ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for SYNJ2

Gene summary

Gene information	Gene symbol	SYNJ2
	Gene ID	8871
	Gene name	synaptojanin 2
	Synonyms	INPP5H
	Cytomap	6q25.3
	Type of gene	protein-coding
	Description	synaptojanin-2inositol phosphate 5'-phosphatase 2inositol polyphosphate-5-phosphatase Hphosphoinositide 5-phosphatasesynaptic inositol 1,4,5-trisphosphate 5-phosphatase 2
	Modification date	20180523
	UniProtAcc	O15056
	Context	PubMed: SYNJ2 [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 SYNJ2 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 SYNJ2

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 SYNJ2

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_455021	6	158438235:158438322:158449787:158450058:158454486:158454712	158449787:158450058	ENSG00000078269.9	ENST00000367121.3,ENST00000367122.2,ENST00000355585.4
exon_skip_455024	6	158454521:158454712:158464347:158464431:158475998:158476060	158464347:158464431	ENSG00000078269.9	ENST00000367121.3,ENST00000367122.2,ENST00000485863.1,ENST00000355585.4,ENST00000449859.2
exon_skip_455025	6	158475998:158476060:158480288:158480385:158483023:158483196	158480288:158480385	ENSG00000078269.9	ENST00000367121.3,ENST00000367122.2,ENST00000355585.4
exon_skip_455028	6	158480288:158480385:158483023:158483196:158484822:158484904	158483023:158483196	ENSG00000078269.9	ENST00000367121.3,ENST00000367122.2,ENST00000355585.4
exon_skip_455030	6	158480288:158480385:158483086:158483196:158484822:158484904	158483086:158483196	ENSG00000078269.9	ENST00000449859.2
exon_skip_455032	6	158485632:158485782:158485857:158486023:158487475:158487667	158485857:158486023	ENSG00000078269.9	ENST00000367121.3,ENST00000367122.2,ENST00000355585.4,ENST00000449859.2
exon_skip_455034	6	158487475:158487667:158489678:158489760:158490564:158490705	158489678:158489760	ENSG00000078269.9	ENST00000367121.3,ENST00000367122.2,ENST00000355585.4
exon_skip_455035	6	158492633:158492826:158495611:158495770:158497657:158497814	158495611:158495770	ENSG00000078269.9	ENST00000367121.3,ENST00000367122.2,ENST00000355585.4
exon_skip_455037	6	158497657:158497814:158499195:158499313:158502140:158502359	158499195:158499313	ENSG00000078269.9	ENST00000367121.3,ENST00000367122.2,ENST00000355585.4
exon_skip_455038	6	158505032:158505206:158507886:158508021:158509691:158509804	158507886:158508021	ENSG00000078269.9	ENST00000367121.3,ENST00000367112.1,ENST00000355585.4
exon_skip_455039	6	158509691:158509804:158510870:158510979:158513957:158514136	158510870:158510979	ENSG00000078269.9	ENST00000367121.3,ENST00000367112.1,ENST00000367122.2,ENST00000355585.4

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for SYNJ2

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_455021	6	158438235:158438322:158449787:158450058:158454486:158454712	158449787:158450058	ENSG00000078269.9	ENST00000367122.2,ENST00000367121.3,ENST00000355585.4
exon_skip_455024	6	158454521:158454712:158464347:158464431:158475998:158476060	158464347:158464431	ENSG00000078269.9	ENST00000367122.2,ENST00000367121.3,ENST00000355585.4,ENST00000449859.2,ENST00000485863.1
exon_skip_455025	6	158475998:158476060:158480288:158480385:158483023:158483196	158480288:158480385	ENSG00000078269.9	ENST00000367122.2,ENST00000367121.3,ENST00000355585.4
exon_skip_455028	6	158480288:158480385:158483023:158483196:158484822:158484904	158483023:158483196	ENSG00000078269.9	ENST00000367122.2,ENST00000367121.3,ENST00000355585.4
exon_skip_455030	6	158480288:158480385:158483086:158483196:158484822:158484904	158483086:158483196	ENSG00000078269.9	ENST00000449859.2
exon_skip_455032	6	158485632:158485782:158485857:158486023:158487475:158487667	158485857:158486023	ENSG00000078269.9	ENST00000367122.2,ENST00000367121.3,ENST00000355585.4,ENST00000449859.2
exon_skip_455034	6	158487475:158487667:158489678:158489760:158490564:158490705	158489678:158489760	ENSG00000078269.9	ENST00000367122.2,ENST00000367121.3,ENST00000355585.4
exon_skip_455037	6	158497657:158497814:158499195:158499313:158502140:158502359	158499195:158499313	ENSG00000078269.9	ENST00000367122.2,ENST00000367121.3,ENST00000355585.4
exon_skip_455038	6	158505032:158505206:158507886:158508021:158509691:158509804	158507886:158508021	ENSG00000078269.9	ENST00000367121.3,ENST00000355585.4,ENST00000367112.1
exon_skip_455039	6	158509691:158509804:158510870:158510979:158513957:158514136	158510870:158510979	ENSG00000078269.9	ENST00000367122.2,ENST00000367121.3,ENST00000355585.4,ENST00000367112.1

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 SYNJ2

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
ENST00000355585	158449787	158450058	Frame-shift
ENST00000355585	158480288	158480385	Frame-shift
ENST00000355585	158483023	158483196	Frame-shift
ENST00000355585	158485857	158486023	Frame-shift
ENST00000355585	158489678	158489760	Frame-shift
ENST00000355585	158499195	158499313	Frame-shift
ENST00000355585	158510870	158510979	Frame-shift
ENST00000355585	158464347	158464431	In-frame
ENST00000355585	158495611	158495770	In-frame
ENST00000355585	158507886	158508021	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
ENST00000355585	158449787	158450058	Frame-shift
ENST00000355585	158480288	158480385	Frame-shift
ENST00000355585	158483023	158483196	Frame-shift
ENST00000355585	158485857	158486023	Frame-shift
ENST00000355585	158489678	158489760	Frame-shift
ENST00000355585	158499195	158499313	Frame-shift
ENST00000355585	158510870	158510979	Frame-shift
ENST00000355585	158464347	158464431	In-frame
ENST00000355585	158507886	158508021	In-frame

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Infer the effects of exon skipping event on protein functional features for SYNJ2

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
ENST00000355585	7395	1496	158464347	158464431	787	870	237	265
ENST00000355585	7395	1496	158495611	158495770	2209	2367	711	764
ENST00000355585	7395	1496	158507886	158508021	3284	3418	1069	1114

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
ENST00000355585	7395	1496	158464347	158464431	787	870	237	265
ENST00000355585	7395	1496	158507886	158508021	3284	3418	1069	1114

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
O15056	237	265	1	1496	Chain	ID=PRO_0000209733;Note=Synaptojanin-2
O15056	237	265	120	444	Domain	Note=SAC;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00183
O15056	711	764	1	1496	Chain	ID=PRO_0000209733;Note=Synaptojanin-2
O15056	1069	1114	1070	1114	Alternative sequence	ID=VSP_012911;Note=In isoform 2B1. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
O15056	1069	1114	1	1496	Chain	ID=PRO_0000209733;Note=Synaptojanin-2
O15056	1069	1114	1099	1114	Compositional bias	Note=Pro-rich

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
O15056	237	265	1	1496	Chain	ID=PRO_0000209733;Note=Synaptojanin-2
O15056	237	265	120	444	Domain	Note=SAC;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00183
O15056	1069	1114	1070	1114	Alternative sequence	ID=VSP_012911;Note=In isoform 2B1. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
O15056	1069	1114	1	1496	Chain	ID=PRO_0000209733;Note=Synaptojanin-2
O15056	1069	1114	1099	1114	Compositional bias	Note=Pro-rich

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SNVs in the skipped exons for SYNJ2

- 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	exon_skip_455034	158489679	158489760	158489710	158489710	Frame_Shift_Del	G	-	p.V583fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_455034	158489679	158489760	158489741	158489741	Frame_Shift_Del	G	-	p.G594fs
LIHC	TCGA-DD-A1EG-01	exon_skip_455035	158495612	158495770	158495622	158495622	Frame_Shift_Del	T	-	p.V715fs
HNSC	TCGA-CN-5369-01	exon_skip_455038	158507887	158508021	158508009	158508009	Frame_Shift_Del	C	-	p.P1114fs
STAD	TCGA-R5-A7ZI-01	exon_skip_455038	158507887	158508021	158508009	158508009	Frame_Shift_Del	C	-	p.P1114fs
UCEC	TCGA-B5-A0K9-01	exon_skip_455038	158507887	158508021	158508009	158508009	Frame_Shift_Del	C	-	p.P1111fs
UCEC	TCGA-D1-A176-01	exon_skip_455038	158507887	158508021	158508009	158508009	Frame_Shift_Del	C	-	p.P1111fs
LIHC	TCGA-BC-A112-01	exon_skip_455035	158495612	158495770	158495766	158495767	Frame_Shift_Ins	-	A	p.E763fs
LIHC	TCGA-BC-A112-01	exon_skip_455037	158499196	158499313	158499203	158499204	Frame_Shift_Ins	-	C	p.Q820fs
CESC	TCGA-EA-A410-01	exon_skip_455038	158507887	158508021	158508008	158508009	Frame_Shift_Ins	-	C	p.P1113fs
ESCA	TCGA-L5-A8NM-01	exon_skip_455038	158507887	158508021	158508008	158508009	Frame_Shift_Ins	-	C	p.P1113fs
ESCA	TCGA-L5-A8NM-01	exon_skip_455038	158507887	158508021	158508008	158508009	Frame_Shift_Ins	-	C	p.SP1110fs
UCEC	TCGA-B5-A11I-01	exon_skip_455038	158507887	158508021	158508008	158508009	Frame_Shift_Ins	-	C	p.R1110fs
UCEC	TCGA-BG-A0MQ-01	exon_skip_455038	158507887	158508021	158508008	158508009	Frame_Shift_Ins	-	C	p.R1110fs
UCEC	TCGA-D1-A17U-01	exon_skip_455038	158507887	158508021	158508008	158508009	Frame_Shift_Ins	-	C	p.R1110fs
STAD	TCGA-BR-8081-01	exon_skip_455038	158507887	158508021	158508009	158508010	Frame_Shift_Ins	-	C	p.R1110fs
STAD	TCGA-BR-8361-01	exon_skip_455038	158507887	158508021	158508009	158508010	Frame_Shift_Ins	-	C	p.R1110fs
STAD	TCGA-CG-5726-01	exon_skip_455038	158507887	158508021	158508009	158508010	Frame_Shift_Ins	-	C	p.R1110fs
SKCM	TCGA-FR-A3YO-06	exon_skip_455021	158449788	158450058	158450041	158450041	Nonsense_Mutation	G	A	p.W156*
SKCM	TCGA-FR-A3YO-06	exon_skip_455021	158449788	158450058	158450041	158450041	Nonsense_Mutation	G	A	p.W156X
HNSC	TCGA-H7-8501-01	exon_skip_455039	158510871	158510979	158510943	158510943	Nonsense_Mutation	G	T	p.E1177*

- 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
SNU1076_UPPER_AERODIGESTIVE_TRACT	158495612	158495770	158495621	158495622	Frame_Shift_Ins	-	T	p.V715fs
LNZTA3WT4_CENTRAL_NERVOUS_SYSTEM	158449788	158450058	158450006	158450006	Missense_Mutation	C	T	p.R145C
LNZ308_CENTRAL_NERVOUS_SYSTEM	158449788	158450058	158450006	158450006	Missense_Mutation	C	T	p.R145C
CALU1_LUNG	158449788	158450058	158450010	158450010	Missense_Mutation	C	T	p.T146M
NCIH2023_LUNG	158464348	158464431	158464366	158464366	Missense_Mutation	G	A	p.G244R
SBC5_LUNG	158480289	158480385	158480344	158480344	Missense_Mutation	G	A	p.G305R
A4FUK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	158483024	158483196	158483046	158483046	Missense_Mutation	A	G	p.H326R
RS5_FIBROBLAST	158483024	158483196	158483058	158483058	Missense_Mutation	C	T	p.T330M
HS944T_SKIN	158483087	158483196	158483153	158483153	Missense_Mutation	G	A	p.E362K
HS944T_SKIN	158483024	158483196	158483153	158483153	Missense_Mutation	G	A	p.E362K
ISTMES2_PLEURA	158485858	158486023	158485910	158485910	Missense_Mutation	A	G	p.N471S
NCIH2073_LUNG	158485858	158486023	158485918	158485918	Missense_Mutation	G	T	p.D474Y
NCIH1993_LUNG	158485858	158486023	158485918	158485918	Missense_Mutation	G	T	p.D474Y
EW1_BONE	158485858	158486023	158486015	158486015	Missense_Mutation	C	T	p.A506V
NCIH1436_LUNG	158489679	158489760	158489717	158489717	Missense_Mutation	G	C	p.E586Q
HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	158489679	158489760	158489753	158489753	Missense_Mutation	A	G	p.N598D
DV90_LUNG	158495612	158495770	158495659	158495659	Missense_Mutation	C	G	p.F727L
RCHACV_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	158495612	158495770	158495666	158495666	Missense_Mutation	C	T	p.R730C
JHUEM7_ENDOMETRIUM	158495612	158495770	158495699	158495699	Missense_Mutation	T	G	p.F741V
DV90_LUNG	158495612	158495770	158495721	158495721	Missense_Mutation	A	C	p.K748T
CA46_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	158499196	158499313	158499208	158499208	Missense_Mutation	A	G	p.N821S
MET2B	158499196	158499313	158499210	158499210	Missense_Mutation	C	T	p.L822F
OVKATE_OVARY	158499196	158499313	158499285	158499285	Missense_Mutation	C	T	p.R847C
SNU520_STOMACH	158499196	158499313	158499307	158499307	Missense_Mutation	A	G	p.D854G
SW48_LARGE_INTESTINE	158507887	158508021	158507893	158507893	Missense_Mutation	C	T	p.A1072V
UACC812_BREAST	158507887	158508021	158507931	158507931	Missense_Mutation	G	A	p.G1085R
LS411N_LARGE_INTESTINE	158507887	158508021	158507985	158507985	Missense_Mutation	C	T	p.R1103W
BHY_UPPER_AERODIGESTIVE_TRACT	158507887	158508021	158508001	158508001	Missense_Mutation	C	A	p.P1108Q
P30OHK_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	158510871	158510979	158510877	158510877	Missense_Mutation	G	A	p.A1155T
TCYIK_CERVIX	158510871	158510979	158510878	158510878	Missense_Mutation	C	T	p.A1155V
59M_OVARY	158510871	158510979	158510907	158510907	Missense_Mutation	G	A	p.V1165I
MFE319_ENDOMETRIUM	158480289	158480385	158480385	158480385	Splice_Site	G	A	p.K318K

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SYNJ2

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
exon_skip_455038	6	158505032:158505206:158507886:158508021:158509691:158509804	158507886:158508021	ENST00000367121.3,ENST00000367112.1,ENST00000355585.4	COAD	rs2296506	chr6:158507981	G/A	3.62e-04
exon_skip_455038	6	158505032:158505206:158507886:158508021:158509691:158509804	158507886:158508021	ENST00000367121.3,ENST00000367112.1,ENST00000355585.4	BRCA	rs2296506	chr6:158507981	G/A	8.93e-05
exon_skip_455038	6	158505032:158505206:158507886:158508021:158509691:158509804	158507886:158508021	ENST00000367121.3,ENST00000367112.1,ENST00000355585.4	LUSC	rs2296506	chr6:158507981	G/A	4.14e-04
exon_skip_455038	6	158505032:158505206:158507886:158508021:158509691:158509804	158507886:158508021	ENST00000367121.3,ENST00000367112.1,ENST00000355585.4	STAD	rs2296506	chr6:158507981	G/A	6.57e-08
exon_skip_455037	6	158497657:158497814:158499195:158499313:158502140:158502359	158499195:158499313	ENST00000367121.3,ENST00000367122.2,ENST00000355585.4	COAD	rs2296507	chr6:158499302	G/T	3.63e-04
exon_skip_455037	6	158497657:158497814:158499195:158499313:158502140:158502359	158499195:158499313	ENST00000367121.3,ENST00000367122.2,ENST00000355585.4	KIRC	rs2296507	chr6:158499302	G/T	1.72e-04
exon_skip_455037	6	158497657:158497814:158499195:158499313:158502140:158502359	158499195:158499313	ENST00000367121.3,ENST00000367122.2,ENST00000355585.4	KIRC	rs2296507	chr6:158499302	G/T	4.77e-04
exon_skip_455037	6	158497657:158497814:158499195:158499313:158502140:158502359	158499195:158499313	ENST00000367121.3,ENST00000367122.2,ENST00000355585.4	LUSC	rs2296507	chr6:158499302	G/T	2.18e-04
exon_skip_455037	6	158497657:158497814:158499195:158499313:158502140:158502359	158499195:158499313	ENST00000367121.3,ENST00000367122.2,ENST00000355585.4	PRAD	rs2296507	chr6:158499302	G/T	1.82e-03
exon_skip_455037	6	158497657:158497814:158499195:158499313:158502140:158502359	158499195:158499313	ENST00000367121.3,ENST00000367122.2,ENST00000355585.4	STAD	rs2296507	chr6:158499302	G/T	3.81e-08

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SYNJ2

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SYNJ2

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RelatedDrugs for SYNJ2

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 SYNJ2

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
SYNJ2	C0086132	Depressive Symptoms	1	PSYGENET
SYNJ2	C1458155	Mammary Neoplasms	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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