ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for ITSN2

Gene summary

Gene information	Gene symbol	ITSN2
	Gene ID	50618
	Gene name	intersectin 2
	Synonyms	PRO2015\|SH3D1B\|SH3P18\|SWA\|SWAP
	Cytomap	2p23.3
	Type of gene	protein-coding
	Description	intersectin-2SH3 domain-containing protein 1BSH3P18-like WASP-associated protein
	Modification date	20180519
	UniProtAcc	Q9NZM3
	Context	PubMed: ITSN2 [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
ITSN2	GO:1903861	positive regulation of dendrite extension	23999003

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Exon skipping events across known transcript of Ensembl for ITSN2 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 ITSN2

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 ITSN2

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_337374	2	24428134:24428166:24429112:24429144:24431105:24431185	24429112:24429144	ENSG00000198399.10	ENST00000449392.1
exon_skip_337375	2	24428134:24428166:24431105:24431188:24431968:24432090	24431105:24431188	ENSG00000198399.10	ENST00000361999.3,ENST00000355123.4,ENST00000479575.1
exon_skip_337377	2	24431105:24431188:24431968:24432090:24432686:24432817	24431968:24432090	ENSG00000198399.10	ENST00000361999.3,ENST00000355123.4,ENST00000479575.1
exon_skip_337378	2	24440775:24440882:24443813:24443935:24468997:24469189	24443813:24443935	ENSG00000198399.10	ENST00000361999.3,ENST00000355123.4
exon_skip_337380	2	24477235:24477300:24480756:24480962:24483974:24484119	24480756:24480962	ENSG00000198399.10	ENST00000406921.3,ENST00000361999.3,ENST00000355123.4
exon_skip_337383	2	24494673:24494810:24498581:24498718:24509080:24509220	24498581:24498718	ENSG00000198399.10	ENST00000361999.3
exon_skip_337384	2	24498581:24498718:24507631:24507712:24509080:24509220	24507631:24507712	ENSG00000198399.10	ENST00000406921.3,ENST00000355123.4
exon_skip_337385	2	24498581:24498718:24509080:24509220:24516556:24516644	24509080:24509220	ENSG00000198399.10	ENST00000361999.3
exon_skip_337388	2	24509191:24509220:24516556:24516644:24518532:24518580	24516556:24516644	ENSG00000198399.10	ENST00000406921.3,ENST00000361999.3,ENST00000355123.4,ENST00000412011.1
exon_skip_337390	2	24521533:24521683:24522777:24523040:24524022:24524108	24522777:24523040	ENSG00000198399.10	ENST00000406921.3,ENST00000361999.3,ENST00000355123.4,ENST00000412011.1
exon_skip_337392	2	24526667:24526731:24531485:24531625:24533152:24533249	24531485:24531625	ENSG00000198399.10	ENST00000406921.3,ENST00000361999.3,ENST00000355123.4
exon_skip_337396	2	24531485:24531625:24531746:24531821:24533152:24533249	24531746:24531821	ENSG00000198399.10	ENST00000412011.1
exon_skip_337398	2	24531485:24531625:24533152:24533249:24533357:24533561	24533152:24533249	ENSG00000198399.10	ENST00000406921.3,ENST00000361999.3,ENST00000355123.4
exon_skip_337401	2	24535080:24535244:24536328:24536392:24538000:24538090	24536328:24536392	ENSG00000198399.10	ENST00000406921.3,ENST00000407704.1,ENST00000443927.1,ENST00000361999.3,ENST00000355123.4,ENST00000412011.1
exon_skip_337406	2	24538000:24538093:24550920:24550984:24583172:24583178	24550920:24550984	ENSG00000198399.10	ENST00000406921.3,ENST00000407704.1,ENST00000361999.3,ENST00000355123.4,ENST00000412011.1
exon_skip_337408	2	24544682:24544749:24549528:24549550:24550920:24550984	24549528:24549550	ENSG00000198399.10	ENST00000443927.1

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for ITSN2

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_337374	2	24428134:24428166:24429112:24429144:24431105:24431185	24429112:24429144	ENSG00000198399.10	ENST00000449392.1
exon_skip_337375	2	24428134:24428166:24431105:24431188:24431968:24432090	24431105:24431188	ENSG00000198399.10	ENST00000361999.3,ENST00000355123.4,ENST00000479575.1
exon_skip_337377	2	24431105:24431188:24431968:24432090:24432686:24432817	24431968:24432090	ENSG00000198399.10	ENST00000361999.3,ENST00000355123.4,ENST00000479575.1
exon_skip_337378	2	24440775:24440882:24443813:24443935:24468997:24469189	24443813:24443935	ENSG00000198399.10	ENST00000361999.3,ENST00000355123.4
exon_skip_337380	2	24477235:24477300:24480756:24480962:24483974:24484119	24480756:24480962	ENSG00000198399.10	ENST00000361999.3,ENST00000355123.4,ENST00000406921.3
exon_skip_337383	2	24494673:24494810:24498581:24498718:24509080:24509220	24498581:24498718	ENSG00000198399.10	ENST00000361999.3
exon_skip_337384	2	24498581:24498718:24507631:24507712:24509080:24509220	24507631:24507712	ENSG00000198399.10	ENST00000355123.4,ENST00000406921.3
exon_skip_337385	2	24498581:24498718:24509080:24509220:24516556:24516644	24509080:24509220	ENSG00000198399.10	ENST00000361999.3
exon_skip_337388	2	24509191:24509220:24516556:24516644:24518532:24518580	24516556:24516644	ENSG00000198399.10	ENST00000361999.3,ENST00000355123.4,ENST00000406921.3,ENST00000412011.1
exon_skip_337390	2	24521533:24521683:24522777:24523040:24524022:24524108	24522777:24523040	ENSG00000198399.10	ENST00000361999.3,ENST00000355123.4,ENST00000406921.3,ENST00000412011.1
exon_skip_337392	2	24526667:24526731:24531485:24531625:24533152:24533249	24531485:24531625	ENSG00000198399.10	ENST00000361999.3,ENST00000355123.4,ENST00000406921.3
exon_skip_337396	2	24531485:24531625:24531746:24531821:24533152:24533249	24531746:24531821	ENSG00000198399.10	ENST00000412011.1
exon_skip_337398	2	24531485:24531625:24533152:24533249:24533357:24533561	24533152:24533249	ENSG00000198399.10	ENST00000361999.3,ENST00000355123.4,ENST00000406921.3
exon_skip_337401	2	24535080:24535244:24536328:24536392:24538000:24538090	24536328:24536392	ENSG00000198399.10	ENST00000361999.3,ENST00000355123.4,ENST00000406921.3,ENST00000412011.1,ENST00000443927.1,ENST00000407704.1
exon_skip_337403	2	24538000:24538093:24544682:24544749:24549528:24549550	24544682:24544749	ENSG00000198399.10	ENST00000443927.1
exon_skip_337406	2	24538000:24538093:24550920:24550984:24583172:24583178	24550920:24550984	ENSG00000198399.10	ENST00000361999.3,ENST00000355123.4,ENST00000406921.3,ENST00000412011.1,ENST00000407704.1
exon_skip_337408	2	24544682:24544749:24549528:24549550:24550920:24550984	24549528:24549550	ENSG00000198399.10	ENST00000443927.1

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 ITSN2

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
ENST00000355123	24550920	24550984	3UTR-3CDS
ENST00000355123	24431105	24431188	Frame-shift
ENST00000355123	24431968	24432090	Frame-shift
ENST00000355123	24443813	24443935	Frame-shift
ENST00000355123	24480756	24480962	Frame-shift
ENST00000355123	24516556	24516644	Frame-shift
ENST00000355123	24522777	24523040	Frame-shift
ENST00000355123	24531485	24531625	Frame-shift
ENST00000355123	24533152	24533249	Frame-shift
ENST00000355123	24536328	24536392	Frame-shift
ENST00000355123	24507631	24507712	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
ENST00000355123	24550920	24550984	3UTR-3CDS
ENST00000355123	24431105	24431188	Frame-shift
ENST00000355123	24431968	24432090	Frame-shift
ENST00000355123	24443813	24443935	Frame-shift
ENST00000355123	24480756	24480962	Frame-shift
ENST00000355123	24516556	24516644	Frame-shift
ENST00000355123	24522777	24523040	Frame-shift
ENST00000355123	24531485	24531625	Frame-shift
ENST00000355123	24533152	24533249	Frame-shift
ENST00000355123	24536328	24536392	Frame-shift
ENST00000355123	24507631	24507712	In-frame

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Infer the effects of exon skipping event on protein functional features for ITSN2

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
ENST00000355123	6317	1697	24507631	24507712	2308	2388	621	648

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
ENST00000355123	6317	1697	24507631	24507712	2308	2388	621	648

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
Q9NZM3	621	648	622	648	Alternative sequence	ID=VSP_003892;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:10574462,ECO:0000303\|PubMed:14702039,ECO:0000303\|Ref.2;Dbxref=PMID:10574462,PMID:14702039
Q9NZM3	621	648	1	1697	Chain	ID=PRO_0000080961;Note=Intersectin-2
Q9NZM3	621	648	361	756	Coiled coil	Ontology_term=ECO:0000255;evidence=ECO:0000255

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
Q9NZM3	621	648	622	648	Alternative sequence	ID=VSP_003892;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:10574462,ECO:0000303\|PubMed:14702039,ECO:0000303\|Ref.2;Dbxref=PMID:10574462,PMID:14702039
Q9NZM3	621	648	1	1697	Chain	ID=PRO_0000080961;Note=Intersectin-2
Q9NZM3	621	648	361	756	Coiled coil	Ontology_term=ECO:0000255;evidence=ECO:0000255

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SNVs in the skipped exons for ITSN2

- 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-DD-A3A0-01	exon_skip_337380	24480757	24480962	24480920	24480920	Frame_Shift_Del	A	-	p.W909fs
LIHC	TCGA-DD-A1EG-01	exon_skip_337383	24498582	24498718	24498606	24498606	Frame_Shift_Del	T	-	p.K687fs
LIHC	TCGA-DD-A39Y-01	exon_skip_337383	24498582	24498718	24498606	24498606	Frame_Shift_Del	T	-	p.K687fs
LIHC	TCGA-DD-A1EG-01	exon_skip_337383	24498582	24498718	24498670	24498670	Frame_Shift_Del	A	-	p.Y665fs
LIHC	TCGA-DD-A3A0-01	exon_skip_337383	24498582	24498718	24498693	24498693	Frame_Shift_Del	T	-	p.Q658fs
LIHC	TCGA-DD-A1EG-01	exon_skip_337385	24509081	24509220	24509192	24509192	Frame_Shift_Del	T	-	p.K584fs
LIHC	TCGA-DD-A39Y-01	exon_skip_337385	24509081	24509220	24509192	24509192	Frame_Shift_Del	T	-	p.K584fs
LIHC	TCGA-DD-A3A0-01	exon_skip_337388	24516557	24516644	24516590	24516590	Frame_Shift_Del	T	-	p.R564fs
LIHC	TCGA-DD-A39Y-01	exon_skip_337390	24522778	24523040	24522850	24522850	Frame_Shift_Del	T	-	p.K424fs
LIHC	TCGA-DD-A1EG-01	exon_skip_337392	24531486	24531625	24531497	24531497	Frame_Shift_Del	C	-	p.G261fs
HNSC	TCGA-CV-6954-01	exon_skip_337383	24498582	24498718	24498605	24498606	Frame_Shift_Ins	-	T	p.K686fs
STAD	TCGA-F1-6177-01	exon_skip_337385	24509081	24509220	24509095	24509096	Frame_Shift_Ins	-	A	p.F616fs
STAD	TCGA-F1-6177-01	exon_skip_337385	24509081	24509220	24509095	24509096	Frame_Shift_Ins	-	A	p.N617_N618delinsX
STAD	TCGA-F1-6177-01	exon_skip_337385	24509081	24509220	24509096	24509097	Frame_Shift_Ins	-	A	p.F616fs
HNSC	TCGA-P3-A5Q5-01	exon_skip_337377	24431969	24432090	24432036	24432036	Nonsense_Mutation	C	A	p.E1510*
LUAD	TCGA-55-6971-01	exon_skip_337383	24498582	24498718	24498701	24498701	Nonsense_Mutation	G	T	p.Y654*
READ	TCGA-AG-A002-01	exon_skip_337383	24498582	24498718	24498709	24498709	Nonsense_Mutation	C	A	p.E652X
UCEC	TCGA-AP-A056-01	exon_skip_337385	24509081	24509220	24509131	24509131	Nonsense_Mutation	C	A	p.E605*
UCEC	TCGA-D1-A16X-01	exon_skip_337385	24509081	24509220	24509155	24509155	Nonsense_Mutation	C	A	p.E597*
UCS	TCGA-ND-A4WC-01	exon_skip_337385	24509081	24509220	24509172	24509172	Nonsense_Mutation	A	C	p.L591*
COAD	TCGA-G4-6588-01	exon_skip_337390	24522778	24523040	24522816	24522816	Nonsense_Mutation	G	A	p.R436X
BLCA	TCGA-ZF-A9R5-01	exon_skip_337390	24522778	24523040	24522981	24522981	Nonsense_Mutation	G	A	p.R381*
PAAD	TCGA-IB-7651-01	exon_skip_337398	24533153	24533249	24533163	24533163	Nonsense_Mutation	C	A	p.G215*
PAAD	TCGA-IB-7651-01	exon_skip_337398	24533153	24533249	24533163	24533163	Nonsense_Mutation	C	A	p.G215X
LUAD	TCGA-55-7907-01	exon_skip_337388	24516557	24516644	24516556	24516556	Splice_Site	C	G	p.D575_splice

- 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
SNU719_STOMACH	24443814	24443935	24443872	24443873	Frame_Shift_Del	AT	-	p.I1214fs
MFE319_ENDOMETRIUM	24498582	24498718	24498606	24498606	Frame_Shift_Del	T	-	p.K687fs
MAC2A_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	24516557	24516644	24516618	24516621	Frame_Shift_Del	CAGA	-	p.YL553fs
639V_URINARY_TRACT	24509081	24509220	24509191	24509192	Frame_Shift_Ins	-	T	p.S585fs
SNU407_LARGE_INTESTINE	24431969	24432090	24432057	24432057	Missense_Mutation	G	A	p.P1503S
CW2_LARGE_INTESTINE	24443814	24443935	24443843	24443843	Missense_Mutation	A	G	p.Y1224H
NAMALWA_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	24443814	24443935	24443887	24443887	Missense_Mutation	T	C	p.K1209R
SNU520_STOMACH	24480757	24480962	24480840	24480840	Missense_Mutation	C	A	p.W935C
HEC251_ENDOMETRIUM	24498582	24498718	24498605	24498605	Missense_Mutation	C	A	p.K686N
MTA_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	24498582	24498718	24498633	24498633	Missense_Mutation	C	A	p.R677M
NMCG1_CENTRAL_NERVOUS_SYSTEM	24498582	24498718	24498633	24498633	Missense_Mutation	C	A	p.R677M
SYO1_SOFT_TISSUE	24498582	24498718	24498633	24498633	Missense_Mutation	C	A	p.R677M
JHUEM7_ENDOMETRIUM	24498582	24498718	24498660	24498660	Missense_Mutation	T	A	p.K668I
BICR18_UPPER_AERODIGESTIVE_TRACT	24509081	24509220	24509187	24509187	Missense_Mutation	A	G	p.L586S
MET2B	24509081	24509220	24509190	24509190	Missense_Mutation	G	A	p.S585L
BICR18_UPPER_AERODIGESTIVE_TRACT	24509081	24509220	24509212	24509212	Missense_Mutation	C	T	p.V578I
BICR18_UPPER_AERODIGESTIVE_TRACT	24516557	24516644	24516572	24516572	Missense_Mutation	A	G	p.F570L
HCC2998_LARGE_INTESTINE	24516557	24516644	24516631	24516631	Missense_Mutation	T	G	p.K550T
FTC238_THYROID	24522778	24523040	24522789	24522789	Missense_Mutation	C	T	p.E445K
JK1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	24522778	24523040	24522803	24522803	Missense_Mutation	C	G	p.R440T
ISHIKAWAHERAKLIO02ER_ENDOMETRIUM	24522778	24523040	24522846	24522846	Missense_Mutation	A	C	p.L426V
NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	24522778	24523040	24522849	24522849	Missense_Mutation	G	A	p.R425C
HCT15_LARGE_INTESTINE	24522778	24523040	24522885	24522885	Missense_Mutation	C	T	p.E413K
SKES1_BONE	24522778	24523040	24522933	24522933	Missense_Mutation	C	A	p.A397S
22RV1_PROSTATE	24531486	24531625	24531533	24531533	Missense_Mutation	C	T	p.R249Q
HT115_LARGE_INTESTINE	24531486	24531625	24531533	24531533	Missense_Mutation	C	T	p.R249Q
DU145_PROSTATE	24531486	24531625	24531609	24531609	Missense_Mutation	C	A	p.A224S
VMRCRCW_KIDNEY	24536329	24536392	24536366	24536366	Missense_Mutation	G	T	p.Q51K
JMSU1_URINARY_TRACT	24550921	24550984	24550927	24550927	Missense_Mutation	T	C	p.M9V
LS411N_LARGE_INTESTINE	24550921	24550984	24550948	24550948	Missense_Mutation	T	A	p.M2L
UMUC14_URINARY_TRACT	24443814	24443935	24443828	24443828	Nonsense_Mutation	G	A	p.Q1229*
CAMA1_BREAST	24536329	24536392	24536362	24536362	Nonsense_Mutation	G	C	p.S52*
MOLT3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	24498582	24498718	24498583	24498583	Splice_Site	T	C	p.R694G
MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	24498582	24498718	24498583	24498583	Splice_Site	T	C	p.R694G

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for ITSN2

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 ITSN2

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for ITSN2

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RelatedDrugs for ITSN2

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 ITSN2

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
ITSN2	C0027643	Neoplasm Recurrence, Local	1	CTD_human
ITSN2	C1458155	Mammary Neoplasms	1	CTD_human
ITSN2	C1527336	Sjogren's Syndrome	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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