ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for CADPS

Gene summary

Gene information	Gene symbol	CADPS
	Gene ID	8618
	Gene name	calcium dependent secretion activator
	Synonyms	CADPS1\|CAPS\|CAPS1\|UNC-31
	Cytomap	3p14.2
	Type of gene	protein-coding
	Description	calcium-dependent secretion activator 1CAPS-1Ca++-dependent secretion activatorCa2+ dependent secretion activatorCa2+-dependent activator protein for secretionCa2+-regulated cytoskeletal proteincalcium-dependent activator protein for secretion 1
	Modification date	20180519
	UniProtAcc	Q9ULU8
	Context	PubMed: CADPS [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 CADPS 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 CADPS

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 CADPS

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_385489	3	62388768:62388860:62423778:62423886:62431439:62431472	62423778:62423886	ENSG00000163618.13	ENST00000283269.9,ENST00000383710.4,ENST00000357948.3,ENST00000473635.1
exon_skip_385492	3	62423814:62423886:62431439:62431472:62451041:62451125	62431439:62431472	ENSG00000163618.13	ENST00000283269.9,ENST00000383710.4,ENST00000357948.3,ENST00000473635.1
exon_skip_385493	3	62451041:62451125:62452013:62452088:62459847:62459995	62452013:62452088	ENSG00000163618.13	ENST00000283269.9,ENST00000466621.2,ENST00000383710.4,ENST00000357948.3
exon_skip_385495	3	62452013:62452088:62452972:62452987:62459847:62459995	62452972:62452987	ENSG00000163618.13	ENST00000473635.1
exon_skip_385496	3	62452013:62452088:62459847:62459995:62463935:62463991	62459847:62459995	ENSG00000163618.13	ENST00000283269.9,ENST00000466621.2,ENST00000383710.4,ENST00000357948.3
exon_skip_385497	3	62463935:62464091:62467397:62467544:62477013:62477155	62467397:62467544	ENSG00000163618.13	ENST00000383710.4
exon_skip_385498	3	62477964:62478121:62479319:62479340:62484836:62484943	62479319:62479340	ENSG00000163618.13	ENST00000383710.4
exon_skip_385499	3	62477964:62478121:62483820:62483829:62484836:62484943	62483820:62483829	ENSG00000163618.13	ENST00000491424.1
exon_skip_385500	3	62477964:62478121:62484836:62484943:62501733:62501857	62484836:62484943	ENSG00000163618.13	ENST00000357948.3
exon_skip_385503	3	62484836:62484943:62498425:62498443:62501733:62501857	62498425:62498443	ENSG00000163618.13	ENST00000491424.1,ENST00000383710.4
exon_skip_385505	3	62484836:62484943:62499312:62499381:62501733:62501857	62499312:62499381	ENSG00000163618.13	ENST00000283269.9
exon_skip_385509	3	62503823:62503925:62516328:62516487:62518545:62518733	62516328:62516487	ENSG00000163618.13	ENST00000468271.1
exon_skip_385510	3	62522170:62522256:62530522:62530534:62535577:62535789	62530522:62530534	ENSG00000163618.13	ENST00000542833.1

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for CADPS

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_385489	3	62388768:62388860:62423778:62423886:62431439:62431472	62423778:62423886	ENSG00000163618.13	ENST00000383710.4,ENST00000473635.1,ENST00000357948.3,ENST00000283269.9
exon_skip_385492	3	62423814:62423886:62431439:62431472:62451041:62451125	62431439:62431472	ENSG00000163618.13	ENST00000383710.4,ENST00000473635.1,ENST00000357948.3,ENST00000283269.9
exon_skip_385493	3	62451041:62451125:62452013:62452088:62459847:62459995	62452013:62452088	ENSG00000163618.13	ENST00000383710.4,ENST00000357948.3,ENST00000283269.9,ENST00000466621.2
exon_skip_385495	3	62452013:62452088:62452972:62452987:62459847:62459995	62452972:62452987	ENSG00000163618.13	ENST00000473635.1
exon_skip_385496	3	62452013:62452088:62459847:62459995:62463935:62463991	62459847:62459995	ENSG00000163618.13	ENST00000383710.4,ENST00000357948.3,ENST00000283269.9,ENST00000466621.2
exon_skip_385497	3	62463935:62464091:62467397:62467544:62477013:62477155	62467397:62467544	ENSG00000163618.13	ENST00000383710.4
exon_skip_385498	3	62477964:62478121:62479319:62479340:62484836:62484943	62479319:62479340	ENSG00000163618.13	ENST00000383710.4
exon_skip_385499	3	62477964:62478121:62483820:62483829:62484836:62484943	62483820:62483829	ENSG00000163618.13	ENST00000491424.1
exon_skip_385500	3	62477964:62478121:62484836:62484943:62501733:62501857	62484836:62484943	ENSG00000163618.13	ENST00000357948.3
exon_skip_385503	3	62484836:62484943:62498425:62498443:62501733:62501857	62498425:62498443	ENSG00000163618.13	ENST00000383710.4,ENST00000491424.1
exon_skip_385505	3	62484836:62484943:62499312:62499381:62501733:62501857	62499312:62499381	ENSG00000163618.13	ENST00000283269.9
exon_skip_385509	3	62503823:62503925:62516328:62516487:62518545:62518733	62516328:62516487	ENSG00000163618.13	ENST00000468271.1
exon_skip_385510	3	62522170:62522256:62530522:62530534:62535577:62535789	62530522:62530534	ENSG00000163618.13	ENST00000542833.1

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 CADPS

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
ENST00000383710	62459847	62459995	Frame-shift
ENST00000383710	62423778	62423886	In-frame
ENST00000383710	62431439	62431472	In-frame
ENST00000383710	62452013	62452088	In-frame
ENST00000383710	62467397	62467544	In-frame
ENST00000383710	62479319	62479340	In-frame
ENST00000383710	62498425	62498443	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
ENST00000383710	62459847	62459995	Frame-shift
ENST00000383710	62423778	62423886	In-frame
ENST00000383710	62431439	62431472	In-frame
ENST00000383710	62452013	62452088	In-frame
ENST00000383710	62467397	62467544	In-frame
ENST00000383710	62479319	62479340	In-frame
ENST00000383710	62498425	62498443	In-frame

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

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
ENST00000383710	5488	1353	62467397	62467544	3377	3523	1009	1057
ENST00000383710	5488	1353	62452013	62452088	3828	3902	1159	1184
ENST00000383710	5488	1353	62431439	62431472	3987	4019	1212	1223
ENST00000383710	5488	1353	62423778	62423886	4020	4127	1223	1259

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
ENST00000383710	5488	1353	62467397	62467544	3377	3523	1009	1057
ENST00000383710	5488	1353	62452013	62452088	3828	3902	1159	1184
ENST00000383710	5488	1353	62431439	62431472	3987	4019	1212	1223
ENST00000383710	5488	1353	62423778	62423886	4020	4127	1223	1259

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
Q9ULU8	1009	1057	458	1353	Alternative sequence	ID=VSP_016802;Note=In isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q9ULU8	1009	1057	1009	1058	Alternative sequence	ID=VSP_016807;Note=In isoform 2 and isoform 3. KSLTSNLPNVNLPNVNLPKVPNLPVNIPLGIPQMPTFSAPSWMAAIYDAD->N;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:12659812,ECO:0000303\|PubMed:17974005;Dbxref=PMID:12659812,PMID:17974005
Q9ULU8	1009	1057	1	1353	Chain	ID=PRO_0000053864;Note=Calcium-dependent secretion activator 1
Q9ULU8	1009	1057	931	1111	Domain	Note=MHD1;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00587
Q9ULU8	1009	1057	790	1129	Region	Note=Interaction with DRD2;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15857609;Dbxref=PMID:15857609
Q9ULU8	1159	1184	458	1353	Alternative sequence	ID=VSP_016802;Note=In isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q9ULU8	1159	1184	1159	1159	Alternative sequence	ID=VSP_016808;Note=In isoform 4. E->EFAKMW;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:15489334,ECO:0000303\|PubMed:9289490;Dbxref=PMID:15489334,PMID:9289490
Q9ULU8	1159	1184	1	1353	Chain	ID=PRO_0000053864;Note=Calcium-dependent secretion activator 1
Q9ULU8	1159	1184	1177	1353	Region	Note=Mediates targeting and association with DCVs;Ontology_term=ECO:0000250;evidence=ECO:0000250
Q9ULU8	1212	1223	458	1353	Alternative sequence	ID=VSP_016802;Note=In isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q9ULU8	1212	1223	1	1353	Chain	ID=PRO_0000053864;Note=Calcium-dependent secretion activator 1
Q9ULU8	1212	1223	1177	1353	Region	Note=Mediates targeting and association with DCVs;Ontology_term=ECO:0000250;evidence=ECO:0000250
Q9ULU8	1223	1259	458	1353	Alternative sequence	ID=VSP_016802;Note=In isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q9ULU8	1223	1259	1	1353	Chain	ID=PRO_0000053864;Note=Calcium-dependent secretion activator 1
Q9ULU8	1223	1259	1177	1353	Region	Note=Mediates targeting and association with DCVs;Ontology_term=ECO:0000250;evidence=ECO:0000250
Q9ULU8	1223	1259	1230	1230	Sequence conflict	Note=A->P;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9ULU8	1223	1259	1237	1237	Sequence conflict	Note=V->G;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9ULU8	1223	1259	1250	1250	Sequence conflict	Note=E->G;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9ULU8	1223	1259	1250	1250	Sequence conflict	Note=E->G;Ontology_term=ECO:0000305;evidence=ECO:0000305

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
Q9ULU8	1009	1057	458	1353	Alternative sequence	ID=VSP_016802;Note=In isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q9ULU8	1009	1057	1009	1058	Alternative sequence	ID=VSP_016807;Note=In isoform 2 and isoform 3. KSLTSNLPNVNLPNVNLPKVPNLPVNIPLGIPQMPTFSAPSWMAAIYDAD->N;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:12659812,ECO:0000303\|PubMed:17974005;Dbxref=PMID:12659812,PMID:17974005
Q9ULU8	1009	1057	1	1353	Chain	ID=PRO_0000053864;Note=Calcium-dependent secretion activator 1
Q9ULU8	1009	1057	931	1111	Domain	Note=MHD1;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00587
Q9ULU8	1009	1057	790	1129	Region	Note=Interaction with DRD2;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15857609;Dbxref=PMID:15857609
Q9ULU8	1159	1184	458	1353	Alternative sequence	ID=VSP_016802;Note=In isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q9ULU8	1159	1184	1159	1159	Alternative sequence	ID=VSP_016808;Note=In isoform 4. E->EFAKMW;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:15489334,ECO:0000303\|PubMed:9289490;Dbxref=PMID:15489334,PMID:9289490
Q9ULU8	1159	1184	1	1353	Chain	ID=PRO_0000053864;Note=Calcium-dependent secretion activator 1
Q9ULU8	1159	1184	1177	1353	Region	Note=Mediates targeting and association with DCVs;Ontology_term=ECO:0000250;evidence=ECO:0000250
Q9ULU8	1212	1223	458	1353	Alternative sequence	ID=VSP_016802;Note=In isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q9ULU8	1212	1223	1	1353	Chain	ID=PRO_0000053864;Note=Calcium-dependent secretion activator 1
Q9ULU8	1212	1223	1177	1353	Region	Note=Mediates targeting and association with DCVs;Ontology_term=ECO:0000250;evidence=ECO:0000250
Q9ULU8	1223	1259	458	1353	Alternative sequence	ID=VSP_016802;Note=In isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:15489334;Dbxref=PMID:15489334
Q9ULU8	1223	1259	1	1353	Chain	ID=PRO_0000053864;Note=Calcium-dependent secretion activator 1
Q9ULU8	1223	1259	1177	1353	Region	Note=Mediates targeting and association with DCVs;Ontology_term=ECO:0000250;evidence=ECO:0000250
Q9ULU8	1223	1259	1230	1230	Sequence conflict	Note=A->P;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9ULU8	1223	1259	1237	1237	Sequence conflict	Note=V->G;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9ULU8	1223	1259	1250	1250	Sequence conflict	Note=E->G;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9ULU8	1223	1259	1250	1250	Sequence conflict	Note=E->G;Ontology_term=ECO:0000305;evidence=ECO:0000305

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SNVs in the skipped exons for CADPS

- 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.

CADPS_READ_exon_skip_385505_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_385492	62431440	62431472	62431455	62431455	Frame_Shift_Del	T	-	p.K1218fs
LIHC	TCGA-DD-A3A0-01	exon_skip_385500	62484837	62484943	62484882	62484882	Frame_Shift_Del	T	-	p.E887fs
LIHC	TCGA-DD-A39Y-01	exon_skip_385505	62499313	62499381	62499321	62499321	Frame_Shift_Del	A	-	p.L881fs
COAD	TCGA-A6-6138-01	exon_skip_385496	62459848	62459995	62459927	62459927	Nonsense_Mutation	G	T	p.S1054X
UCEC	TCGA-AP-A0LM-01	exon_skip_385505	62499313	62499381	62499370	62499370	Nonsense_Mutation	C	A	p.E865*
BRCA	TCGA-A8-A09C-01	exon_skip_385505	62499313	62499381	62499312	62499312	Splice_Site	C	T	e17+1
READ	TCGA-DY-A1DG-01	exon_skip_385505	62499313	62499381	62499312	62499312	Splice_Site	C	T	.
SARC	TCGA-DX-A8BJ-01	exon_skip_385505	62499313	62499381	62499312	62499312	Splice_Site	C	T	e17+1

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

Depth of coverage in three exons	Mutation description
	Sample: TCGA-DY-A1DG-01
	Cancer type: READ
	ESID: exon_skip_385505
	Skipped exon start: 62499313
	Skipped exon end: 62499381
	Mutation start: 62499312
	Mutation end: 62499312
	Mutation type: Splice_Site
	Reference seq: C
	Mutation seq: T
	AAchange: .
exon_skip_385505_READ_TCGA-DY-A1DG-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
LC2AD_LUNG	62423779	62423886	62423850	62423850	Missense_Mutation	A	C	p.F1236V
NBTU110_AUTONOMIC_GANGLIA	62423779	62423886	62423856	62423856	Missense_Mutation	C	T	p.V1234M
HCC1954_BREAST	62423779	62423886	62423864	62423864	Missense_Mutation	T	C	p.D1231G
EN_ENDOMETRIUM	62431440	62431472	62431444	62431444	Missense_Mutation	A	G	p.V1222A
SKGT4_OESOPHAGUS	62452014	62452088	62452064	62452064	Missense_Mutation	C	T	p.E1168K
LS180_LARGE_INTESTINE	62459848	62459995	62459921	62459921	Missense_Mutation	C	T	p.C1135Y
MCF7_BREAST	62459848	62459995	62459976	62459976	Missense_Mutation	C	A	p.V1117F
KYSE50_OESOPHAGUS	62467398	62467544	62467434	62467434	Missense_Mutation	G	A	p.S1046L
HEC59_ENDOMETRIUM	62467398	62467544	62467477	62467477	Missense_Mutation	G	A	p.P1032S
HEC251_ENDOMETRIUM	62467398	62467544	62467516	62467516	Missense_Mutation	T	C	p.N1019D
REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	62484837	62484943	62484842	62484842	Missense_Mutation	C	T	p.A901T
JHH7_LIVER	62498426	62498443	62498428	62498428	Missense_Mutation	G	T	p.A866E
OCILY132_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	62431440	62431472	62431471	62431471	Splice_Site	A	T	p.V1213E
KPNYN_AUTONOMIC_GANGLIA	62452014	62452088	62452014	62452014	Splice_Site	C	A	p.K1184N

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

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 CADPS

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

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RelatedDrugs for CADPS

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
	Q9ULU8	DB11348	Calcium Phosphate	Calcium-dependent secretion activator 1	small molecule	approved
	Q9ULU8	DB11093	Calcium Citrate	Calcium-dependent secretion activator 1	small molecule	approved\|investigational

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RelatedDiseases for CADPS

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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