ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for NAPA

Gene summary

Gene information	Gene symbol	NAPA
	Gene ID	8775
	Gene name	NSF attachment protein alpha
	Synonyms	SNAPA
	Cytomap	19q13.32-q13.33
	Type of gene	protein-coding
	Description	alpha-soluble NSF attachment proteinN-ethylmaleimide-sensitive factor attachment protein, alphaalpha-SNAP
	Modification date	20180523
	UniProtAcc	P54920
	Context	PubMed: NAPA [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 NAPA 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 NAPA

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 NAPA

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_319959	19	47990898:47991147:47991491:47991646:47992967:47993018	47991491:47991646	ENSG00000105402.3	ENST00000594217.1
exon_skip_319963	19	47991491:47991646:47992967:47993018:47994044:47994113	47992967:47993018	ENSG00000105402.3	ENST00000594217.1,ENST00000595227.1,ENST00000597778.1,ENST00000597271.1,ENST00000263354.3,ENST00000594001.1
exon_skip_319967	19	47993010:47993018:47994044:47994113:47995271:47995301	47994044:47994113	ENSG00000105402.3	ENST00000594217.1,ENST00000595227.1,ENST00000597778.1,ENST00000593905.1,ENST00000263354.3,ENST00000593761.1,ENST00000594001.1
exon_skip_319970	19	47994100:47994113:47995271:47995376:47996217:47996302	47995271:47995376	ENSG00000105402.3	ENST00000595227.1,ENST00000593905.1,ENST00000263354.3,ENST00000593761.1,ENST00000594001.1,ENST00000601208.1
exon_skip_319975	19	47995317:47995376:47996217:47996302:47996375:47996431	47996217:47996302	ENSG00000105402.3	ENST00000595227.1,ENST00000593905.1,ENST00000263354.3,ENST00000593761.1,ENST00000598615.1,ENST00000594001.1,ENST00000601208.1
exon_skip_319980	19	47995317:47995376:47996672:47996750:47998806:47998853	47996672:47996750	ENSG00000105402.3	ENST00000594155.1
exon_skip_319981	19	47996217:47996302:47996375:47996431:47996672:47996750	47996375:47996431	ENSG00000105402.3	ENST00000597118.1,ENST00000595227.1,ENST00000593905.1,ENST00000263354.3,ENST00000593761.1,ENST00000598615.1,ENST00000594001.1,ENST00000601208.1
exon_skip_319982	19	47996375:47996431:47996672:47996750:47998806:47998853	47996672:47996750	ENSG00000105402.3	ENST00000602174.1,ENST00000597118.1,ENST00000595227.1,ENST00000602082.1,ENST00000601927.1,ENST00000597274.1,ENST00000263354.3,ENST00000596892.1,ENST00000593761.1,ENST00000598615.1,ENST00000594001.1,ENST00000601208.1,ENST00000594288.1,ENST00000595826.1
exon_skip_319986	19	47996672:47996750:47998806:47998853:48003889:48004006	47998806:47998853	ENSG00000105402.3	ENST00000602174.1,ENST00000597118.1,ENST00000597274.1,ENST00000594740.1,ENST00000263354.3,ENST00000594155.1,ENST00000593761.1,ENST00000601208.1,ENST00000594288.1,ENST00000595826.1
exon_skip_319987	19	47996672:47996750:47998806:47998853:48006679:48006759	47998806:47998853	ENSG00000105402.3	ENST00000595227.1
exon_skip_319988	19	47996672:47996750:47998806:47998853:48018099:48018202	47998806:47998853	ENSG00000105402.3	ENST00000602082.1,ENST00000594001.1
exon_skip_319993	19	47998806:47998853:48003889:48004006:48006679:48006759	48003889:48004006	ENSG00000105402.3	ENST00000597118.1,ENST00000594740.1,ENST00000263354.3,ENST00000601208.1,ENST00000594288.1,ENST00000595826.1
exon_skip_319995	19	47998806:47998853:48003889:48004006:48018099:48018202	48003889:48004006	ENSG00000105402.3	ENST00000602174.1,ENST00000597274.1
exon_skip_319998	19	47998806:47998853:48006679:48006759:48018099:48018202	48006679:48006759	ENSG00000105402.3	ENST00000595227.1
exon_skip_320005	19	48003889:48004006:48006649:48006759:48018099:48018202	48006649:48006759	ENSG00000105402.3	ENST00000593761.1
exon_skip_320007	19	48003889:48004006:48006679:48006759:48015969:48016023	48006679:48006759	ENSG00000105402.3	ENST00000597118.1,ENST00000594288.1
exon_skip_320009	19	48003889:48004006:48006679:48006759:48018099:48018202	48006679:48006759	ENSG00000105402.3	ENST00000594740.1,ENST00000593785.1
exon_skip_320013	19	48006679:48006759:48008593:48008800:48018099:48018202	48008593:48008800	ENSG00000105402.3	ENST00000601208.1
exon_skip_320017	19	48006679:48006759:48010088:48010231:48018099:48018202	48010088:48010231	ENSG00000105402.3	ENST00000595826.1

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for NAPA

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_319963	19	47991491:47991646:47992967:47993018:47994044:47994113	47992967:47993018	ENSG00000105402.3	ENST00000263354.3,ENST00000597778.1,ENST00000594217.1,ENST00000597271.1,ENST00000595227.1,ENST00000594001.1
exon_skip_319967	19	47993010:47993018:47994044:47994113:47995271:47995301	47994044:47994113	ENSG00000105402.3	ENST00000263354.3,ENST00000597778.1,ENST00000594217.1,ENST00000595227.1,ENST00000594001.1,ENST00000593761.1,ENST00000593905.1
exon_skip_319970	19	47994100:47994113:47995271:47995376:47996217:47996302	47995271:47995376	ENSG00000105402.3	ENST00000263354.3,ENST00000595227.1,ENST00000594001.1,ENST00000593761.1,ENST00000593905.1,ENST00000601208.1
exon_skip_319975	19	47995317:47995376:47996217:47996302:47996375:47996431	47996217:47996302	ENSG00000105402.3	ENST00000263354.3,ENST00000595227.1,ENST00000594001.1,ENST00000593761.1,ENST00000593905.1,ENST00000601208.1,ENST00000598615.1
exon_skip_319980	19	47995317:47995376:47996672:47996750:47998806:47998853	47996672:47996750	ENSG00000105402.3	ENST00000594155.1
exon_skip_319981	19	47996217:47996302:47996375:47996431:47996672:47996750	47996375:47996431	ENSG00000105402.3	ENST00000263354.3,ENST00000595227.1,ENST00000594001.1,ENST00000593761.1,ENST00000593905.1,ENST00000601208.1,ENST00000598615.1,ENST00000597118.1
exon_skip_319982	19	47996375:47996431:47996672:47996750:47998806:47998853	47996672:47996750	ENSG00000105402.3	ENST00000263354.3,ENST00000595227.1,ENST00000594001.1,ENST00000593761.1,ENST00000601208.1,ENST00000598615.1,ENST00000602082.1,ENST00000602174.1,ENST00000595826.1,ENST00000597118.1,ENST00000596892.1,ENST00000594288.1,ENST00000597274.1,ENST00000601927.1
exon_skip_319986	19	47996672:47996750:47998806:47998853:48003889:48004006	47998806:47998853	ENSG00000105402.3	ENST00000263354.3,ENST00000593761.1,ENST00000594155.1,ENST00000601208.1,ENST00000602174.1,ENST00000595826.1,ENST00000597118.1,ENST00000594288.1,ENST00000594740.1,ENST00000597274.1
exon_skip_319987	19	47996672:47996750:47998806:47998853:48006679:48006759	47998806:47998853	ENSG00000105402.3	ENST00000595227.1
exon_skip_319988	19	47996672:47996750:47998806:47998853:48018099:48018202	47998806:47998853	ENSG00000105402.3	ENST00000594001.1,ENST00000602082.1
exon_skip_319993	19	47998806:47998853:48003889:48004006:48006679:48006759	48003889:48004006	ENSG00000105402.3	ENST00000263354.3,ENST00000601208.1,ENST00000595826.1,ENST00000597118.1,ENST00000594288.1,ENST00000594740.1
exon_skip_319995	19	47998806:47998853:48003889:48004006:48018099:48018202	48003889:48004006	ENSG00000105402.3	ENST00000602174.1,ENST00000597274.1
exon_skip_319998	19	47998806:47998853:48006679:48006759:48018099:48018202	48006679:48006759	ENSG00000105402.3	ENST00000595227.1
exon_skip_320005	19	48003889:48004006:48006649:48006759:48018099:48018202	48006649:48006759	ENSG00000105402.3	ENST00000593761.1
exon_skip_320007	19	48003889:48004006:48006679:48006759:48015969:48016023	48006679:48006759	ENSG00000105402.3	ENST00000597118.1,ENST00000594288.1
exon_skip_320009	19	48003889:48004006:48006679:48006759:48018099:48018202	48006679:48006759	ENSG00000105402.3	ENST00000594740.1,ENST00000593785.1
exon_skip_320013	19	48006679:48006759:48008593:48008800:48018099:48018202	48008593:48008800	ENSG00000105402.3	ENST00000601208.1
exon_skip_320017	19	48006679:48006759:48010088:48010231:48018099:48018202	48010088:48010231	ENSG00000105402.3	ENST00000595826.1

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 NAPA

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
ENST00000263354	47996217	47996302	Frame-shift
ENST00000263354	47996375	47996431	Frame-shift
ENST00000263354	47998806	47998853	Frame-shift
ENST00000263354	47992967	47993018	In-frame
ENST00000263354	47994044	47994113	In-frame
ENST00000263354	47995271	47995376	In-frame
ENST00000263354	47996672	47996750	In-frame
ENST00000263354	48003889	48004006	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
ENST00000263354	47996217	47996302	Frame-shift
ENST00000263354	47996375	47996431	Frame-shift
ENST00000263354	47998806	47998853	Frame-shift
ENST00000263354	47992967	47993018	In-frame
ENST00000263354	47994044	47994113	In-frame
ENST00000263354	47995271	47995376	In-frame
ENST00000263354	47996672	47996750	In-frame
ENST00000263354	48003889	48004006	In-frame

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

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
ENST00000263354	1856	295	48003889	48004006	479	595	59	98
ENST00000263354	1856	295	47996672	47996750	643	720	114	140
ENST00000263354	1856	295	47995271	47995376	862	966	187	222
ENST00000263354	1856	295	47994044	47994113	967	1035	222	245
ENST00000263354	1856	295	47992967	47993018	1036	1086	245	262

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
ENST00000263354	1856	295	48003889	48004006	479	595	59	98
ENST00000263354	1856	295	47996672	47996750	643	720	114	140
ENST00000263354	1856	295	47995271	47995376	862	966	187	222
ENST00000263354	1856	295	47994044	47994113	967	1035	222	245
ENST00000263354	1856	295	47992967	47993018	1036	1086	245	262

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
P54920	59	98	1	295	Chain	ID=PRO_0000219056;Note=Alpha-soluble NSF attachment protein
P54920	114	140	1	295	Chain	ID=PRO_0000219056;Note=Alpha-soluble NSF attachment protein
P54920	114	140	122	122	Mutagenesis	Note=Does not affect interaction with GNA12. K->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15980433;Dbxref=PMID:15980433
P54920	114	140	140	140	Mutagenesis	Note=Increases interaction with GNA12. K->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15980433;Dbxref=PMID:15980433
P54920	187	222	1	295	Chain	ID=PRO_0000219056;Note=Alpha-soluble NSF attachment protein
P54920	187	222	195	195	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:24275569;Dbxref=PMID:24275569
P54920	187	222	195	195	Sequence conflict	Note=S->T;Ontology_term=ECO:0000305;evidence=ECO:0000305
P54920	222	245	1	295	Chain	ID=PRO_0000219056;Note=Alpha-soluble NSF attachment protein
P54920	245	262	1	295	Chain	ID=PRO_0000219056;Note=Alpha-soluble NSF attachment 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
P54920	59	98	1	295	Chain	ID=PRO_0000219056;Note=Alpha-soluble NSF attachment protein
P54920	114	140	1	295	Chain	ID=PRO_0000219056;Note=Alpha-soluble NSF attachment protein
P54920	114	140	122	122	Mutagenesis	Note=Does not affect interaction with GNA12. K->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15980433;Dbxref=PMID:15980433
P54920	114	140	140	140	Mutagenesis	Note=Increases interaction with GNA12. K->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:15980433;Dbxref=PMID:15980433
P54920	187	222	1	295	Chain	ID=PRO_0000219056;Note=Alpha-soluble NSF attachment protein
P54920	187	222	195	195	Modified residue	Note=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244\|PubMed:24275569;Dbxref=PMID:24275569
P54920	187	222	195	195	Sequence conflict	Note=S->T;Ontology_term=ECO:0000305;evidence=ECO:0000305
P54920	222	245	1	295	Chain	ID=PRO_0000219056;Note=Alpha-soluble NSF attachment protein
P54920	245	262	1	295	Chain	ID=PRO_0000219056;Note=Alpha-soluble NSF attachment protein

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SNVs in the skipped exons for NAPA

- 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-BC-A112-01	exon_skip_319970	47995272	47995376	47995348	47995349	Frame_Shift_Ins	-	G	p.L197fs
LIHC	TCGA-BC-A112-01	exon_skip_319970	47995272	47995376	47995348	47995349	Frame_Shift_Ins	-	G	p.P197fs
HNSC	TCGA-CV-7097-01	exon_skip_319981	47996376	47996431	47996389	47996390	Frame_Shift_Ins	-	G	p.G154fs
HNSC	TCGA-CV-7097-01	exon_skip_319981	47996376	47996431	47996389	47996390	Frame_Shift_Ins	-	G	p.G155fs
COAD	TCGA-AA-A00J-01	exon_skip_319980 exon_skip_319982	47996673	47996750	47996727	47996728	Frame_Shift_Ins	-	T	p.K122fs
THYM	TCGA-YT-A95G-01	exon_skip_319993 exon_skip_319995	48003890	48004006	48004007	48004007	Splice_Site	C	A	.

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

Depth of coverage in three exons	Mutation description
	Sample: TCGA-YT-A95G-01
	Cancer type: THYM
	ESID: exon_skip_319995
	Skipped exon start: 48003890
	Skipped exon end: 48004006
	Mutation start: 48004007
	Mutation end: 48004007
	Mutation type: Splice_Site
	Reference seq: C
	Mutation seq: A
	AAchange: .
exon_skip_312820_THYM_TCGA-YT-A95G-01.png
exon_skip_312822_THYM_TCGA-YT-A95G-01.png
exon_skip_319993_THYM_TCGA-YT-A95G-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
COLO679_SKIN	47991492	47991646	47991550	47991550	Missense_Mutation	G	A	p.R295C
HCC2998_LARGE_INTESTINE	47991492	47991646	47991634	47991634	Missense_Mutation	C	T	p.D267N
HEC108_ENDOMETRIUM	47992968	47993018	47992988	47992988	Missense_Mutation	C	T	p.V256M
NB1_AUTONOMIC_GANGLIA	47992968	47993018	47992991	47992991	Missense_Mutation	T	A	p.N255Y
NCIH2141_LUNG	47992968	47993018	47992998	47992998	Missense_Mutation	C	G	p.E252D
CHSA0108_BONE	47992968	47993018	47993008	47993008	Missense_Mutation	T	C	p.E249G
DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	47995272	47995376	47995366	47995366	Missense_Mutation	T	C	p.N191S
HCT116_LARGE_INTESTINE	47996218	47996302	47996237	47996237	Missense_Mutation	G	A	p.A181V
CJM_SKIN	47996218	47996302	47996261	47996261	Missense_Mutation	G	A	p.A173V
SW48_LARGE_INTESTINE	48003890	48004006	48003914	48003914	Missense_Mutation	C	T	p.A91T
HEC6_ENDOMETRIUM	48003890	48004006	48003923	48003923	Missense_Mutation	C	T	p.A88T
SNU1040_LARGE_INTESTINE	48003890	48004006	48003944	48003944	Missense_Mutation	C	T	p.A81T
SNU719_STOMACH	48003890	48004006	48003952	48003952	Missense_Mutation	T	C	p.K78R
SNU175_LARGE_INTESTINE	48006680	48006759	48006722	48006722	Missense_Mutation	C	T	p.A46T
SNU175_LARGE_INTESTINE	48006650	48006759	48006722	48006722	Missense_Mutation	C	T	p.A46T
SKNDZ_AUTONOMIC_GANGLIA	48006680	48006759	48006731	48006731	Missense_Mutation	C	T	p.E43K
SKNDZ_AUTONOMIC_GANGLIA	48006650	48006759	48006731	48006731	Missense_Mutation	C	T	p.E43K
MDAMB453_BREAST	47992968	47993018	47993018	47993018	Splice_Site	T	C	p.K246E
SKES1_BONE	47994045	47994113	47994045	47994045	Splice_Site	T	-	p.K246fs
DU145_PROSTATE	47998807	47998853	47998807	47998807	Splice_Site	C	T	p.M114I

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

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 NAPA

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

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RelatedDrugs for NAPA

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 NAPA

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 NAPA

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

Gene isoform structures and expression levels for NAPA

Exon skipping events with PSIs in TCGA for NAPA

Exon skipping events with PSIs in GTEx for NAPA

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

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

SNVs in the skipped exons for NAPA

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

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

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

RelatedDrugs for NAPA

RelatedDiseases for NAPA