ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for VAV2

Gene summary

Gene information	Gene symbol	VAV2
	Gene ID	7410
	Gene name	vav guanine nucleotide exchange factor 2
	Synonyms	VAV-2
	Cytomap	9q34.2
	Type of gene	protein-coding
	Description	guanine nucleotide exchange factor VAV2vav 2 guanine nucleotide exchange factorvav 2 oncogene
	Modification date	20180519
	UniProtAcc	P52735
	Context	PubMed: VAV2 [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 VAV2 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 VAV2

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 VAV2

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_508128	9	136627015:136629231:136633563:136633718:136635499:136635623	136633563:136633718	ENSG00000160293.12	ENST00000406606.3
exon_skip_508131	9	136633563:136633718:136634538:136634625:136635499:136635620	136634538:136634625	ENSG00000160293.12	ENST00000371851.1,ENST00000371850.3
exon_skip_508133	9	136633563:136633718:136635499:136635623:136637080:136637168	136635499:136635623	ENSG00000160293.12	ENST00000406606.3
exon_skip_508135	9	136640056:136640173:136641149:136641202:136642510:136642585	136641149:136641202	ENSG00000160293.12	ENST00000371851.1,ENST00000406606.3,ENST00000371850.3
exon_skip_508136	9	136643883:136644011:136645039:136645061:136645815:136645832	136645039:136645061	ENSG00000160293.12	ENST00000371851.1,ENST00000406606.3,ENST00000371850.3
exon_skip_508141	9	136645039:136645061:136645815:136645832:136648624:136648713	136645815:136645832	ENSG00000160293.12	ENST00000371851.1,ENST00000406606.3,ENST00000371850.3
exon_skip_508145	9	136648624:136648713:136649438:136649540:136650897:136651007	136649438:136649540	ENSG00000160293.12	ENST00000371851.1,ENST00000406606.3,ENST00000371850.3
exon_skip_508147	9	136650897:136651007:136652367:136652382:136653475:136653586	136652367:136652382	ENSG00000160293.12	ENST00000371850.3
exon_skip_508154	9	136671202:136671303:136672379:136672448:136674161:136674260	136672379:136672448	ENSG00000160293.12	ENST00000371851.1,ENST00000406606.3,ENST00000371850.3
exon_skip_508155	9	136674161:136674260:136675312:136675327:136677235:136677338	136675312:136675327	ENSG00000160293.12	ENST00000371850.3
exon_skip_508156	9	136674161:136674260:136677235:136677338:136699393:136699462	136677235:136677338	ENSG00000160293.12	ENST00000371851.1,ENST00000406606.3
exon_skip_508159	9	136677235:136677338:136699393:136699462:136726495:136726554	136699393:136699462	ENSG00000160293.12	ENST00000371851.1,ENST00000406606.3,ENST00000371850.3
exon_skip_508160	9	136699393:136699462:136726495:136726554:136804224:136804341	136726495:136726554	ENSG00000160293.12	ENST00000371851.1,ENST00000406606.3,ENST00000371850.3
exon_skip_508163	9	136726495:136726554:136804224:136804341:136857196:136857381	136804224:136804341	ENSG00000160293.12	ENST00000371851.1,ENST00000486113.1,ENST00000371850.3
exon_skip_508164	9	136790972:136791070:136791337:136791449:136792917:136793014	136791337:136791449	ENSG00000160293.12	ENST00000472905.1

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for VAV2

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_508128	9	136627015:136629231:136633563:136633718:136635499:136635623	136633563:136633718	ENSG00000160293.12	ENST00000406606.3
exon_skip_508131	9	136633563:136633718:136634538:136634625:136635499:136635620	136634538:136634625	ENSG00000160293.12	ENST00000371850.3,ENST00000371851.1
exon_skip_508133	9	136633563:136633718:136635499:136635623:136637080:136637168	136635499:136635623	ENSG00000160293.12	ENST00000406606.3
exon_skip_508135	9	136640056:136640173:136641149:136641202:136642510:136642585	136641149:136641202	ENSG00000160293.12	ENST00000406606.3,ENST00000371850.3,ENST00000371851.1
exon_skip_508136	9	136643883:136644011:136645039:136645061:136645815:136645832	136645039:136645061	ENSG00000160293.12	ENST00000406606.3,ENST00000371850.3,ENST00000371851.1
exon_skip_508141	9	136645039:136645061:136645815:136645832:136648624:136648713	136645815:136645832	ENSG00000160293.12	ENST00000406606.3,ENST00000371850.3,ENST00000371851.1
exon_skip_508145	9	136648624:136648713:136649438:136649540:136650897:136651007	136649438:136649540	ENSG00000160293.12	ENST00000406606.3,ENST00000371850.3,ENST00000371851.1
exon_skip_508147	9	136650897:136651007:136652367:136652382:136653475:136653586	136652367:136652382	ENSG00000160293.12	ENST00000371850.3
exon_skip_508154	9	136671202:136671303:136672379:136672448:136674161:136674260	136672379:136672448	ENSG00000160293.12	ENST00000406606.3,ENST00000371850.3,ENST00000371851.1
exon_skip_508155	9	136674161:136674260:136675312:136675327:136677235:136677338	136675312:136675327	ENSG00000160293.12	ENST00000371850.3
exon_skip_508156	9	136674161:136674260:136677235:136677338:136699393:136699462	136677235:136677338	ENSG00000160293.12	ENST00000406606.3,ENST00000371851.1
exon_skip_508159	9	136677235:136677338:136699393:136699462:136726495:136726554	136699393:136699462	ENSG00000160293.12	ENST00000406606.3,ENST00000371850.3,ENST00000371851.1
exon_skip_508160	9	136699393:136699462:136726495:136726554:136804224:136804341	136726495:136726554	ENSG00000160293.12	ENST00000406606.3,ENST00000371850.3,ENST00000371851.1
exon_skip_508163	9	136726495:136726554:136804224:136804341:136857196:136857381	136804224:136804341	ENSG00000160293.12	ENST00000371850.3,ENST00000371851.1,ENST00000486113.1
exon_skip_508167	9	136791337:136791449:136792917:136793014:136804224:136804341	136792917:136793014	ENSG00000160293.12	ENST00000472905.1

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 VAV2

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
ENST00000371850	136641149	136641202	Frame-shift
ENST00000371850	136645039	136645061	Frame-shift
ENST00000371850	136645815	136645832	Frame-shift
ENST00000371850	136726495	136726554	Frame-shift
ENST00000371850	136634538	136634625	In-frame
ENST00000371850	136649438	136649540	In-frame
ENST00000371850	136652367	136652382	In-frame
ENST00000371850	136672379	136672448	In-frame
ENST00000371850	136675312	136675327	In-frame
ENST00000371850	136699393	136699462	In-frame
ENST00000371850	136804224	136804341	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
ENST00000371850	136641149	136641202	Frame-shift
ENST00000371850	136645039	136645061	Frame-shift
ENST00000371850	136645815	136645832	Frame-shift
ENST00000371850	136726495	136726554	Frame-shift
ENST00000371850	136634538	136634625	In-frame
ENST00000371850	136649438	136649540	In-frame
ENST00000371850	136652367	136652382	In-frame
ENST00000371850	136672379	136672448	In-frame
ENST00000371850	136675312	136675327	In-frame
ENST00000371850	136699393	136699462	In-frame
ENST00000371850	136804224	136804341	In-frame

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Infer the effects of exon skipping event on protein functional features for VAV2

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
ENST00000371850	4854	878	136804224	136804341	237	353	68	107
ENST00000371850	4854	878	136699393	136699462	413	481	127	149
ENST00000371850	4854	878	136672379	136672448	699	767	222	245
ENST00000371850	4854	878	136649438	136649540	1565	1666	511	544
ENST00000371850	4854	878	136634538	136634625	2380	2466	782	811

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
ENST00000371850	4854	878	136804224	136804341	237	353	68	107
ENST00000371850	4854	878	136699393	136699462	413	481	127	149
ENST00000371850	4854	878	136672379	136672448	699	767	222	245
ENST00000371850	4854	878	136649438	136649540	1565	1666	511	544
ENST00000371850	4854	878	136634538	136634625	2380	2466	782	811

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 VAV2

- 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-A39Y-01		136635500	136635623	136635539	136635539	Frame_Shift_Del	G	-	p.R760fs
THCA	TCGA-EM-A1CU-01		136635500	136635623	136635556	136635556	Frame_Shift_Del	T	-	p.K754fs
LUAD	TCGA-95-A4VN-01	exon_skip_508163	136804225	136804341	136804229	136804229	Frame_Shift_Del	C	-	p.G106fs

- 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
MOLT3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	136633564	136633718	136633599	136633599	Missense_Mutation	C	T	p.D852N
CH157MN_CENTRAL_NERVOUS_SYSTEM	136633564	136633718	136633602	136633602	Missense_Mutation	C	T	p.G851R
HEC1A_ENDOMETRIUM	136633564	136633718	136633610	136633610	Missense_Mutation	C	T	p.R848H
HEC1_ENDOMETRIUM	136633564	136633718	136633610	136633610	Missense_Mutation	C	T	p.R848H
HEC1B_ENDOMETRIUM	136633564	136633718	136633610	136633610	Missense_Mutation	C	T	p.R848H
CCK81_LARGE_INTESTINE	136633564	136633718	136633695	136633695	Missense_Mutation	T	C	p.T820A
22RV1_PROSTATE	136634539	136634625	136634571	136634571	Missense_Mutation	G	T	p.A801D
SARC9371_BONE	136634539	136634625	136634589	136634589	Missense_Mutation	G	A	p.P795L
NCIH520_LUNG	136635500	136635623	136635517	136635517	Missense_Mutation	G	A	p.A777V
NCIH196_LUNG	136641150	136641202	136641166	136641166	Missense_Mutation	A	C	p.Y668D
SUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	136645040	136645061	136645042	136645042	Missense_Mutation	G	A	p.P587L
CORL32_LUNG	136649439	136649540	136649484	136649484	Missense_Mutation	G	A	p.T530M
RS411_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	136652368	136652382	136652376	136652376	Missense_Mutation	C	T	p.G472R
BICR18_UPPER_AERODIGESTIVE_TRACT	136672380	136672448	136672439	136672439	Missense_Mutation	T	C	p.S226G
JHH7_LIVER	136677236	136677338	136677292	136677292	Missense_Mutation	C	A	p.D166Y
JURKAT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	136677236	136677338	136677300	136677300	Missense_Mutation	G	A	p.P163L
MET2B	136677236	136677338	136677301	136677301	Missense_Mutation	G	A	p.P163S
MN60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	136699394	136699462	136699415	136699415	Missense_Mutation	C	T	p.R143H
SUPHD1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	136699394	136699462	136699424	136699424	Missense_Mutation	T	C	p.D140G
MOLM13_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	136726496	136726554	136726502	136726502	Missense_Mutation	C	T	p.G125E
MDAPCA2B_PROSTATE	136726496	136726554	136726514	136726514	Missense_Mutation	G	A	p.A121V
GP2D_LARGE_INTESTINE	136804225	136804341	136804282	136804282	Missense_Mutation	T	A	p.L88F
GP5D_LARGE_INTESTINE	136804225	136804341	136804282	136804282	Missense_Mutation	T	A	p.L88F
SNU1040_LARGE_INTESTINE	136804225	136804341	136804319	136804319	Missense_Mutation	C	T	p.R76H
COV504_OVARY	136804225	136804341	136804225	136804225	Splice_Site	C	G	p.K107N

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for VAV2

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 VAV2

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for VAV2

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RelatedDrugs for VAV2

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 VAV2

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 VAV2

Exon skipping events across known transcript of Ensembl for VAV2 from UCSC genome browser

Gene isoform structures and expression levels for VAV2

Exon skipping events with PSIs in TCGA for VAV2

Exon skipping events with PSIs in GTEx for VAV2

Open reading frame (ORF) annotation in the exon skipping event for VAV2

Infer the effects of exon skipping event on protein functional features for VAV2

SNVs in the skipped exons for VAV2

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for VAV2

Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for VAV2

Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for VAV2

RelatedDrugs for VAV2

RelatedDiseases for VAV2