ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for ICA1L

Gene summary

Gene information	Gene symbol	ICA1L
	Gene ID	130026
	Gene name	islet cell autoantigen 1 like
	Synonyms	ALS2CR14\|ALS2CR15
	Cytomap	2q33.2
	Type of gene	protein-coding
	Description	islet cell autoantigen 1-like proteinIca69-related proteinamyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 14amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 15amyotrophic lateral sclerosis 2 chromosomal r
	Modification date	20180519
	UniProtAcc	Q8NDH6
	Context	PubMed: ICA1L [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract] - Title (PMID)

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

Gene

GO ID

GO term

PubMed ID

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Exon skipping events across known transcript of Ensembl for ICA1L 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 ICA1L

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 ICA1L

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_346154	2	203643792:203644371:203650640:203650730:203653552:203653810	203650640:203650730	ENSG00000163596.12	ENST00000358299.2,ENST00000392237.2
exon_skip_346155	2	203650640:203650730:203651398:203651498:203653552:203653810	203651398:203651498	ENSG00000163596.12	ENST00000438804.1
exon_skip_346156	2	203650640:203650730:203653552:203653810:203661612:203661687	203653552:203653810	ENSG00000163596.12	ENST00000358299.2,ENST00000392237.2
exon_skip_346159	2	203653712:203653810:203661612:203661687:203676468:203676512	203661612:203661687	ENSG00000163596.12	ENST00000438804.1,ENST00000358299.2,ENST00000392237.2
exon_skip_346160	2	203661612:203661687:203676468:203676512:203679424:203679507	203676468:203676512	ENSG00000163596.12	ENST00000438804.1,ENST00000358299.2,ENST00000392237.2
exon_skip_346162	2	203680633:203680732:203682140:203682266:203684423:203684622	203682140:203682266	ENSG00000163596.12	ENST00000494560.1,ENST00000438804.1,ENST00000358299.2,ENST00000392237.2
exon_skip_346165	2	203684609:203684622:203686080:203686204:203690417:203690471	203686080:203686204	ENSG00000163596.12	ENST00000438804.1,ENST00000419460.1,ENST00000450143.1,ENST00000435143.1,ENST00000358299.2,ENST00000425178.1,ENST00000392237.2
exon_skip_346171	2	203686149:203686204:203690417:203690471:203693570:203693739	203690417:203690471	ENSG00000163596.12	ENST00000437978.1
exon_skip_346172	2	203686149:203686204:203690417:203690490:203693570:203693739	203690417:203690490	ENSG00000163596.12	ENST00000438804.1,ENST00000419460.1,ENST00000412210.1,ENST00000450143.1,ENST00000435143.1,ENST00000454326.1,ENST00000358299.2,ENST00000457524.1,ENST00000416760.1,ENST00000425178.1,ENST00000441547.1,ENST00000432273.1,ENST00000392237.2
exon_skip_346177	2	203693605:203693739:203724869:203724967:203734258:203734320	203724869:203724967	ENSG00000163596.12	ENST00000441547.1
exon_skip_346178	2	203693605:203693739:203734258:203734328:203735252:203735379	203734258:203734328	ENSG00000163596.12	ENST00000438804.1,ENST00000412210.1,ENST00000454326.1,ENST00000484561.1,ENST00000411681.1,ENST00000437978.1
exon_skip_346180	2	203693605:203693739:203735252:203735379:203735652:203735769	203735252:203735379	ENSG00000163596.12	ENST00000421334.1

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for ICA1L

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_346154	2	203643792:203644371:203650640:203650730:203653552:203653810	203650640:203650730	ENSG00000163596.12	ENST00000392237.2,ENST00000358299.2
exon_skip_346155	2	203650640:203650730:203651398:203651498:203653552:203653810	203651398:203651498	ENSG00000163596.12	ENST00000438804.1
exon_skip_346156	2	203650640:203650730:203653552:203653810:203661612:203661687	203653552:203653810	ENSG00000163596.12	ENST00000392237.2,ENST00000358299.2
exon_skip_346159	2	203653712:203653810:203661612:203661687:203676468:203676512	203661612:203661687	ENSG00000163596.12	ENST00000392237.2,ENST00000358299.2,ENST00000438804.1
exon_skip_346160	2	203661612:203661687:203676468:203676512:203679424:203679507	203676468:203676512	ENSG00000163596.12	ENST00000392237.2,ENST00000358299.2,ENST00000438804.1
exon_skip_346162	2	203680633:203680732:203682140:203682266:203684423:203684622	203682140:203682266	ENSG00000163596.12	ENST00000392237.2,ENST00000358299.2,ENST00000438804.1,ENST00000494560.1
exon_skip_346165	2	203684609:203684622:203686080:203686204:203690417:203690471	203686080:203686204	ENSG00000163596.12	ENST00000392237.2,ENST00000358299.2,ENST00000438804.1,ENST00000425178.1,ENST00000450143.1,ENST00000435143.1,ENST00000419460.1
exon_skip_346171	2	203686149:203686204:203690417:203690471:203693570:203693739	203690417:203690471	ENSG00000163596.12	ENST00000437978.1
exon_skip_346172	2	203686149:203686204:203690417:203690490:203693570:203693739	203690417:203690490	ENSG00000163596.12	ENST00000392237.2,ENST00000358299.2,ENST00000438804.1,ENST00000425178.1,ENST00000450143.1,ENST00000435143.1,ENST00000419460.1,ENST00000441547.1,ENST00000412210.1,ENST00000457524.1,ENST00000432273.1,ENST00000416760.1,ENST00000454326.1
exon_skip_346173	2	203693570:203693739:203708959:203709105:203709224:203709310	203708959:203709105	ENSG00000163596.12	ENST00000416760.1
exon_skip_346177	2	203693605:203693739:203724869:203724967:203734258:203734320	203724869:203724967	ENSG00000163596.12	ENST00000441547.1
exon_skip_346178	2	203693605:203693739:203734258:203734328:203735252:203735379	203734258:203734328	ENSG00000163596.12	ENST00000438804.1,ENST00000412210.1,ENST00000437978.1,ENST00000454326.1,ENST00000484561.1,ENST00000411681.1
exon_skip_346179	2	203693605:203693739:203734258:203734328:203736341:203736458	203734258:203734328	ENSG00000163596.12	ENST00000419460.1
exon_skip_346180	2	203693605:203693739:203735252:203735379:203735652:203735769	203735252:203735379	ENSG00000163596.12	ENST00000421334.1
exon_skip_346188	2	203734258:203734328:203735252:203735379:203736341:203736458	203735252:203735379	ENSG00000163596.12	ENST00000412210.1

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 ICA1L

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
ENST00000358299	203676468	203676512	Frame-shift
ENST00000392237	203676468	203676512	Frame-shift
ENST00000358299	203686080	203686204	Frame-shift
ENST00000392237	203686080	203686204	Frame-shift
ENST00000358299	203690417	203690490	Frame-shift
ENST00000392237	203690417	203690490	Frame-shift
ENST00000358299	203650640	203650730	In-frame
ENST00000392237	203650640	203650730	In-frame
ENST00000358299	203653552	203653810	In-frame
ENST00000392237	203653552	203653810	In-frame
ENST00000358299	203661612	203661687	In-frame
ENST00000392237	203661612	203661687	In-frame
ENST00000358299	203682140	203682266	In-frame
ENST00000392237	203682140	203682266	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
ENST00000358299	203676468	203676512	Frame-shift
ENST00000392237	203676468	203676512	Frame-shift
ENST00000358299	203686080	203686204	Frame-shift
ENST00000392237	203686080	203686204	Frame-shift
ENST00000358299	203690417	203690490	Frame-shift
ENST00000392237	203690417	203690490	Frame-shift
ENST00000358299	203650640	203650730	In-frame
ENST00000392237	203650640	203650730	In-frame
ENST00000358299	203653552	203653810	In-frame
ENST00000392237	203653552	203653810	In-frame
ENST00000358299	203661612	203661687	In-frame
ENST00000392237	203661612	203661687	In-frame
ENST00000358299	203682140	203682266	In-frame
ENST00000392237	203682140	203682266	In-frame

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Infer the effects of exon skipping event on protein functional features for ICA1L

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
ENST00000358299	3474	482	203682140	203682266	933	1058	186	228
ENST00000392237	5190	482	203682140	203682266	717	842	186	228
ENST00000358299	3474	482	203661612	203661687	1285	1359	303	328
ENST00000392237	5190	482	203661612	203661687	1069	1143	303	328
ENST00000358299	3474	482	203653552	203653810	1360	1617	328	414
ENST00000392237	5190	482	203653552	203653810	1144	1401	328	414
ENST00000358299	3474	482	203650640	203650730	1618	1707	414	444
ENST00000392237	5190	482	203650640	203650730	1402	1491	414	444

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
ENST00000358299	3474	482	203682140	203682266	933	1058	186	228
ENST00000392237	5190	482	203682140	203682266	717	842	186	228
ENST00000358299	3474	482	203661612	203661687	1285	1359	303	328
ENST00000392237	5190	482	203661612	203661687	1069	1143	303	328
ENST00000358299	3474	482	203653552	203653810	1360	1617	328	414
ENST00000392237	5190	482	203653552	203653810	1144	1401	328	414
ENST00000358299	3474	482	203650640	203650730	1618	1707	414	444
ENST00000392237	5190	482	203650640	203650730	1402	1491	414	444

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
Q8NDH6	186	228	188	482	Alternative sequence	ID=VSP_017107;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q8NDH6	186	228	188	482	Alternative sequence	ID=VSP_017107;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q8NDH6	186	228	1	482	Chain	ID=PRO_0000076175;Note=Islet cell autoantigen 1-like protein
Q8NDH6	186	228	1	482	Chain	ID=PRO_0000076175;Note=Islet cell autoantigen 1-like protein
Q8NDH6	186	228	44	247	Domain	Note=AH;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00294
Q8NDH6	186	228	44	247	Domain	Note=AH;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00294
Q8NDH6	303	328	188	482	Alternative sequence	ID=VSP_017107;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q8NDH6	303	328	188	482	Alternative sequence	ID=VSP_017107;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q8NDH6	303	328	1	482	Chain	ID=PRO_0000076175;Note=Islet cell autoantigen 1-like protein
Q8NDH6	303	328	1	482	Chain	ID=PRO_0000076175;Note=Islet cell autoantigen 1-like protein
Q8NDH6	328	414	188	482	Alternative sequence	ID=VSP_017107;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q8NDH6	328	414	188	482	Alternative sequence	ID=VSP_017107;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q8NDH6	328	414	1	482	Chain	ID=PRO_0000076175;Note=Islet cell autoantigen 1-like protein
Q8NDH6	328	414	1	482	Chain	ID=PRO_0000076175;Note=Islet cell autoantigen 1-like protein
Q8NDH6	328	414	334	334	Sequence conflict	Note=P->S;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q8NDH6	328	414	334	334	Sequence conflict	Note=P->S;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q8NDH6	414	444	188	482	Alternative sequence	ID=VSP_017107;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q8NDH6	414	444	188	482	Alternative sequence	ID=VSP_017107;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q8NDH6	414	444	1	482	Chain	ID=PRO_0000076175;Note=Islet cell autoantigen 1-like protein
Q8NDH6	414	444	1	482	Chain	ID=PRO_0000076175;Note=Islet cell autoantigen 1-like protein

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
Q8NDH6	186	228	188	482	Alternative sequence	ID=VSP_017107;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q8NDH6	186	228	188	482	Alternative sequence	ID=VSP_017107;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q8NDH6	186	228	1	482	Chain	ID=PRO_0000076175;Note=Islet cell autoantigen 1-like protein
Q8NDH6	186	228	1	482	Chain	ID=PRO_0000076175;Note=Islet cell autoantigen 1-like protein
Q8NDH6	186	228	44	247	Domain	Note=AH;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00294
Q8NDH6	186	228	44	247	Domain	Note=AH;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00294
Q8NDH6	303	328	188	482	Alternative sequence	ID=VSP_017107;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q8NDH6	303	328	188	482	Alternative sequence	ID=VSP_017107;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q8NDH6	303	328	1	482	Chain	ID=PRO_0000076175;Note=Islet cell autoantigen 1-like protein
Q8NDH6	303	328	1	482	Chain	ID=PRO_0000076175;Note=Islet cell autoantigen 1-like protein
Q8NDH6	328	414	188	482	Alternative sequence	ID=VSP_017107;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q8NDH6	328	414	188	482	Alternative sequence	ID=VSP_017107;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q8NDH6	328	414	1	482	Chain	ID=PRO_0000076175;Note=Islet cell autoantigen 1-like protein
Q8NDH6	328	414	1	482	Chain	ID=PRO_0000076175;Note=Islet cell autoantigen 1-like protein
Q8NDH6	328	414	334	334	Sequence conflict	Note=P->S;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q8NDH6	328	414	334	334	Sequence conflict	Note=P->S;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q8NDH6	414	444	188	482	Alternative sequence	ID=VSP_017107;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q8NDH6	414	444	188	482	Alternative sequence	ID=VSP_017107;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q8NDH6	414	444	1	482	Chain	ID=PRO_0000076175;Note=Islet cell autoantigen 1-like protein
Q8NDH6	414	444	1	482	Chain	ID=PRO_0000076175;Note=Islet cell autoantigen 1-like protein

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SNVs in the skipped exons for ICA1L

- 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
BLCA	TCGA-CF-A1HS-01	exon_skip_346154	203650641	203650730	203650667	203650667	Nonsense_Mutation	G	C	p.S436*
UCS	TCGA-ND-A4WC-01	exon_skip_346156	203653553	203653810	203653775	203653775	Nonsense_Mutation	C	A	p.E341*
UCS	TCGA-ND-A4WC-01	exon_skip_346156	203653553	203653810	203653775	203653775	Nonsense_Mutation	C	A	p.E341X
HNSC	TCGA-CQ-A4CD-01	exon_skip_346165	203686081	203686204	203686198	203686198	Nonsense_Mutation	G	C	p.S81*
SKCM	TCGA-EE-A2GB-06	exon_skip_346162	203682141	203682266	203682140	203682140	Splice_Site	C	-	.

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

Depth of coverage in three exons

Mutation description

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

Sample	Skipped exon start	Skipped exon end	Mutation start	Mutation end	Mutation type	Reference seq	Mutation seq	AAchange
NCIH820_LUNG	203653553	203653810	203653622	203653622	Missense_Mutation	C	T	p.A392T
SF295_CENTRAL_NERVOUS_SYSTEM	203653553	203653810	203653673	203653673	Missense_Mutation	G	T	p.P375T
NCIH1568_LUNG	203653553	203653810	203653766	203653766	Missense_Mutation	C	G	p.E344Q
M00921_SKIN	203653553	203653810	203653770	203653770	Missense_Mutation	A	C	p.D342E
NCIH661_LUNG	203653553	203653810	203653773	203653773	Missense_Mutation	T	A	p.E341D
LNCAPCLONEFGC_PROSTATE	203686081	203686204	203686171	203686171	Missense_Mutation	A	G	p.F90S
SNUC5_LARGE_INTESTINE	203661613	203661687	203661687	203661687	Splice_Site	G	T	p.A304E
MN60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	203676469	203676512	203676511	203676511	Splice_Site	G	A	p.L290L

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for ICA1L

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 ICA1L

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for ICA1L

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RelatedDrugs for ICA1L

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 ICA1L

Diseases associated with this gene.
(DisGeNet 4.0)

Gene

Disease ID

Disease name

# pubmeds

Source

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

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Gene summary for ICA1L

Exon skipping events across known transcript of Ensembl for ICA1L from UCSC genome browser

Gene isoform structures and expression levels for ICA1L

Exon skipping events with PSIs in TCGA for ICA1L

Exon skipping events with PSIs in GTEx for ICA1L

Open reading frame (ORF) annotation in the exon skipping event for ICA1L

Infer the effects of exon skipping event on protein functional features for ICA1L

SNVs in the skipped exons for ICA1L

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for ICA1L

Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for ICA1L

Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for ICA1L

RelatedDrugs for ICA1L

RelatedDiseases for ICA1L