ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for SPTBN2

Gene summary

Gene information	Gene symbol	SPTBN2
	Gene ID	6712
	Gene name	spectrin beta, non-erythrocytic 2
	Synonyms	GTRAP41\|SCA5\|SCAR14
	Cytomap	11q13.2
	Type of gene	protein-coding
	Description	spectrin beta chain, non-erythrocytic 2beta-III spectringlutamate transporter EAAT4-associated protein 41spectrin beta III sigma 2spectrin beta chain, brain 2spectrin, non-erythroid beta chain 2spinocerebellar ataxia 5 protein
	Modification date	20180522
	UniProtAcc	O15020
	Context	PubMed: SPTBN2 [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
SPTBN2	GO:0016192	vesicle-mediated transport	9826670

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Exon skipping events across known transcript of Ensembl for SPTBN2 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 SPTBN2

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 SPTBN2

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_74736	11	66454464:66454638:66454897:66455118:66455338:66455389	66454897:66455118	ENSG00000173898.7	ENST00000529997.1,ENST00000309996.2,ENST00000533211.1
exon_skip_74738	11	66455474:66455550:66455639:66455782:66456123:66456320	66455639:66455782	ENSG00000173898.7	ENST00000529997.1,ENST00000309996.2,ENST00000533211.1,ENST00000532650.1
exon_skip_74740	11	66457509:66457754:66458754:66459129:66460006:66460211	66458754:66459129	ENSG00000173898.7	ENST00000529997.1,ENST00000309996.2,ENST00000533211.1
exon_skip_74741	11	66461242:66461332:66461609:66461834:66463747:66464011	66461609:66461834	ENSG00000173898.7	ENST00000529997.1,ENST00000309996.2,ENST00000533211.1
exon_skip_74746	11	66466876:66467079:66467996:66468753:66469054:66469192	66467996:66468753	ENSG00000173898.7	ENST00000529997.1,ENST00000309996.2,ENST00000533211.1
exon_skip_74751	11	66475611:66475770:66476372:66476490:66478052:66478240	66476372:66476490	ENSG00000173898.7	ENST00000529997.1,ENST00000309996.2,ENST00000533211.1

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for SPTBN2

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_74736	11	66454464:66454638:66454897:66455118:66455338:66455389	66454897:66455118	ENSG00000173898.7	ENST00000533211.1,ENST00000309996.2,ENST00000529997.1
exon_skip_74738	11	66455474:66455550:66455639:66455782:66456123:66456320	66455639:66455782	ENSG00000173898.7	ENST00000533211.1,ENST00000309996.2,ENST00000529997.1,ENST00000532650.1
exon_skip_74740	11	66457509:66457754:66458754:66459129:66460006:66460211	66458754:66459129	ENSG00000173898.7	ENST00000533211.1,ENST00000309996.2,ENST00000529997.1
exon_skip_74746	11	66466876:66467079:66467996:66468753:66469054:66469192	66467996:66468753	ENSG00000173898.7	ENST00000533211.1,ENST00000309996.2,ENST00000529997.1
exon_skip_74751	11	66475611:66475770:66476372:66476490:66478052:66478240	66476372:66476490	ENSG00000173898.7	ENST00000533211.1,ENST00000309996.2,ENST00000529997.1

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 SPTBN2

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
ENST00000309996	66454897	66455118	Frame-shift
ENST00000533211	66454897	66455118	Frame-shift
ENST00000309996	66455639	66455782	Frame-shift
ENST00000533211	66455639	66455782	Frame-shift
ENST00000309996	66467996	66468753	Frame-shift
ENST00000533211	66467996	66468753	Frame-shift
ENST00000309996	66476372	66476490	Frame-shift
ENST00000533211	66476372	66476490	Frame-shift
ENST00000309996	66458754	66459129	In-frame
ENST00000533211	66458754	66459129	In-frame
ENST00000309996	66461609	66461834	In-frame
ENST00000533211	66461609	66461834	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
ENST00000309996	66454897	66455118	Frame-shift
ENST00000533211	66454897	66455118	Frame-shift
ENST00000309996	66455639	66455782	Frame-shift
ENST00000533211	66455639	66455782	Frame-shift
ENST00000309996	66467996	66468753	Frame-shift
ENST00000533211	66467996	66468753	Frame-shift
ENST00000309996	66476372	66476490	Frame-shift
ENST00000533211	66476372	66476490	Frame-shift
ENST00000309996	66458754	66459129	In-frame
ENST00000533211	66458754	66459129	In-frame

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Infer the effects of exon skipping event on protein functional features for SPTBN2

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
ENST00000309996	7883	2390	66461609	66461834	4351	4575	1426	1501
ENST00000533211	8145	2390	66461609	66461834	4611	4835	1426	1501
ENST00000309996	7883	2390	66458754	66459129	5263	5637	1730	1855
ENST00000533211	8145	2390	66458754	66459129	5523	5897	1730	1855

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
ENST00000309996	7883	2390	66458754	66459129	5263	5637	1730	1855
ENST00000533211	8145	2390	66458754	66459129	5523	5897	1730	1855

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
O15020	1426	1501	2	2390	Chain	ID=PRO_0000073463;Note=Spectrin beta chain%2C non-erythrocytic 2
O15020	1426	1501	2	2390	Chain	ID=PRO_0000073463;Note=Spectrin beta chain%2C non-erythrocytic 2
O15020	1426	1501	1384	1485	Repeat	Note=Spectrin 11;Ontology_term=ECO:0000255;evidence=ECO:0000255
O15020	1426	1501	1384	1485	Repeat	Note=Spectrin 11;Ontology_term=ECO:0000255;evidence=ECO:0000255
O15020	1426	1501	1489	1586	Repeat	Note=Spectrin 12;Ontology_term=ECO:0000255;evidence=ECO:0000255
O15020	1426	1501	1489	1586	Repeat	Note=Spectrin 12;Ontology_term=ECO:0000255;evidence=ECO:0000255
O15020	1730	1855	2	2390	Chain	ID=PRO_0000073463;Note=Spectrin beta chain%2C non-erythrocytic 2
O15020	1730	1855	2	2390	Chain	ID=PRO_0000073463;Note=Spectrin beta chain%2C non-erythrocytic 2
O15020	1730	1855	1696	1797	Repeat	Note=Spectrin 14;Ontology_term=ECO:0000255;evidence=ECO:0000255
O15020	1730	1855	1696	1797	Repeat	Note=Spectrin 14;Ontology_term=ECO:0000255;evidence=ECO:0000255
O15020	1730	1855	1801	1904	Repeat	Note=Spectrin 15;Ontology_term=ECO:0000255;evidence=ECO:0000255
O15020	1730	1855	1801	1904	Repeat	Note=Spectrin 15;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
O15020	1730	1855	2	2390	Chain	ID=PRO_0000073463;Note=Spectrin beta chain%2C non-erythrocytic 2
O15020	1730	1855	2	2390	Chain	ID=PRO_0000073463;Note=Spectrin beta chain%2C non-erythrocytic 2
O15020	1730	1855	1696	1797	Repeat	Note=Spectrin 14;Ontology_term=ECO:0000255;evidence=ECO:0000255
O15020	1730	1855	1696	1797	Repeat	Note=Spectrin 14;Ontology_term=ECO:0000255;evidence=ECO:0000255
O15020	1730	1855	1801	1904	Repeat	Note=Spectrin 15;Ontology_term=ECO:0000255;evidence=ECO:0000255
O15020	1730	1855	1801	1904	Repeat	Note=Spectrin 15;Ontology_term=ECO:0000255;evidence=ECO:0000255

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SNVs in the skipped exons for SPTBN2

- 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.

SPTBN2_BRCA_exon_skip_74746_psi_boxplot.png
boxplot

- 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_74736	66454898	66455118	66454998	66454998	Frame_Shift_Del	G	-	p.L2208fs
LIHC	TCGA-DD-A39Y-01	exon_skip_74740	66458755	66459129	66458757	66458757	Frame_Shift_Del	G	-	p.Q1855fs
STAD	TCGA-D7-6818-01	exon_skip_74746	66467997	66468753	66468026	66468026	Frame_Shift_Del	G	-	p.R1182fs
SARC	TCGA-PT-A8TR-01A-11D-A37C-09	exon_skip_74746	66467997	66468753	66468674	66468675	Frame_Shift_Ins	-	TT	p.E965fs
CESC	TCGA-EK-A2RN-01	exon_skip_74741	66461610	66461834	66461714	66461714	Nonsense_Mutation	C	A	p.E1467*
SKCM	TCGA-EE-A2MS-06	exon_skip_74746	66467997	66468753	66468095	66468095	Nonsense_Mutation	G	A	p.R1159*
SKCM	TCGA-EE-A2MS-06	exon_skip_74746	66467997	66468753	66468095	66468095	Nonsense_Mutation	G	A	p.R1159X
UCEC	TCGA-B5-A0JY-01	exon_skip_74746	66467997	66468753	66468401	66468401	Nonsense_Mutation	G	A	p.R1057*
HNSC	TCGA-CV-A45U-01	exon_skip_74746	66467997	66468753	66468476	66468476	Nonsense_Mutation	G	A	p.Q1032*
BRCA	TCGA-A8-A09G-01	exon_skip_74746	66467997	66468753	66468703	66468703	Nonsense_Mutation	G	C	p.S956*

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

Depth of coverage in three exons	Mutation description
	Sample: TCGA-A8-A09G-01
	Cancer type: BRCA
	ESID: exon_skip_74746
	Skipped exon start: 66467997
	Skipped exon end: 66468753
	Mutation start: 66468703
	Mutation end: 66468703
	Mutation type: Nonsense_Mutation
	Reference seq: G
	Mutation seq: C
	AAchange: p.S956*
exon_skip_74746_BRCA_TCGA-A8-A09G-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
OC316_OVARY	66461610	66461834	66461804	66461805	Frame_Shift_Del	TC	-	p.K1437fs
OC314_OVARY	66461610	66461834	66461804	66461805	Frame_Shift_Del	TC	-	p.K1437fs
IGROV1_OVARY	66454898	66455118	66454940	66454940	Missense_Mutation	C	T	p.R2227H
ISHIKAWAHERAKLIO02ER_ENDOMETRIUM	66454898	66455118	66454941	66454941	Missense_Mutation	G	A	p.R2227C
SCH_STOMACH	66454898	66455118	66454973	66454973	Missense_Mutation	G	A	p.S2216F
CTV1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	66454898	66455118	66455084	66455084	Missense_Mutation	C	T	p.R2179Q
MDAMB361_BREAST	66455640	66455782	66455731	66455731	Missense_Mutation	G	A	p.R2095W
REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	66455640	66455782	66455736	66455736	Missense_Mutation	T	C	p.E2093G
REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	66455640	66455782	66455736	66455737	Missense_Mutation	TC	CG	p.E2093R
REH_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	66455640	66455782	66455737	66455737	Missense_Mutation	C	G	p.E2093Q
SW756_CERVIX	66455640	66455782	66455756	66455756	Missense_Mutation	C	G	p.K2086N
NCIH1944_LUNG	66455640	66455782	66455760	66455760	Missense_Mutation	C	T	p.R2085Q
JHH5_LIVER	66455640	66455782	66455773	66455773	Missense_Mutation	G	A	p.R2081W
CTB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	66458755	66459129	66458805	66458805	Missense_Mutation	G	T	p.Q1839K
SNUC2A_LARGE_INTESTINE	66458755	66459129	66458820	66458820	Missense_Mutation	C	T	p.A1834T
SNUC2B_LARGE_INTESTINE	66458755	66459129	66458820	66458820	Missense_Mutation	C	T	p.A1834T
UACC812_BREAST	66458755	66459129	66458863	66458863	Missense_Mutation	G	T	p.H1819Q
IM95_STOMACH	66458755	66459129	66459020	66459020	Missense_Mutation	G	T	p.A1767D
GB1_CENTRAL_NERVOUS_SYSTEM	66458755	66459129	66459027	66459027	Missense_Mutation	C	T	p.G1765S
GP5D_LARGE_INTESTINE	66458755	66459129	66459033	66459033	Missense_Mutation	C	T	p.A1763T
NCIBL128_MATCHED_NORMAL_TISSUE	66461610	66461834	66461633	66461633	Missense_Mutation	G	A	p.H1494Y
HCC202_BREAST	66461610	66461834	66461637	66461637	Missense_Mutation	C	A	p.Q1492H
HCC2998_LARGE_INTESTINE	66461610	66461834	66461651	66461651	Missense_Mutation	G	A	p.R1488C
T47D_BREAST	66461610	66461834	66461675	66461675	Missense_Mutation	G	A	p.R1480C
ES8_BONE	66461610	66461834	66461675	66461675	Missense_Mutation	G	A	p.R1480C
CW2_LARGE_INTESTINE	66461610	66461834	66461704	66461704	Missense_Mutation	A	T	p.F1470Y
HSC39_STOMACH	66467997	66468753	66468001	66468001	Missense_Mutation	C	G	p.S1190T
KPNYS_AUTONOMIC_GANGLIA	66467997	66468753	66468001	66468001	Missense_Mutation	C	G	p.S1190T
SNU520_STOMACH	66467997	66468753	66468008	66468008	Missense_Mutation	G	A	p.L1188F
NCIH1155_LUNG	66467997	66468753	66468011	66468011	Missense_Mutation	C	T	p.V1187M
PEO1_OVARY	66467997	66468753	66468090	66468090	Missense_Mutation	C	T	p.M1160I
MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	66467997	66468753	66468094	66468094	Missense_Mutation	C	T	p.R1159Q
HEC1_ENDOMETRIUM	66467997	66468753	66468130	66468130	Missense_Mutation	A	G	p.L1147P
HS746T_STOMACH	66467997	66468753	66468212	66468212	Missense_Mutation	C	T	p.E1120K
TYKNU_OVARY	66467997	66468753	66468311	66468311	Missense_Mutation	C	G	p.A1087P
NCIH650_LUNG	66467997	66468753	66468322	66468322	Missense_Mutation	C	A	p.R1083L
HARA_LUNG	66467997	66468753	66468326	66468326	Missense_Mutation	C	A	p.G1082C
MDAMB453_BREAST	66467997	66468753	66468373	66468373	Missense_Mutation	C	T	p.R1066Q
HCC70_BREAST	66467997	66468753	66468391	66468391	Missense_Mutation	G	A	p.S1060L
MOLT3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	66467997	66468753	66468434	66468434	Missense_Mutation	C	A	p.G1046C
HMEL_BREAST	66467997	66468753	66468479	66468479	Missense_Mutation	C	T	p.A1031T
JEG3_PLACENTA	66467997	66468753	66468517	66468517	Missense_Mutation	A	T	p.L1018Q
AU565_BREAST	66467997	66468753	66468553	66468553	Missense_Mutation	C	T	p.R1006Q
SKBR3_BREAST	66467997	66468753	66468553	66468553	Missense_Mutation	C	T	p.R1006Q
PACADD137_PANCREAS	66467997	66468753	66468607	66468607	Missense_Mutation	C	T	p.G988D
KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	66467997	66468753	66468632	66468632	Missense_Mutation	C	A	p.V980F
MESSA_SOFT_TISSUE	66467997	66468753	66468710	66468710	Missense_Mutation	G	T	p.L954I
HEC251_ENDOMETRIUM	66467997	66468753	66468742	66468742	Missense_Mutation	A	C	p.F943C
MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	66467997	66468753	66468744	66468744	Missense_Mutation	C	G	p.Q942H
SNU175_LARGE_INTESTINE	66476373	66476490	66476386	66476386	Missense_Mutation	G	A	p.S393L
KM12_LARGE_INTESTINE	66476373	66476490	66476393	66476393	Missense_Mutation	G	A	p.L391F
BC3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	66476373	66476490	66476421	66476421	Missense_Mutation	C	A	p.Q381H
NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	66458755	66459129	66458756	66458757	Splice_Site	-	G	p.Q1855fs

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for SPTBN2

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 SPTBN2

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for SPTBN2

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RelatedDrugs for SPTBN2

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 SPTBN2

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
SPTBN2	C0752123	Spinocerebellar Ataxia Type 5	2	ORPHANET;UNIPROT
SPTBN2	C0036341	Schizophrenia	1	PSYGENET

	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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