ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for RYR3

Gene summary

Gene information	Gene symbol	RYR3
	Gene ID	6263
	Gene name	ryanodine receptor 3
	Synonyms	RYR-3
	Cytomap	15q13.3-q14
	Type of gene	protein-coding
	Description	ryanodine receptor 3brain ryanodine receptor-calcium release channelbrain-type ryanodine receptortype 3 ryanodine receptor
	Modification date	20180523
	UniProtAcc	Q15413
	Context	PubMed: RYR3 [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 RYR3 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 RYR3

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 RYR3

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_120691	15	33873708:33873844:33876595:33876691:33878198:33878317	33876595:33876691	ENSG00000198838.7	ENST00000389232.4,ENST00000415757.3
exon_skip_120692	15	34018586:34018707:34021057:34021227:34023674:34023895	34021057:34021227	ENSG00000198838.7	ENST00000389232.4,ENST00000415757.3
exon_skip_120693	15	34048506:34048574:34049675:34049797:34060858:34060908	34049675:34049797	ENSG00000198838.7	ENST00000389232.4,ENST00000415757.3
exon_skip_120696	15	34049675:34049797:34060858:34060908:34061312:34061373	34060858:34060908	ENSG00000198838.7	ENST00000389232.4,ENST00000415757.3
exon_skip_120698	15	34065734:34065816:34072411:34072542:34077862:34078183	34072411:34072542	ENSG00000198838.7	ENST00000389232.4,ENST00000415757.3
exon_skip_120699	15	34094069:34094162:34099755:34099770:34102679:34102850	34099755:34099770	ENSG00000198838.7	ENST00000389232.4
exon_skip_120702	15	34105667:34105780:34109062:34109159:34110778:34110885	34109062:34109159	ENSG00000198838.7	ENST00000389232.4,ENST00000415757.3
exon_skip_120703	15	34117803:34117877:34118452:34118470:34118872:34118953	34118452:34118470	ENSG00000198838.7	ENST00000389232.4,ENST00000415757.3
exon_skip_120710	15	34127168:34127273:34129106:34129188:34129831:34130727	34129106:34129188	ENSG00000198838.7	ENST00000389232.4,ENST00000415757.3
exon_skip_120713	15	34129106:34129188:34129831:34131159:34133025:34133084	34129831:34131159	ENSG00000198838.7	ENST00000389232.4,ENST00000415757.3
exon_skip_120715	15	34134064:34134236:34135688:34135775:34137062:34137263	34135688:34135775	ENSG00000198838.7	ENST00000389232.4,ENST00000415757.3
exon_skip_120718	15	34146966:34147113:34149980:34150115:34151775:34151932	34149980:34150115	ENSG00000198838.7	ENST00000389232.4,ENST00000415757.3
exon_skip_120719	15	34152795:34152860:34153278:34153379:34156338:34156390	34153278:34153379	ENSG00000198838.7	ENST00000389232.4,ENST00000415757.3

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for RYR3

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_120691	15	33873708:33873844:33876595:33876691:33878198:33878317	33876595:33876691	ENSG00000198838.7	ENST00000415757.3,ENST00000389232.4
exon_skip_120692	15	34018586:34018707:34021057:34021227:34023674:34023895	34021057:34021227	ENSG00000198838.7	ENST00000415757.3,ENST00000389232.4
exon_skip_120693	15	34048506:34048574:34049675:34049797:34060858:34060908	34049675:34049797	ENSG00000198838.7	ENST00000415757.3,ENST00000389232.4
exon_skip_120696	15	34049675:34049797:34060858:34060908:34061312:34061373	34060858:34060908	ENSG00000198838.7	ENST00000415757.3,ENST00000389232.4
exon_skip_120698	15	34065734:34065816:34072411:34072542:34077862:34078183	34072411:34072542	ENSG00000198838.7	ENST00000415757.3,ENST00000389232.4
exon_skip_120699	15	34094069:34094162:34099755:34099770:34102679:34102850	34099755:34099770	ENSG00000198838.7	ENST00000389232.4
exon_skip_120702	15	34105667:34105780:34109062:34109159:34110778:34110885	34109062:34109159	ENSG00000198838.7	ENST00000415757.3,ENST00000389232.4
exon_skip_120703	15	34117803:34117877:34118452:34118470:34118872:34118953	34118452:34118470	ENSG00000198838.7	ENST00000415757.3,ENST00000389232.4
exon_skip_120710	15	34127168:34127273:34129106:34129188:34129831:34130727	34129106:34129188	ENSG00000198838.7	ENST00000415757.3,ENST00000389232.4
exon_skip_120713	15	34129106:34129188:34129831:34131159:34133025:34133084	34129831:34131159	ENSG00000198838.7	ENST00000415757.3,ENST00000389232.4
exon_skip_120715	15	34134064:34134236:34135688:34135775:34137062:34137263	34135688:34135775	ENSG00000198838.7	ENST00000415757.3,ENST00000389232.4
exon_skip_120718	15	34146966:34147113:34149980:34150115:34151775:34151932	34149980:34150115	ENSG00000198838.7	ENST00000415757.3,ENST00000389232.4
exon_skip_120719	15	34152795:34152860:34153278:34153379:34156338:34156390	34153278:34153379	ENSG00000198838.7	ENST00000415757.3,ENST00000389232.4

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 RYR3

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

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

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Infer the effects of exon skipping event on protein functional features for RYR3

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

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

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 RYR3

- 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-BC-A3KG-01	exon_skip_120692	34021058	34021227	34021174	34021174	Frame_Shift_Del	T	-	p.L2385fs
LIHC	TCGA-DD-A1EG-01	exon_skip_120693	34049676	34049797	34049780	34049780	Frame_Shift_Del	G	-	p.E2896fs
BLCA	TCGA-UY-A78K-01	exon_skip_120696	34060859	34060908	34060893	34060894	Frame_Shift_Del	AG	-	p.R2914fs
LIHC	TCGA-G3-A7M5-01	exon_skip_120702	34109063	34109159	34109120	34109120	Frame_Shift_Del	G	-	p.E3520fs
LIHC	TCGA-G3-A7M5-01	exon_skip_120702	34109063	34109159	34109120	34109120	Frame_Shift_Del	G	-	p.E3521fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_120702	34109063	34109159	34109126	34109126	Frame_Shift_Del	T	-	p.Y3522fs
SKCM	TCGA-RP-A695-06	exon_skip_120713	34129832	34131159	34129961	34129961	Frame_Shift_Del	C	-	p.T3927fs
KIRP	TCGA-GL-A59R-01	exon_skip_120713	34129832	34131159	34130027	34130027	Frame_Shift_Del	A	-	p.E3949fs
LIHC	TCGA-DD-A39Y-01	exon_skip_120713	34129832	34131159	34130740	34130740	Frame_Shift_Del	T	-	p.F4188fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_120713	34129832	34131159	34130760	34130760	Frame_Shift_Del	G	-	p.V4193fs
LIHC	TCGA-DD-A3A0-01	exon_skip_120713	34129832	34131159	34131043	34131043	Frame_Shift_Del	A	-	p.K4288fs
LIHC	TCGA-DD-A3A0-01	exon_skip_120719	34153279	34153379	34153325	34153325	Frame_Shift_Del	C	-	p.T4804fs
GBM	TCGA-06-0126-01	exon_skip_120713	34129832	34131159	34130001	34130002	Frame_Shift_Ins	-	A	p.S3940fs
CESC	TCGA-EK-A2RJ-01	exon_skip_120692	34021058	34021227	34021064	34021064	Nonsense_Mutation	C	A	p.S2347*
UCEC	TCGA-BS-A0UF-01	exon_skip_120693	34049676	34049797	34049784	34049784	Nonsense_Mutation	G	T	p.E2898*
SKCM	TCGA-EE-A2GU-06	exon_skip_120702	34109063	34109159	34109108	34109108	Nonsense_Mutation	G	A	p.W3516*
UCEC	TCGA-AP-A0LM-01	exon_skip_120713	34129832	34131159	34130377	34130377	Nonsense_Mutation	C	T	p.R4066*
LUSC	TCGA-46-3769-01	exon_skip_120713	34129832	34131159	34131112	34131112	Nonsense_Mutation	G	T	p.E4311*
COAD	TCGA-AZ-6601-01	exon_skip_120713	34129832	34131159	34129831	34129831	Splice_Site	G	T	.
SKCM	TCGA-GF-A6C9-06	exon_skip_120718	34149981	34150115	34150116	34150116	Splice_Site	G	A	.

- 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
NCIH69_LUNG	34072412	34072542	34072479	34072479	Frame_Shift_Del	C	-	p.P3069fs
MFE319_ENDOMETRIUM	34072412	34072542	34072483	34072483	Frame_Shift_Del	C	-	p.T3070fs
MOLT16_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	33876596	33876691	33876610	33876610	Missense_Mutation	G	A	p.G530R
HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	33876596	33876691	33876650	33876650	Missense_Mutation	A	C	p.D543A
NALM6_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	33876596	33876691	33876686	33876686	Missense_Mutation	C	T	p.S555F
NCIH2110_LUNG	34021058	34021227	34021083	34021084	Missense_Mutation	GG	TT	p.2353_2354MA>IS
K2_SKIN	34021058	34021227	34021102	34021102	Missense_Mutation	G	A	p.D2360N
MET2B	34021058	34021227	34021131	34021132	Missense_Mutation	GG	TA	p.2369_2370LD>FN
D423MG_CENTRAL_NERVOUS_SYSTEM	34021058	34021227	34021142	34021142	Missense_Mutation	A	T	p.Y2373F
AN3CA_ENDOMETRIUM	34021058	34021227	34021172	34021172	Missense_Mutation	A	G	p.H2383R
BALL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	34049676	34049797	34049773	34049773	Missense_Mutation	A	C	p.H2894P
451LU_SKIN	34060859	34060908	34060900	34060900	Missense_Mutation	C	T	p.S2916F
639V_URINARY_TRACT	34072412	34072542	34072420	34072420	Missense_Mutation	C	A	p.P3049H
HCC1143_BREAST	34072412	34072542	34072491	34072491	Missense_Mutation	C	T	p.R3073C
LS411N_LARGE_INTESTINE	34072412	34072542	34072492	34072492	Missense_Mutation	G	A	p.R3073H
OACM51_OESOPHAGUS	34072412	34072542	34072498	34072498	Missense_Mutation	A	G	p.N3075S
JURKAT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	34072412	34072542	34072507	34072507	Missense_Mutation	C	T	p.S3078L
HEC108_ENDOMETRIUM	34072412	34072542	34072527	34072527	Missense_Mutation	C	T	p.P3085S
SKCO1_LARGE_INTESTINE	34072412	34072542	34072533	34072533	Missense_Mutation	G	A	p.E3087K
HT_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	34072412	34072542	34072535	34072535	Missense_Mutation	G	C	p.E3087D
KYSE520_OESOPHAGUS	34109063	34109159	34109071	34109071	Missense_Mutation	C	G	p.S3504C
MFE319_ENDOMETRIUM	34129107	34129188	34129153	34129153	Missense_Mutation	A	G	p.Q3872R
HT115_LARGE_INTESTINE	34129832	34131159	34129870	34129870	Missense_Mutation	G	T	p.D3897Y
JHUEM7_ENDOMETRIUM	34129832	34131159	34129917	34129917	Missense_Mutation	C	A	p.F3912L
BT12_SOFT_TISSUE	34129832	34131159	34129936	34129936	Missense_Mutation	C	G	p.L3919V
SNU81_LARGE_INTESTINE	34129832	34131159	34129937	34129937	Missense_Mutation	T	G	p.L3919R
8305C_THYROID	34129832	34131159	34129957	34129957	Missense_Mutation	G	T	p.D3926Y
MUTZ5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	34129832	34131159	34130029	34130029	Missense_Mutation	G	T	p.G3950W
NCIH2228_LUNG	34129832	34131159	34130100	34130100	Missense_Mutation	G	A	p.M3973I
HCT15_LARGE_INTESTINE	34129832	34131159	34130101	34130101	Missense_Mutation	T	G	p.F3974V
WM88_SKIN	34129832	34131159	34130213	34130213	Missense_Mutation	T	G	p.L4011R
SW480_LARGE_INTESTINE	34129832	34131159	34130272	34130272	Missense_Mutation	C	T	p.R4031C
SW620_LARGE_INTESTINE	34129832	34131159	34130272	34130272	Missense_Mutation	C	T	p.R4031C
HEC108_ENDOMETRIUM	34129832	34131159	34130309	34130309	Missense_Mutation	G	A	p.R4043H
SNUC4_LARGE_INTESTINE	34129832	34131159	34130322	34130322	Missense_Mutation	G	T	p.E4047D
SNU175_LARGE_INTESTINE	34129832	34131159	34130351	34130351	Missense_Mutation	A	G	p.E4057G
HS936T_SKIN	34129832	34131159	34130419	34130419	Missense_Mutation	G	A	p.E4080K
TOV21G_OVARY	34129832	34131159	34130450	34130450	Missense_Mutation	A	C	p.E4090A
SISO_CERVIX	34129832	34131159	34130497	34130497	Missense_Mutation	G	A	p.D4106N
GRST_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	34129832	34131159	34130497	34130497	Missense_Mutation	G	A	p.D4106N
CW2_LARGE_INTESTINE	34129832	34131159	34130561	34130561	Missense_Mutation	C	T	p.A4127V
BICR16_UPPER_AERODIGESTIVE_TRACT	34129832	34131159	34130638	34130638	Missense_Mutation	G	A	p.V4153I
MERO25_LUNG	34129832	34131159	34130657	34130657	Missense_Mutation	G	A	p.R4159K
COLO668_LUNG	34129832	34131159	34130738	34130738	Missense_Mutation	C	A	p.S4186Y
NCIH630_LARGE_INTESTINE	34129832	34131159	34130828	34130828	Missense_Mutation	G	A	p.G4216E
TE4_OESOPHAGUS	34129832	34131159	34130842	34130842	Missense_Mutation	G	A	p.E4221K
DMS79_LUNG	34129832	34131159	34130901	34130901	Missense_Mutation	A	C	p.Q4240H
MYM12_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	34129832	34131159	34130938	34130938	Missense_Mutation	G	T	p.A4253S
HUNS1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	34129832	34131159	34130952	34130952	Missense_Mutation	G	T	p.E4257D
NCIH1436_LUNG	34129832	34131159	34131008	34131008	Missense_Mutation	A	G	p.D4276G
SNU175_LARGE_INTESTINE	34129832	34131159	34131065	34131065	Missense_Mutation	G	A	p.G4295E
DANG_PANCREAS	34129832	34131159	34131144	34131144	Missense_Mutation	G	C	p.K4321N
MCAS_OVARY	34149981	34150115	34150054	34150054	Missense_Mutation	A	G	p.K4694R
SNU81_LARGE_INTESTINE	34149981	34150115	34150063	34150063	Missense_Mutation	A	C	p.N4697T
LS411N_LARGE_INTESTINE	34149981	34150115	34150071	34150071	Missense_Mutation	G	A	p.E4700K
KNS81_CENTRAL_NERVOUS_SYSTEM	34149981	34150115	34150089	34150089	Missense_Mutation	G	A	p.D4706N
KNS81FD_CENTRAL_NERVOUS_SYSTEM	34149981	34150115	34150089	34150089	Missense_Mutation	G	A	p.D4706N
HEC108_ENDOMETRIUM	34149981	34150115	34150113	34150113	Missense_Mutation	A	G	p.T4714A
HCC56_LARGE_INTESTINE	34153279	34153379	34153334	34153334	Missense_Mutation	G	C	p.G4807A
DU145_PROSTATE	33876596	33876691	33876627	33876627	Nonsense_Mutation	C	A	p.C535*
LB996RCC_KIDNEY	34021058	34021227	34021180	34021180	Nonsense_Mutation	G	T	p.E2386*
NCIH2087_LUNG	34129832	34131159	34131092	34131092	Nonsense_Mutation	C	A	p.S4304*

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for RYR3

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 RYR3

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for RYR3

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RelatedDrugs for RYR3

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 RYR3

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 RYR3

Exon skipping events across known transcript of Ensembl for RYR3 from UCSC genome browser

Gene isoform structures and expression levels for RYR3

Exon skipping events with PSIs in TCGA for RYR3

Exon skipping events with PSIs in GTEx for RYR3

Open reading frame (ORF) annotation in the exon skipping event for RYR3

Infer the effects of exon skipping event on protein functional features for RYR3

SNVs in the skipped exons for RYR3

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for RYR3

Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for RYR3

Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for RYR3

RelatedDrugs for RYR3

RelatedDiseases for RYR3