225964.5
exon_skip_291402	17	48267903:48267957:48268177:48268285:48268743:48268851	48268177:48268285	ENSG00000108821.9	ENST00000225964.5
exon_skip_291408	17	48268269:48268285:48268743:48268851:48269148:48269247	48268743:48268851	ENSG00000108821.9	ENST00000476387.1,ENST00000225964.5
exon_skip_291411	17	48269340:48269385:48269835:48269889:48270000:48270054	48269835:48269889	ENSG00000108821.9	ENST00000476387.1,ENST00000225964.5
exon_skip_291414	17	48270035:48270054:48270157:48270211:48270354:48270408	48270157:48270211	ENSG00000108821.9	ENST00000476387.1,ENST00000225964.5
exon_skip_291430	17	48270157:48270211:48270354:48270408:48271303:48271402	48270354:48270408	ENSG00000108821.9	ENST00000476387.1,ENST00000225964.5
exon_skip_291438	17	48270354:48270408:48271303:48271402:48271490:48271544	48271303:48271402	ENSG00000108821.9	ENST00000225964.5
exon_skip_291444	17	48271512:48271544:48271709:48271808:48271933:48271987	48271709:48271808	ENSG00000108821.9	ENST00000225964.5,ENST00000471344.1
exon_skip_291446	17	48271709:48271808:48271933:48271987:48272081:48272189	48271933:48271987	ENSG00000108821.9	ENST00000225964.5,ENST00000471344.1
exon_skip_291448	17	48272081:48272189:48272407:48272461:48272592:48272691	48272407:48272461	ENSG00000108821.9	ENST00000225964.5,ENST00000471344.1
exon_skip_291449	17	48272407:48272461:48272592:48272691:48272794:48272839	48272592:48272691	ENSG00000108821.9	ENST00000225964.5,ENST00000471344.1
exon_skip_291452	17	48272592:48272691:48272794:48272839:48272927:48273026	48272794:48272839	ENSG00000108821.9	ENST00000225964.5,ENST00000471344.1
exon_skip_291457	17	48272794:48272839:48272927:48273026:48273283:48273337	48272927:48273026	ENSG00000108821.9	ENST00000225964.5
exon_skip_291462	17	48273283:48273337:48273515:48273560:48273674:48273728	48273515:48273560	ENSG00000108821.9	ENST00000225964.5
exon_skip_291463	17	48273515:48273560:48273674:48273728:48273844:48273889	48273674:48273728	ENSG00000108821.9	ENST00000225964.5
exon_skip_291467	17	48275092:48275146:48275309:48275363:48275521:48275566	48275309:48275363	ENSG00000108821.9	ENST00000495677.1,ENST00000225964.5
exon_skip_291468	17	48275309:48275363:48275521:48275566:48275793:48275865	48275521:48275566	ENSG00000108821.9	ENST00000495677.1,ENST00000225964.5
exon_skip_291472	17	48275521:48275566:48275793:48275865:48276586:48276688	48275793:48275865	ENSG00000108821.9	ENST00000225964.5
exon_skip_291473	17	48276649:48276688:48276778:48276814:48276916:48276951	48276778:48276814	ENSG00000108821.9	ENST00000507689.1,ENST00000225964.5

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for COL1A1

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_291308	17	48264193:48264283:48264375:48264483:48264844:48264879	48264375:48264483	ENSG00000108821.9	ENST00000225964.5
exon_skip_291318	17	48264375:48264483:48264844:48264898:48265236:48265254	48264844:48264898	ENSG00000108821.9	ENST00000225964.5
exon_skip_291339	17	48265236:48265344:48265456:48265510:48265890:48265998	48265456:48265510	ENSG00000108821.9	ENST00000225964.5
exon_skip_291346	17	48266263:48266371:48266528:48266636:48266737:48266763	48266528:48266636	ENSG00000108821.9	ENST00000225964.5
exon_skip_291361	17	48266528:48266636:48266737:48266899:48267039:48267093	48266737:48266899	ENSG00000108821.9	ENST00000225964.5
exon_skip_291380	17	48266737:48266899:48267039:48267093:48267219:48267273	48267039:48267093	ENSG00000108821.9	ENST00000225964.5
exon_skip_291390	17	48267039:48267093:48267219:48267273:48267361:48267469	48267219:48267273	ENSG00000108821.9	ENST00000225964.5
exon_skip_291397	17	48267219:48267273:48267361:48267469:48267687:48267741	48267361:48267469	ENSG00000108821.9	ENST00000225964.5
exon_skip_291398	17	48267687:48267741:48267903:48267957:48268177:48268285	48267903:48267957	ENSG00000108821.9	ENST00000225964.5
exon_skip_291402	17	48267903:48267957:48268177:48268285:48268743:48268851	48268177:48268285	ENSG00000108821.9	ENST00000225964.5
exon_skip_291408	17	48268269:48268285:48268743:48268851:48269148:48269247	48268743:48268851	ENSG00000108821.9	ENST00000225964.5,ENST00000476387.1
exon_skip_291411	17	48269340:48269385:48269835:48269889:48270000:48270054	48269835:48269889	ENSG00000108821.9	ENST00000225964.5,ENST00000476387.1
exon_skip_291414	17	48270035:48270054:48270157:48270211:48270354:48270408	48270157:48270211	ENSG00000108821.9	ENST00000225964.5,ENST00000476387.1
exon_skip_291430	17	48270157:48270211:48270354:48270408:48271303:48271402	48270354:48270408	ENSG00000108821.9	ENST00000225964.5,ENST00000476387.1
exon_skip_291438	17	48270354:48270408:48271303:48271402:48271490:48271544	48271303:48271402	ENSG00000108821.9	ENST00000225964.5
exon_skip_291444	17	48271512:48271544:48271709:48271808:48271933:48271987	48271709:48271808	ENSG00000108821.9	ENST00000225964.5,ENST00000471344.1
exon_skip_291446	17	48271709:48271808:48271933:48271987:48272081:48272189	48271933:48271987	ENSG00000108821.9	ENST00000225964.5,ENST00000471344.1
exon_skip_291448	17	48272081:48272189:48272407:48272461:48272592:48272691	48272407:48272461	ENSG00000108821.9	ENST00000225964.5,ENST00000471344.1
exon_skip_291449	17	48272407:48272461:48272592:48272691:48272794:48272839	48272592:48272691	ENSG00000108821.9	ENST00000225964.5,ENST00000471344.1
exon_skip_291452	17	48272592:48272691:48272794:48272839:48272927:48273026	48272794:48272839	ENSG00000108821.9	ENST00000225964.5,ENST00000471344.1
exon_skip_291457	17	48272794:48272839:48272927:48273026:48273283:48273337	48272927:48273026	ENSG00000108821.9	ENST00000225964.5
exon_skip_291462	17	48273283:48273337:48273515:48273560:48273674:48273728	48273515:48273560	ENSG00000108821.9	ENST00000225964.5
exon_skip_291463	17	48273515:48273560:48273674:48273728:48273844:48273889	48273674:48273728	ENSG00000108821.9	ENST00000225964.5
exon_skip_291467	17	48275092:48275146:48275309:48275363:48275521:48275566	48275309:48275363	ENSG00000108821.9	ENST00000225964.5,ENST00000495677.1
exon_skip_291468	17	48275309:48275363:48275521:48275566:48275793:48275865	48275521:48275566	ENSG00000108821.9	ENST00000225964.5,ENST00000495677.1
exon_skip_291472	17	48275521:48275566:48275793:48275865:48276586:48276688	48275793:48275865	ENSG00000108821.9	ENST00000225964.5
exon_skip_291473	17	48276649:48276688:48276778:48276814:48276916:48276951	48276778:48276814	ENSG00000108821.9	ENST00000225964.5,ENST00000507689.1

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 COL1A1

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
ENST00000225964	48264375	48264483	In-frame
ENST00000225964	48264844	48264898	In-frame
ENST00000225964	48265456	48265510	In-frame
ENST00000225964	48266528	48266636	In-frame
ENST00000225964	48266737	48266899	In-frame
ENST00000225964	48267039	48267093	In-frame
ENST00000225964	48267219	48267273	In-frame
ENST00000225964	48267361	48267469	In-frame
ENST00000225964	48267903	48267957	In-frame
ENST00000225964	48268177	48268285	In-frame
ENST00000225964	48268743	48268851	In-frame
ENST00000225964	48269835	48269889	In-frame
ENST00000225964	48270157	48270211	In-frame
ENST00000225964	48270354	48270408	In-frame
ENST00000225964	48271303	48271402	In-frame
ENST00000225964	48271709	48271808	In-frame
ENST00000225964	48271933	48271987	In-frame
ENST00000225964	48272407	48272461	In-frame
ENST00000225964	48272592	48272691	In-frame
ENST00000225964	48272794	48272839	In-frame
ENST00000225964	48272927	48273026	In-frame
ENST00000225964	48273515	48273560	In-frame
ENST00000225964	48273674	48273728	In-frame
ENST00000225964	48275309	48275363	In-frame
ENST00000225964	48275521	48275566	In-frame
ENST00000225964	48275793	48275865	In-frame
ENST00000225964	48276778	48276814	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
ENST00000225964	48264375	48264483	In-frame
ENST00000225964	48264844	48264898	In-frame
ENST00000225964	48265456	48265510	In-frame
ENST00000225964	48266528	48266636	In-frame
ENST00000225964	48266737	48266899	In-frame
ENST00000225964	48267039	48267093	In-frame
ENST00000225964	48267219	48267273	In-frame
ENST00000225964	48267361	48267469	In-frame
ENST00000225964	48267903	48267957	In-frame
ENST00000225964	48268177	48268285	In-frame
ENST00000225964	48268743	48268851	In-frame
ENST00000225964	48269835	48269889	In-frame
ENST00000225964	48270157	48270211	In-frame
ENST00000225964	48270354	48270408	In-frame
ENST00000225964	48271303	48271402	In-frame
ENST00000225964	48271709	48271808	In-frame
ENST00000225964	48271933	48271987	In-frame
ENST00000225964	48272407	48272461	In-frame
ENST00000225964	48272592	48272691	In-frame
ENST00000225964	48272794	48272839	In-frame
ENST00000225964	48272927	48273026	In-frame
ENST00000225964	48273515	48273560	In-frame
ENST00000225964	48273674	48273728	In-frame
ENST00000225964	48275309	48275363	In-frame
ENST00000225964	48275521	48275566	In-frame
ENST00000225964	48275793	48275865	In-frame
ENST00000225964	48276778	48276814	In-frame

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Infer the effects of exon skipping event on protein functional features for COL1A1

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
ENST00000225964	6744	1464	48276778	48276814	453	488	111	123
ENST00000225964	6744	1464	48275793	48275865	591	662	157	181
ENST00000225964	6744	1464	48275521	48275566	663	707	181	196
ENST00000225964	6744	1464	48275309	48275363	708	761	196	214
ENST00000225964	6744	1464	48273674	48273728	1023	1076	301	319
ENST00000225964	6744	1464	48273515	48273560	1077	1121	319	334
ENST00000225964	6744	1464	48272927	48273026	1176	1274	352	385
ENST00000225964	6744	1464	48272794	48272839	1275	1319	385	400
ENST00000225964	6744	1464	48272592	48272691	1320	1418	400	433
ENST00000225964	6744	1464	48272407	48272461	1419	1472	433	451
ENST00000225964	6744	1464	48271933	48271987	1581	1634	487	505
ENST00000225964	6744	1464	48271709	48271808	1635	1733	505	538
ENST00000225964	6744	1464	48271303	48271402	1788	1886	556	589
ENST00000225964	6744	1464	48270354	48270408	1887	1940	589	607
ENST00000225964	6744	1464	48270157	48270211	1941	1994	607	625
ENST00000225964	6744	1464	48269835	48269889	2049	2102	643	661
ENST00000225964	6744	1464	48268743	48268851	2247	2354	709	745
ENST00000225964	6744	1464	48268177	48268285	2355	2462	745	781
ENST00000225964	6744	1464	48267903	48267957	2463	2516	781	799
ENST00000225964	6744	1464	48267361	48267469	2571	2678	817	853
ENST00000225964	6744	1464	48267219	48267273	2679	2732	853	871
ENST00000225964	6744	1464	48267039	48267093	2733	2786	871	889
ENST00000225964	6744	1464	48266737	48266899	2787	2948	889	943
ENST00000225964	6744	1464	48266528	48266636	2949	3056	943	979
ENST00000225964	6744	1464	48265456	48265510	3327	3380	1069	1087
ENST00000225964	6744	1464	48264844	48264898	3489	3542	1123	1141
ENST00000225964	6744	1464	48264375	48264483	3543	3650	1141	1177

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
ENST00000225964	6744	1464	48276778	48276814	453	488	111	123
ENST00000225964	6744	1464	48275793	48275865	591	662	157	181
ENST00000225964	6744	1464	48275521	48275566	663	707	181	196
ENST00000225964	6744	1464	48275309	48275363	708	761	196	214
ENST00000225964	6744	1464	48273674	48273728	1023	1076	301	319
ENST00000225964	6744	1464	48273515	48273560	1077	1121	319	334
ENST00000225964	6744	1464	48272927	48273026	1176	1274	352	385
ENST00000225964	6744	1464	48272794	48272839	1275	1319	385	400
ENST00000225964	6744	1464	48272592	48272691	1320	1418	400	433
ENST00000225964	6744	1464	48272407	48272461	1419	1472	433	451
ENST00000225964	6744	1464	48271933	48271987	1581	1634	487	505
ENST00000225964	6744	1464	48271709	48271808	1635	1733	505	538
ENST00000225964	6744	1464	48271303	48271402	1788	1886	556	589
ENST00000225964	6744	1464	48270354	48270408	1887	1940	589	607
ENST00000225964	6744	1464	48270157	48270211	1941	1994	607	625
ENST00000225964	6744	1464	48269835	48269889	2049	2102	643	661
ENST00000225964	6744	1464	48268743	48268851	2247	2354	709	745
ENST00000225964	6744	1464	48268177	48268285	2355	2462	745	781
ENST00000225964	6744	1464	48267903	48267957	2463	2516	781	799
ENST00000225964	6744	1464	48267361	48267469	2571	2678	817	853
ENST00000225964	6744	1464	48267219	48267273	2679	2732	853	871
ENST00000225964	6744	1464	48267039	48267093	2733	2786	871	889
ENST00000225964	6744	1464	48266737	48266899	2787	2948	889	943
ENST00000225964	6744	1464	48266528	48266636	2949	3056	943	979
ENST00000225964	6744	1464	48265456	48265510	3327	3380	1069	1087
ENST00000225964	6744	1464	48264844	48264898	3489	3542	1123	1141
ENST00000225964	6744	1464	48264375	48264483	3543	3650	1141	1177

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 COL1A1

- 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.

COL1A1_LIHC_exon_skip_291361_psi_boxplot.png
boxplot

COL1A1_LUSC_exon_skip_291361_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-A1EG-01	exon_skip_291361	48266738	48266899	48266742	48266742	Frame_Shift_Del	G	-	p.P942fs
LIHC	TCGA-DD-A39Y-01	exon_skip_291361	48266738	48266899	48266883	48266883	Frame_Shift_Del	G	-	p.P895fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_291397	48267362	48267469	48267372	48267372	Frame_Shift_Del	G	-	p.P850fs
LIHC	TCGA-DD-A39Y-01	exon_skip_291397	48267362	48267469	48267399	48267399	Frame_Shift_Del	G	-	p.P841fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_291402	48268178	48268285	48268217	48268217	Frame_Shift_Del	G	-	p.P768fs
UCEC	TCGA-D1-A17C-01	exon_skip_291408	48268744	48268851	48268763	48268763	Frame_Shift_Del	G	-	p.P739fs
STAD	TCGA-BR-6452-01	exon_skip_291414	48270158	48270211	48270162	48270162	Frame_Shift_Del	G	-	p.P624fs
STAD	TCGA-F1-6874-01	exon_skip_291457	48272928	48273026	48272956	48272956	Frame_Shift_Del	G	-	p.P376fs
LIHC	TCGA-DD-A39Y-01	exon_skip_291463	48273675	48273728	48273722	48273722	Frame_Shift_Del	G	-	p.R304fs
LIHC	TCGA-DD-A39Y-01	exon_skip_291472	48275794	48275865	48275860	48275860	Frame_Shift_Del	A	-	p.F159fs
LUAD	TCGA-55-A494-01	exon_skip_291449	48272593	48272691	48272649	48272649	Nonsense_Mutation	G	A	p.R415*
HNSC	TCGA-CR-7376-01	exon_skip_291457	48272928	48273026	48273002	48273002	Nonsense_Mutation	G	A	p.R361*
LUSC	TCGA-43-3394-01	exon_skip_291361	48266738	48266899	48266736	48266736	Splice_Site	A	G	p.A943_splice
SKCM	TCGA-ER-A42L-06	exon_skip_291444	48271710	48271808	48271809	48271809	Splice_Site	C	T	.
UCEC	TCGA-AX-A0J0-01	exon_skip_291472	48275794	48275865	48275866	48275866	Splice_Site	C	A	e6-1

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

Depth of coverage in three exons	Mutation description
	Sample: TCGA-43-3394-01
	Cancer type: LUSC
	ESID: exon_skip_291361
	Skipped exon start: 48266738
	Skipped exon end: 48266899
	Mutation start: 48266736
	Mutation end: 48266736
	Mutation type: Splice_Site
	Reference seq: A
	Mutation seq: G
	AAchange: p.A943_splice
exon_skip_291361_LUSC_TCGA-43-3394-01.png
exon_skip_433795_LUSC_TCGA-43-3394-01.png
exon_skip_512323_LUSC_TCGA-43-3394-01.png
exon_skip_92560_LUSC_TCGA-43-3394-01.png
exon_skip_92567_LUSC_TCGA-43-3394-01.png
exon_skip_92572_LUSC_TCGA-43-3394-01.png
exon_skip_92573_LUSC_TCGA-43-3394-01.png
	Sample: TCGA-DD-A1EG-01
	Cancer type: LIHC
	ESID: exon_skip_291361
	Skipped exon start: 48266738
	Skipped exon end: 48266899
	Mutation start: 48266742
	Mutation end: 48266742
	Mutation type: Frame_Shift_Del
	Reference seq: G
	Mutation seq: -
	AAchange: p.P942fs
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	Sample: TCGA-DD-A39Y-01
	Cancer type: LIHC
	ESID: exon_skip_291361
	Skipped exon start: 48266738
	Skipped exon end: 48266899
	Mutation start: 48266883
	Mutation end: 48266883
	Mutation type: Frame_Shift_Del
	Reference seq: G
	Mutation seq: -
	AAchange: p.P895fs
	Sample: TCGA-DD-A39Y-01
	Cancer type: LIHC
	ESID: exon_skip_291397
	Skipped exon start: 48267362
	Skipped exon end: 48267469
	Mutation start: 48267399
	Mutation end: 48267399
	Mutation type: Frame_Shift_Del
	Reference seq: G
	Mutation seq: -
	AAchange: p.P841fs
	Sample: TCGA-DD-A39Y-01
	Cancer type: LIHC
	ESID: exon_skip_291463
	Skipped exon start: 48273675
	Skipped exon end: 48273728
	Mutation start: 48273722
	Mutation end: 48273722
	Mutation type: Frame_Shift_Del
	Reference seq: G
	Mutation seq: -
	AAchange: p.R304fs
	Sample: TCGA-DD-A39Y-01
	Cancer type: LIHC
	ESID: exon_skip_291472
	Skipped exon start: 48275794
	Skipped exon end: 48275865
	Mutation start: 48275860
	Mutation end: 48275860
	Mutation type: Frame_Shift_Del
	Reference seq: A
	Mutation seq: -
	AAchange: p.F159fs
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exon_skip_459683_LIHC_TCGA-DD-A39Y-01.png
exon_skip_460515_LIHC_TCGA-DD-A39Y-01.png
exon_skip_463936_LIHC_TCGA-DD-A39Y-01.png
exon_skip_464994_LIHC_TCGA-DD-A39Y-01.png
exon_skip_465641_LIHC_TCGA-DD-A39Y-01.png
exon_skip_469364_LIHC_TCGA-DD-A39Y-01.png
exon_skip_470206_LIHC_TCGA-DD-A39Y-01.png
exon_skip_470208_LIHC_TCGA-DD-A39Y-01.png
exon_skip_470470_LIHC_TCGA-DD-A39Y-01.png
exon_skip_470485_LIHC_TCGA-DD-A39Y-01.png
exon_skip_471015_LIHC_TCGA-DD-A39Y-01.png
exon_skip_471018_LIHC_TCGA-DD-A39Y-01.png
exon_skip_471458_LIHC_TCGA-DD-A39Y-01.png
exon_skip_472524_LIHC_TCGA-DD-A39Y-01.png
exon_skip_472955_LIHC_TCGA-DD-A39Y-01.png
exon_skip_475132_LIHC_TCGA-DD-A39Y-01.png
exon_skip_47552_LIHC_TCGA-DD-A39Y-01.png
exon_skip_476535_LIHC_TCGA-DD-A39Y-01.png
exon_skip_477211_LIHC_TCGA-DD-A39Y-01.png
exon_skip_477637_LIHC_TCGA-DD-A39Y-01.png
exon_skip_478117_LIHC_TCGA-DD-A39Y-01.png
exon_skip_47838_LIHC_TCGA-DD-A39Y-01.png
exon_skip_478401_LIHC_TCGA-DD-A39Y-01.png
exon_skip_478926_LIHC_TCGA-DD-A39Y-01.png
exon_skip_483792_LIHC_TCGA-DD-A39Y-01.png
exon_skip_487634_LIHC_TCGA-DD-A39Y-01.png
exon_skip_489575_LIHC_TCGA-DD-A39Y-01.png
exon_skip_490603_LIHC_TCGA-DD-A39Y-01.png
exon_skip_491406_LIHC_TCGA-DD-A39Y-01.png
exon_skip_492075_LIHC_TCGA-DD-A39Y-01.png
exon_skip_492152_LIHC_TCGA-DD-A39Y-01.png
exon_skip_493904_LIHC_TCGA-DD-A39Y-01.png
exon_skip_493918_LIHC_TCGA-DD-A39Y-01.png
exon_skip_493920_LIHC_TCGA-DD-A39Y-01.png
exon_skip_494000_LIHC_TCGA-DD-A39Y-01.png
exon_skip_494030_LIHC_TCGA-DD-A39Y-01.png
exon_skip_494170_LIHC_TCGA-DD-A39Y-01.png
exon_skip_494284_LIHC_TCGA-DD-A39Y-01.png
exon_skip_499522_LIHC_TCGA-DD-A39Y-01.png
exon_skip_503301_LIHC_TCGA-DD-A39Y-01.png
exon_skip_503593_LIHC_TCGA-DD-A39Y-01.png
exon_skip_503665_LIHC_TCGA-DD-A39Y-01.png
exon_skip_504513_LIHC_TCGA-DD-A39Y-01.png
exon_skip_507316_LIHC_TCGA-DD-A39Y-01.png
exon_skip_507513_LIHC_TCGA-DD-A39Y-01.png
exon_skip_50803_LIHC_TCGA-DD-A39Y-01.png
exon_skip_50804_LIHC_TCGA-DD-A39Y-01.png
exon_skip_510119_LIHC_TCGA-DD-A39Y-01.png
exon_skip_512208_LIHC_TCGA-DD-A39Y-01.png
exon_skip_513207_LIHC_TCGA-DD-A39Y-01.png
exon_skip_513240_LIHC_TCGA-DD-A39Y-01.png
exon_skip_5141_LIHC_TCGA-DD-A39Y-01.png
exon_skip_52393_LIHC_TCGA-DD-A39Y-01.png
exon_skip_54542_LIHC_TCGA-DD-A39Y-01.png
exon_skip_55185_LIHC_TCGA-DD-A39Y-01.png
exon_skip_56398_LIHC_TCGA-DD-A39Y-01.png
exon_skip_56399_LIHC_TCGA-DD-A39Y-01.png
exon_skip_56834_LIHC_TCGA-DD-A39Y-01.png
exon_skip_58444_LIHC_TCGA-DD-A39Y-01.png
exon_skip_58452_LIHC_TCGA-DD-A39Y-01.png
exon_skip_5861_LIHC_TCGA-DD-A39Y-01.png
exon_skip_60290_LIHC_TCGA-DD-A39Y-01.png
exon_skip_60294_LIHC_TCGA-DD-A39Y-01.png
exon_skip_60561_LIHC_TCGA-DD-A39Y-01.png
exon_skip_61147_LIHC_TCGA-DD-A39Y-01.png
exon_skip_6331_LIHC_TCGA-DD-A39Y-01.png
exon_skip_6399_LIHC_TCGA-DD-A39Y-01.png
exon_skip_64652_LIHC_TCGA-DD-A39Y-01.png
exon_skip_64657_LIHC_TCGA-DD-A39Y-01.png
exon_skip_65996_LIHC_TCGA-DD-A39Y-01.png
exon_skip_66666_LIHC_TCGA-DD-A39Y-01.png
exon_skip_67549_LIHC_TCGA-DD-A39Y-01.png
exon_skip_68080_LIHC_TCGA-DD-A39Y-01.png
exon_skip_6817_LIHC_TCGA-DD-A39Y-01.png
exon_skip_69250_LIHC_TCGA-DD-A39Y-01.png
exon_skip_70509_LIHC_TCGA-DD-A39Y-01.png
exon_skip_71759_LIHC_TCGA-DD-A39Y-01.png
exon_skip_71774_LIHC_TCGA-DD-A39Y-01.png
exon_skip_73487_LIHC_TCGA-DD-A39Y-01.png
exon_skip_73796_LIHC_TCGA-DD-A39Y-01.png
exon_skip_74728_LIHC_TCGA-DD-A39Y-01.png
exon_skip_75089_LIHC_TCGA-DD-A39Y-01.png
exon_skip_75391_LIHC_TCGA-DD-A39Y-01.png
exon_skip_77962_LIHC_TCGA-DD-A39Y-01.png
exon_skip_78386_LIHC_TCGA-DD-A39Y-01.png
exon_skip_82069_LIHC_TCGA-DD-A39Y-01.png
exon_skip_82070_LIHC_TCGA-DD-A39Y-01.png
exon_skip_83493_LIHC_TCGA-DD-A39Y-01.png
exon_skip_83494_LIHC_TCGA-DD-A39Y-01.png
exon_skip_83512_LIHC_TCGA-DD-A39Y-01.png
exon_skip_83602_LIHC_TCGA-DD-A39Y-01.png
exon_skip_84090_LIHC_TCGA-DD-A39Y-01.png
exon_skip_84528_LIHC_TCGA-DD-A39Y-01.png
exon_skip_87720_LIHC_TCGA-DD-A39Y-01.png
exon_skip_87721_LIHC_TCGA-DD-A39Y-01.png
exon_skip_89597_LIHC_TCGA-DD-A39Y-01.png
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exon_skip_94842_LIHC_TCGA-DD-A39Y-01.png
exon_skip_94844_LIHC_TCGA-DD-A39Y-01.png
exon_skip_96282_LIHC_TCGA-DD-A39Y-01.png
exon_skip_96298_LIHC_TCGA-DD-A39Y-01.png
exon_skip_96557_LIHC_TCGA-DD-A39Y-01.png
exon_skip_96886_LIHC_TCGA-DD-A39Y-01.png
exon_skip_97738_LIHC_TCGA-DD-A39Y-01.png
exon_skip_97739_LIHC_TCGA-DD-A39Y-01.png
exon_skip_9807_LIHC_TCGA-DD-A39Y-01.png
exon_skip_98550_LIHC_TCGA-DD-A39Y-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
HCT116_LARGE_INTESTINE	48266529	48266636	48266555	48266556	Frame_Shift_Del	CT	-	p.G971fs
MFE319_ENDOMETRIUM	48275522	48275566	48275532	48275532	Frame_Shift_Del	G	-	p.P193fs
NB12_AUTONOMIC_GANGLIA	48275310	48275363	48275354	48275355	Frame_Shift_Ins	-	T	p.G200fs
NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	48264376	48264483	48264438	48264438	Missense_Mutation	C	T	p.G1157S
BICR18_UPPER_AERODIGESTIVE_TRACT	48264376	48264483	48264462	48264462	Missense_Mutation	C	A	p.A1149S
KE39_STOMACH	48265457	48265510	48265465	48265465	Missense_Mutation	C	A	p.G1085C
PF382_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	48266529	48266636	48266581	48266581	Missense_Mutation	C	T	p.G962D
HT55_LARGE_INTESTINE	48266738	48266899	48266799	48266799	Missense_Mutation	C	T	p.G923D
CASKI_CERVIX	48266738	48266899	48266805	48266805	Missense_Mutation	T	A	p.E921V
NCIH1155_LUNG	48266738	48266899	48266821	48266821	Missense_Mutation	C	T	p.A916T
SNU1040_LARGE_INTESTINE	48267220	48267273	48267239	48267239	Missense_Mutation	C	T	p.R865H
NCIH1563_LUNG	48267362	48267469	48267439	48267439	Missense_Mutation	C	T	p.E828K
HCC15_LUNG	48267362	48267469	48267450	48267450	Missense_Mutation	C	A	p.G824V
CALU6_LUNG	48267904	48267957	48267927	48267927	Missense_Mutation	G	A	p.P792S
NB13_AUTONOMIC_GANGLIA	48267904	48267957	48267930	48267930	Missense_Mutation	C	T	p.G791S
HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	48267904	48267957	48267936	48267936	Missense_Mutation	G	A	p.P789S
BHY_UPPER_AERODIGESTIVE_TRACT	48267904	48267957	48267954	48267954	Missense_Mutation	C	T	p.E783K
ECC12_STOMACH	48268744	48268851	48268763	48268763	Missense_Mutation	G	A	p.P739L
NCIH727_LUNG	48268744	48268851	48268838	48268838	Missense_Mutation	G	A	p.A714V
BICR18_UPPER_AERODIGESTIVE_TRACT	48268744	48268851	48268845	48268845	Missense_Mutation	C	T	p.A712T
NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	48270158	48270211	48270162	48270162	Missense_Mutation	G	A	p.P624L
HEC59_ENDOMETRIUM	48270355	48270408	48270360	48270360	Missense_Mutation	C	T	p.A606T
EN_ENDOMETRIUM	48271304	48271402	48271335	48271335	Missense_Mutation	A	G	p.V579A
HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	48271304	48271402	48271350	48271350	Missense_Mutation	C	T	p.R574H
KMOE2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	48272593	48272691	48272603	48272603	Missense_Mutation	T	A	p.K430M
SW780_URINARY_TRACT	48272593	48272691	48272622	48272622	Missense_Mutation	C	T	p.G424S
MOLT13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	48272593	48272691	48272675	48272675	Missense_Mutation	G	A	p.A406V
SQ1_LUNG	48273516	48273560	48273530	48273530	Missense_Mutation	C	T	p.A330T
CALU3_LUNG	48273516	48273560	48273548	48273548	Missense_Mutation	T	G	p.N324H
EN_ENDOMETRIUM	48273516	48273560	48273554	48273554	Missense_Mutation	G	A	p.R322C
M14_SKIN	48273675	48273728	48273698	48273698	Missense_Mutation	G	A	p.R312C
HEC108_ENDOMETRIUM	48273675	48273728	48273721	48273721	Missense_Mutation	C	T	p.R304H
JHUEM7_ENDOMETRIUM	48275310	48275363	48275324	48275324	Missense_Mutation	C	T	p.E210K
NCIH1770_LUNG	48275310	48275363	48275360	48275360	Missense_Mutation	G	A	p.P198S
NCIH2106_LUNG	48275310	48275363	48275360	48275360	Missense_Mutation	G	A	p.P198S
SNU1_STOMACH	48275794	48275865	48275801	48275801	Missense_Mutation	C	G	p.G179A
HCT116_LARGE_INTESTINE	48264845	48264898	48264847	48264847	Nonsense_Mutation	G	A	p.R1141*
RERFLCAD2_LUNG	48267220	48267273	48267272	48267272	Splice_Site	C	A	p.G854V
SKMEL30_SKIN	48268744	48268851	48268850	48268850	Splice_Site	C	T	p.G710D
SARC9371_BONE	48272408	48272461	48272461	48272461	Splice_Site	C	T	p.G434S

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for COL1A1

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 COL1A1

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for COL1A1

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RelatedDrugs for COL1A1

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
	P02452	DB00048	Collagenase clostridium histolyticum	Collagen alpha-1(I) chain	biotech	approved\|investigational
	P02452	DB13133	Von Willebrand Factor Human	Collagen alpha-1(I) chain	biotech	approved\|investigational

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RelatedDiseases for COL1A1

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
COL1A1	C0268358	Osteogenesis imperfecta, dominant perinatal lethal	39	CTD_human;ORPHANET;UNIPROT
COL1A1	C0268362	Osteogenesis imperfecta type III (disorder)	18	CTD_human;ORPHANET;UNIPROT
COL1A1	C0268363	Osteogenesis imperfecta type IV (disorder)	14	CTD_human;ORPHANET;UNIPROT
COL1A1	C0023931	Lobstein's Disease	12	ORPHANET;UNIPROT
COL1A1	C0023890	Liver Cirrhosis	4	CTD_human
COL1A1	C0023893	Liver Cirrhosis, Experimental	3	CTD_human
COL1A1	C4225429	Ehlers-Danlos syndrome classic type	2	UNIPROT
COL1A1	C0000786	Spontaneous abortion	1	CTD_human
COL1A1	C0002949	Aneurysm, Dissecting	1	CTD_human
COL1A1	C0003504	Aortic Valve Insufficiency	1	CTD_human
COL1A1	C0004364	Autoimmune Diseases	1	CTD_human
COL1A1	C0006663	Calcinosis	1	CTD_human
COL1A1	C0008311	Cholangitis	1	CTD_human
COL1A1	C0016059	Fibrosis	1	CTD_human
COL1A1	C0018824	Heart valve disease	1	CTD_human
COL1A1	C0020497	Cortical Congenital Hyperostosis	1	CTD_human;ORPHANET;UNIPROT
COL1A1	C0020538	Hypertensive disease	1	CTD_human
COL1A1	C0022548	Keloid	1	CTD_human
COL1A1	C0027726	Nephrotic Syndrome	1	CTD_human
COL1A1	C0029172	Oral Submucous Fibrosis	1	CTD_human
COL1A1	C0029434	Osteogenesis Imperfecta	1	CTD_human
COL1A1	C0149721	Left Ventricular Hypertrophy	1	CTD_human
COL1A1	C1619692	Nephrogenic Fibrosing Dermopathy	1	CTD_human

	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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