ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for RIMS2

Gene summary

Gene information	Gene symbol	RIMS2
	Gene ID	9699
	Gene name	regulating synaptic membrane exocytosis 2
	Synonyms	OBOE\|RAB3IP3\|RIM2
	Cytomap	8q22.3
	Type of gene	protein-coding
	Description	regulating synaptic membrane exocytosis protein 2RAB3 interacting protein 3Rab3-interacting proteinnon-small cell lung cancer RimL3a proteinnon-small cell lung cancer RimL3c proteinnuclear proteinrab-3-interacting molecule 2rab-3-interacting protei
	Modification date	20180523
	UniProtAcc	Q9UQ26
	Context	PubMed: RIMS2 [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
RIMS2	GO:1903861	positive regulation of dendrite extension	23999003

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Exon skipping events across known transcript of Ensembl for RIMS2 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 RIMS2

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 RIMS2

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_485425	8	104897525:104898451:104922361:104922429:104924280:104924400	104922361:104922429	ENSG00000176406.16	ENST00000515551.1,ENST00000507740.1,ENST00000504942.2,ENST00000436393.2,ENST00000408894.2,ENST00000406091.3
exon_skip_485426	8	104897525:104898451:104922548:104922757:104924280:104924400	104922548:104922757	ENSG00000176406.16	ENST00000262231.10
exon_skip_485428	8	104924359:104924400:104927722:104927822:104928641:104928765	104927722:104927822	ENSG00000176406.16	ENST00000262231.10,ENST00000515551.1,ENST00000507677.1,ENST00000507740.1,ENST00000504942.2,ENST00000436393.2,ENST00000408894.2,ENST00000406091.3
exon_skip_485429	8	104933899:104934012:104940069:104940117:104943490:104943621	104940069:104940117	ENSG00000176406.16	ENST00000504942.2,ENST00000436393.2,ENST00000406091.3
exon_skip_485430	8	105001532:105001649:105010412:105010478:105025669:105025849	105010412:105010478	ENSG00000176406.16	ENST00000507740.1,ENST00000408894.2
exon_skip_485431	8	105001532:105001649:105010412:105010478:105026733:105026843	105010412:105010478	ENSG00000176406.16	ENST00000436393.2
exon_skip_485432	8	105001532:105001649:105025669:105025849:105026733:105026843	105025669:105025849	ENSG00000176406.16	ENST00000262231.10,ENST00000504942.2,ENST00000406091.3
exon_skip_485433	8	105010412:105010478:105025669:105025849:105026733:105026843	105025669:105025849	ENSG00000176406.16	ENST00000507740.1,ENST00000408894.2
exon_skip_485435	8	105026733:105026843:105027651:105027684:105053553:105053586	105027651:105027684	ENSG00000176406.16	ENST00000436393.2
exon_skip_485436	8	105026733:105026843:105027651:105027684:105053556:105053586	105027651:105027684	ENSG00000176406.16	ENST00000408894.2
exon_skip_485446	8	105027651:105027684:105053553:105053586:105080739:105080840	105053553:105053586	ENSG00000176406.16	ENST00000436393.2
exon_skip_485447	8	105027651:105027684:105053556:105053586:105080739:105080840	105053556:105053586	ENSG00000176406.16	ENST00000408894.2
exon_skip_485450	8	105105817:105105871:105106705:105106957:105160834:105161076	105106705:105106957	ENSG00000176406.16	ENST00000436393.2
exon_skip_485451	8	105105698:105105871:105160834:105161076:105257143:105257285	105160834:105161076	ENSG00000176406.16	ENST00000408894.2

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for RIMS2

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_485425	8	104897525:104898451:104922361:104922429:104924280:104924400	104922361:104922429	ENSG00000176406.16	ENST00000504942.2,ENST00000406091.3,ENST00000515551.1,ENST00000507740.1,ENST00000408894.2,ENST00000436393.2
exon_skip_485426	8	104897525:104898451:104922548:104922757:104924280:104924400	104922548:104922757	ENSG00000176406.16	ENST00000262231.10
exon_skip_485428	8	104924359:104924400:104927722:104927822:104928641:104928765	104927722:104927822	ENSG00000176406.16	ENST00000504942.2,ENST00000406091.3,ENST00000515551.1,ENST00000262231.10,ENST00000507740.1,ENST00000408894.2,ENST00000436393.2,ENST00000507677.1
exon_skip_485429	8	104933899:104934012:104940069:104940117:104943490:104943621	104940069:104940117	ENSG00000176406.16	ENST00000504942.2,ENST00000406091.3,ENST00000436393.2
exon_skip_485430	8	105001532:105001649:105010412:105010478:105025669:105025849	105010412:105010478	ENSG00000176406.16	ENST00000507740.1,ENST00000408894.2
exon_skip_485431	8	105001532:105001649:105010412:105010478:105026733:105026843	105010412:105010478	ENSG00000176406.16	ENST00000436393.2
exon_skip_485432	8	105001532:105001649:105025669:105025849:105026733:105026843	105025669:105025849	ENSG00000176406.16	ENST00000504942.2,ENST00000406091.3,ENST00000262231.10
exon_skip_485433	8	105010412:105010478:105025669:105025849:105026733:105026843	105025669:105025849	ENSG00000176406.16	ENST00000507740.1,ENST00000408894.2
exon_skip_485435	8	105026733:105026843:105027651:105027684:105053553:105053586	105027651:105027684	ENSG00000176406.16	ENST00000436393.2
exon_skip_485436	8	105026733:105026843:105027651:105027684:105053556:105053586	105027651:105027684	ENSG00000176406.16	ENST00000408894.2
exon_skip_485446	8	105027651:105027684:105053553:105053586:105080739:105080840	105053553:105053586	ENSG00000176406.16	ENST00000436393.2
exon_skip_485447	8	105027651:105027684:105053556:105053586:105080739:105080840	105053556:105053586	ENSG00000176406.16	ENST00000408894.2
exon_skip_485450	8	105105817:105105871:105106705:105106957:105160834:105161076	105106705:105106957	ENSG00000176406.16	ENST00000436393.2
exon_skip_485451	8	105105698:105105871:105160834:105161076:105257143:105257285	105160834:105161076	ENSG00000176406.16	ENST00000408894.2

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 RIMS2

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
ENST00000262231	104922548	104922757	Frame-shift
ENST00000262231	104927722	104927822	Frame-shift
ENST00000262231	105025669	105025849	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
ENST00000262231	104922548	104922757	Frame-shift
ENST00000262231	104927722	104927822	Frame-shift
ENST00000262231	105025669	105025849	In-frame

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Infer the effects of exon skipping event on protein functional features for RIMS2

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
ENST00000262231	3871	1411	105025669	105025849	2810	2989	854	913

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
ENST00000262231	3871	1411	105025669	105025849	2810	2989	854	913

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
Q9UQ26	854	913	1	1126	Alternative sequence	ID=VSP_040864;Note=In isoform 7. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9UQ26	854	913	802	1411	Alternative sequence	ID=VSP_040871;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.6
Q9UQ26	854	913	825	1411	Alternative sequence	ID=VSP_040870;Note=In isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.6
Q9UQ26	854	913	854	857	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1V27
Q9UQ26	854	913	890	898	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1V27
Q9UQ26	854	913	900	903	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1V27
Q9UQ26	854	913	910	915	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1V27
Q9UQ26	854	913	1	1411	Chain	ID=PRO_0000190201;Note=Regulating synaptic membrane exocytosis protein 2
Q9UQ26	854	913	807	913	Domain	Note=C2 1;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00041
Q9UQ26	854	913	885	887	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1V27

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
Q9UQ26	854	913	1	1126	Alternative sequence	ID=VSP_040864;Note=In isoform 7. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9UQ26	854	913	802	1411	Alternative sequence	ID=VSP_040871;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.6
Q9UQ26	854	913	825	1411	Alternative sequence	ID=VSP_040870;Note=In isoform 5. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.6
Q9UQ26	854	913	854	857	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1V27
Q9UQ26	854	913	890	898	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1V27
Q9UQ26	854	913	900	903	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1V27
Q9UQ26	854	913	910	915	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1V27
Q9UQ26	854	913	1	1411	Chain	ID=PRO_0000190201;Note=Regulating synaptic membrane exocytosis protein 2
Q9UQ26	854	913	807	913	Domain	Note=C2 1;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU00041
Q9UQ26	854	913	885	887	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1V27

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SNVs in the skipped exons for RIMS2

- 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-A39Z-01	exon_skip_485426	104922549	104922757	104922585	104922585	Frame_Shift_Del	A	-	p.Q362fs
STAD	TCGA-BR-4292-01	exon_skip_485428	104927723	104927822	104927779	104927779	Frame_Shift_Del	A	-	p.V401fs
STAD	TCGA-BR-4292-01	exon_skip_485428	104927723	104927822	104927779	104927779	Frame_Shift_Del	A	-	p.V623fs
STAD	TCGA-BR-6802-01	exon_skip_485428	104927723	104927822	104927779	104927779	Frame_Shift_Del	A	-	p.V401fs
STAD	TCGA-BR-6802-01	exon_skip_485428	104927723	104927822	104927779	104927779	Frame_Shift_Del	A	-	p.V623fs
STAD	TCGA-BR-8487-01	exon_skip_485428	104927723	104927822	104927779	104927779	Frame_Shift_Del	A	-	p.V401fs
STAD	TCGA-BR-8487-01	exon_skip_485428	104927723	104927822	104927779	104927779	Frame_Shift_Del	A	-	p.V623fs
HNSC	TCGA-CN-5373-01	exon_skip_485451	105160835	105161076	105160892	105160892	Frame_Shift_Del	A	-	p.T1068fs
LUAD	TCGA-MN-A4N4-01	exon_skip_485425	104922362	104922429	104922381	104922381	Nonsense_Mutation	G	A	p.W356*
LUSC	TCGA-66-2782-01	exon_skip_485451	105160835	105161076	105161076	105161076	Nonsense_Mutation	G	T	p.E1130_splice
ESCA	TCGA-L5-A88Y-01	exon_skip_485446 exon_skip_485447	105053557	105053586	105053555	105053555	Splice_Site	A	C	p.E863_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
HEC151_ENDOMETRIUM	104927723	104927822	104927779	104927779	Frame_Shift_Del	A	-	p.V401fs
IM95_STOMACH	104927723	104927822	104927779	104927779	Frame_Shift_Del	A	-	p.V401fs
RKO_LARGE_INTESTINE	104927723	104927822	104927779	104927779	Frame_Shift_Del	A	-	p.V401fs
CCK81_LARGE_INTESTINE	104927723	104927822	104927779	104927779	Frame_Shift_Del	A	-	p.V401fs
LOVO_LARGE_INTESTINE	104927723	104927822	104927779	104927779	Frame_Shift_Del	A	-	p.V401fs
SNU1040_LARGE_INTESTINE	104927723	104927822	104927779	104927779	Frame_Shift_Del	A	-	p.V401fs
SAS_UPPER_AERODIGESTIVE_TRACT	105025670	105025849	105025767	105025767	Frame_Shift_Del	G	-	p.E862fs
IGROV1_OVARY	105106706	105106957	105106867	105106867	Frame_Shift_Del	A	-	p.E1019fs
HEC265_ENDOMETRIUM	104927723	104927822	104927733	104927734	Frame_Shift_Ins	-	A	p.GK386fs
HS939T_SKIN	105160835	105161076	105160884	105160892	In_Frame_Del	AACATGACA	-	p.NMT1066del
HEC251_ENDOMETRIUM	104922362	104922429	104922374	104922374	Missense_Mutation	A	C	p.Y324S
NCIH1688_LUNG	104922362	104922429	104922388	104922388	Missense_Mutation	C	A	p.H329N
SF126_CENTRAL_NERVOUS_SYSTEM	104922362	104922429	104922424	104922424	Missense_Mutation	T	A	p.S341T
HEC251_ENDOMETRIUM	104922549	104922757	104922570	104922570	Missense_Mutation	G	T	p.R357I
DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	104922549	104922757	104922588	104922588	Missense_Mutation	C	G	p.A363G
REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	104922549	104922757	104922597	104922597	Missense_Mutation	C	T	p.S366L
DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	104922549	104922757	104922629	104922629	Missense_Mutation	G	A	p.E377K
DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	104922549	104922757	104922642	104922642	Missense_Mutation	T	A	p.F381Y
RKO_LARGE_INTESTINE	104922549	104922757	104922664	104922664	Missense_Mutation	G	T	p.E388D
SW1417_LARGE_INTESTINE	104922549	104922757	104922683	104922683	Missense_Mutation	C	A	p.P395T
NCIH520_LUNG	104927723	104927822	104927740	104927740	Missense_Mutation	G	A	p.M388I
NCIH661_LUNG	104927723	104927822	104927751	104927751	Missense_Mutation	G	A	p.G392D
PANC1_PANCREAS	104927723	104927822	104927795	104927795	Missense_Mutation	G	T	p.A407S
KP1N_PANCREAS	104927723	104927822	104927795	104927795	Missense_Mutation	G	T	p.A407S
KP1NL_PANCREAS	104927723	104927822	104927795	104927795	Missense_Mutation	G	T	p.A407S
SKLU1_LUNG	104927723	104927822	104927796	104927796	Missense_Mutation	C	T	p.A407V
LN18_CENTRAL_NERVOUS_SYSTEM	104927723	104927822	104927798	104927798	Missense_Mutation	G	A	p.D408N
DMS454_LUNG	104927723	104927822	104927802	104927802	Missense_Mutation	C	A	p.T409N
MDST8_LARGE_INTESTINE	104940070	104940117	104940113	104940113	Missense_Mutation	T	C	p.V525A
SW403_LARGE_INTESTINE	105010413	105010478	105010421	105010421	Missense_Mutation	T	A	p.L796H
TMK1_STOMACH	105025670	105025849	105025701	105025701	Missense_Mutation	C	G	p.H840D
S117_SOFT_TISSUE	105025670	105025849	105025721	105025721	Missense_Mutation	A	T	p.E846D
HRT18_LARGE_INTESTINE	105025670	105025849	105025746	105025746	Missense_Mutation	A	T	p.T855S
ESO51_OESOPHAGUS	105025670	105025849	105025752	105025752	Missense_Mutation	C	T	p.R857C
HUPT4_PANCREAS	105025670	105025849	105025755	105025755	Missense_Mutation	T	C	p.S858P
BICR18_UPPER_AERODIGESTIVE_TRACT	105025670	105025849	105025764	105025764	Missense_Mutation	A	T	p.T861S
DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	105025670	105025849	105025764	105025764	Missense_Mutation	A	T	p.T861S
DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	105025670	105025849	105025764	105025764	Missense_Mutation	A	T	p.T861S
S117_SOFT_TISSUE	105025670	105025849	105025764	105025764	Missense_Mutation	A	T	p.T861S
NCIH2110_LUNG	105025670	105025849	105025771	105025771	Missense_Mutation	G	A	p.R863H
MDAMB361_BREAST	105025670	105025849	105025790	105025790	Missense_Mutation	G	A	p.M869I
C75_LARGE_INTESTINE	105025670	105025849	105025809	105025809	Missense_Mutation	A	G	p.M876V
NCIH1793_LUNG	105025670	105025849	105025827	105025827	Missense_Mutation	C	A	p.P882T
MEWO_SKIN	105025670	105025849	105025846	105025846	Missense_Mutation	C	T	p.S888L
MEWO_SKIN	105053554	105053586	105053572	105053572	Missense_Mutation	G	A	p.R869K
MEWO_SKIN	105053557	105053586	105053572	105053572	Missense_Mutation	G	A	p.R869K
NCIH1793_LUNG	105106706	105106957	105106729	105106729	Missense_Mutation	G	T	p.G973V
HT115_LARGE_INTESTINE	105106706	105106957	105106878	105106878	Missense_Mutation	G	T	p.D1023Y
ES8_BONE	105106706	105106957	105106902	105106902	Missense_Mutation	A	G	p.K1031E
LNCAPCLONEFGC_PROSTATE	105160835	105161076	105160853	105160853	Missense_Mutation	G	A	p.M1055I
HCT15_LARGE_INTESTINE	105160835	105161076	105160869	105160869	Missense_Mutation	G	T	p.G1061C
NCIH2342_LUNG	105160835	105161076	105160879	105160879	Missense_Mutation	G	C	p.G1064A
PCM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	105160835	105161076	105160904	105160904	Missense_Mutation	C	G	p.S1072R
NCIH1373_LUNG	105160835	105161076	105160909	105160909	Missense_Mutation	G	T	p.S1074I
HOP92_LUNG	105160835	105161076	105160969	105160969	Missense_Mutation	C	T	p.T1094I
SNU1040_LARGE_INTESTINE	105160835	105161076	105160996	105160997	Missense_Mutation	GC	AA	p.R1103Q
CW2_LARGE_INTESTINE	105160835	105161076	105161023	105161023	Missense_Mutation	C	T	p.A1112V
ANGMCSS_CENTRAL_NERVOUS_SYSTEM	105160835	105161076	105161047	105161047	Missense_Mutation	G	T	p.S1120I
DG75_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	104922549	104922757	104922671	104922671	Nonsense_Mutation	G	T	p.E391*
SNU81_LARGE_INTESTINE	104927723	104927822	104927807	104927807	Nonsense_Mutation	G	T	p.G411*
NCIH345_LUNG	104922549	104922757	104922549	104922549	Splice_Site	G	T	p.G350V
NUGC3_STOMACH	105025670	105025849	105025849	105025849	Splice_Site	G	A	p.R889K
NCIH1930_LUNG	105053554	105053586	105053586	105053586	Splice_Site	G	A	p.G874S
NCIH1930_LUNG	105053557	105053586	105053586	105053586	Splice_Site	G	A	p.G874S

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for RIMS2

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 RIMS2

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for RIMS2

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RelatedDrugs for RIMS2

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 RIMS2

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
RIMS2	C0036341	Schizophrenia	1	PSYGENET
RIMS2	C0149925	Small cell carcinoma of lung	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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