ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for RNF213

Gene summary

Gene information	Gene symbol	RNF213
	Gene ID	57674
	Gene name	ring finger protein 213
	Synonyms	ALO17\|C17orf27\|KIAA1618\|MYMY2\|MYSTR\|NET57
	Cytomap	17q25.3
	Type of gene	protein-coding
	Description	E3 ubiquitin-protein ligase RNF213ALK lymphoma oligomerization partner on chromosome 17RING-type E3 ubiquitin transferase RNF213mysterin
	Modification date	20180527
	UniProtAcc	Q63HN8
	Context	PubMed: RNF213 [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
RNF213	GO:0016567	protein ubiquitination	21799892
RNF213	GO:0051260	protein homooligomerization	24658080\|26126547
RNF213	GO:0051865	protein autoubiquitination	21799892

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Exon skipping events across known transcript of Ensembl for RNF213 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 RNF213

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 RNF213

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_284208	17	78234668:78234701:78237372:78237577:78247039:78247203	78237372:78237577	ENSG00000173821.15	ENST00000319921.4,ENST00000582970.1,ENST00000456466.1
exon_skip_284213	17	78247039:78247203:78252562:78252709:78261613:78261856	78252562:78252709	ENSG00000173821.15	ENST00000508628.2
exon_skip_284215	17	78272120:78272318:78280051:78280268:78280927:78281001	78280051:78280268	ENSG00000173821.15	ENST00000319921.4,ENST00000508628.2,ENST00000559070.1,ENST00000582970.1,ENST00000456466.1
exon_skip_284218	17	78292989:78293112:78298829:78298998:78301615:78301789	78298829:78298998	ENSG00000173821.15	ENST00000508628.2,ENST00000559070.1,ENST00000582970.1,ENST00000456466.1
exon_skip_284222	17	78311632:78311797:78313000:78314156:78316931:78317125	78313000:78314156	ENSG00000173821.15	ENST00000508628.2,ENST00000582970.1
exon_skip_284223	17	78318477:78322086:78323569:78323706:78324100:78324196	78323569:78323706	ENSG00000173821.15	ENST00000336301.6,ENST00000508628.2,ENST00000582970.1
exon_skip_284239	17	78343301:78343471:78343567:78343667:78345673:78345785	78343567:78343667	ENSG00000173821.15	ENST00000336301.6,ENST00000508628.2,ENST00000582970.1,ENST00000558116.1
exon_skip_284241	17	78343567:78343667:78345673:78345785:78346320:78346534	78345673:78345785	ENSG00000173821.15	ENST00000336301.6,ENST00000508628.2,ENST00000582970.1,ENST00000558116.1
exon_skip_284247	17	78351561:78351596:78353419:78353514:78354630:78354691	78353419:78353514	ENSG00000173821.15	ENST00000336301.6,ENST00000508628.2,ENST00000411702.3,ENST00000582970.1,ENST00000558116.1
exon_skip_284252	17	78357476:78357728:78358838:78358971:78359337:78359421	78358838:78358971	ENSG00000173821.15	ENST00000427003.3,ENST00000336301.6,ENST00000508628.2,ENST00000411702.3,ENST00000582970.1
exon_skip_284255	17	78362972:78363167:78363627:78363717:78363811:78363996	78363627:78363717	ENSG00000173821.15	ENST00000427003.3,ENST00000336301.6,ENST00000508628.2,ENST00000411702.3,ENST00000582970.1,ENST00000560083.1
exon_skip_284257	17	78363627:78363717:78363811:78363996:78367144:78369053	78363811:78363996	ENSG00000173821.15	ENST00000427003.3,ENST00000336301.6,ENST00000508628.2,ENST00000411702.3,ENST00000582970.1,ENST00000560083.1

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for RNF213

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_284208	17	78234668:78234701:78237372:78237577:78247039:78247203	78237372:78237577	ENSG00000173821.15	ENST00000582970.1,ENST00000456466.1,ENST00000319921.4
exon_skip_284213	17	78247039:78247203:78252562:78252709:78261613:78261856	78252562:78252709	ENSG00000173821.15	ENST00000508628.2
exon_skip_284215	17	78272120:78272318:78280051:78280268:78280927:78281001	78280051:78280268	ENSG00000173821.15	ENST00000508628.2,ENST00000582970.1,ENST00000456466.1,ENST00000319921.4,ENST00000559070.1
exon_skip_284218	17	78292989:78293112:78298829:78298998:78301615:78301789	78298829:78298998	ENSG00000173821.15	ENST00000508628.2,ENST00000582970.1,ENST00000456466.1,ENST00000559070.1
exon_skip_284222	17	78311632:78311797:78313000:78314156:78316931:78317125	78313000:78314156	ENSG00000173821.15	ENST00000508628.2,ENST00000582970.1
exon_skip_284223	17	78318477:78322086:78323569:78323706:78324100:78324196	78323569:78323706	ENSG00000173821.15	ENST00000508628.2,ENST00000582970.1,ENST00000336301.6
exon_skip_284239	17	78343301:78343471:78343567:78343667:78345673:78345785	78343567:78343667	ENSG00000173821.15	ENST00000508628.2,ENST00000582970.1,ENST00000336301.6,ENST00000558116.1
exon_skip_284241	17	78343567:78343667:78345673:78345785:78346320:78346534	78345673:78345785	ENSG00000173821.15	ENST00000508628.2,ENST00000582970.1,ENST00000336301.6,ENST00000558116.1
exon_skip_284247	17	78351561:78351596:78353419:78353514:78354630:78354691	78353419:78353514	ENSG00000173821.15	ENST00000508628.2,ENST00000582970.1,ENST00000336301.6,ENST00000558116.1,ENST00000411702.3
exon_skip_284252	17	78357476:78357728:78358838:78358971:78359337:78359421	78358838:78358971	ENSG00000173821.15	ENST00000508628.2,ENST00000582970.1,ENST00000336301.6,ENST00000411702.3,ENST00000427003.3
exon_skip_284255	17	78362972:78363167:78363627:78363717:78363811:78363996	78363627:78363717	ENSG00000173821.15	ENST00000508628.2,ENST00000582970.1,ENST00000336301.6,ENST00000411702.3,ENST00000427003.3,ENST00000560083.1
exon_skip_284257	17	78363627:78363717:78363811:78363996:78367144:78369053	78363811:78363996	ENSG00000173821.15	ENST00000508628.2,ENST00000582970.1,ENST00000336301.6,ENST00000411702.3,ENST00000427003.3,ENST00000560083.1

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 RNF213

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 RNF213

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 RNF213

- 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-A1EG-01	exon_skip_284208	78237373	78237577	78237521	78237521	Frame_Shift_Del	C	-	p.T14fs
LIHC	TCGA-DD-A3A0-01	exon_skip_284208	78237373	78237577	78237521	78237521	Frame_Shift_Del	C	-	p.T14fs
COAD	TCGA-D5-6930-01	exon_skip_284215	78280052	78280268	78280073	78280074	Frame_Shift_Del	GA	-	p.744_744del
LIHC	TCGA-DD-A1EG-01	exon_skip_284222	78313001	78314156	78313961	78313961	Frame_Shift_Del	G	-	p.G1932fs
STAD	TCGA-BR-A4QL-01	exon_skip_284222	78313001	78314156	78314019	78314019	Frame_Shift_Del	C	-	p.T1951fs
STAD	TCGA-BR-A4QL-01	exon_skip_284222	78313001	78314156	78314019	78314019	Frame_Shift_Del	C	-	p.T24fs
LIHC	TCGA-DD-A3A0-01	exon_skip_284222	78313001	78314156	78314030	78314030	Frame_Shift_Del	C	-	p.P1955fs
LIHC	TCGA-DD-A39Y-01	exon_skip_284241	78345674	78345785	78345719	78345719	Frame_Shift_Del	A	-	p.L4157fs
LIHC	TCGA-DD-A3A0-01	exon_skip_284257	78363812	78363996	78363821	78363821	Frame_Shift_Del	G	-	p.G5099fs
LIHC	TCGA-DD-A3A0-01	exon_skip_284257	78363812	78363996	78363955	78363955	Frame_Shift_Del	C	-	p.N5143fs
KIRC	TCGA-BP-4968-01	exon_skip_284239	78343568	78343667	78343583	78343584	Frame_Shift_Ins	-	A	p.K4114fs
KIRC	TCGA-BP-4968-01	exon_skip_284239	78343568	78343667	78343583	78343584	Frame_Shift_Ins	-	A	p.T4114fs
THYM	TCGA-5U-AB0E-01	exon_skip_284222	78313001	78314156	78313781	78313781	Nonsense_Mutation	G	T	p.E1872X
BLCA	TCGA-E5-A4U1-01	exon_skip_284222	78313001	78314156	78314024	78314024	Nonsense_Mutation	C	T	p.Q1953*
SKCM	TCGA-D3-A8GM-06	exon_skip_284223	78323570	78323706	78323688	78323688	Nonsense_Mutation	C	A	p.S3357*
STAD	TCGA-F1-6874-01	exon_skip_284215	78280052	78280268	78280270	78280270	Splice_Site	T	G	.

- 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
CMLT1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	78313001	78314156	78314019	78314019	Frame_Shift_Del	C	-	p.T1951fs
HEC6_ENDOMETRIUM	78280052	78280268	78280090	78280090	Missense_Mutation	T	C	p.L750S
HOP62_LUNG	78280052	78280268	78280099	78280099	Missense_Mutation	T	C	p.I753T
HEC108_ENDOMETRIUM	78280052	78280268	78280180	78280180	Missense_Mutation	A	G	p.H780R
KG1C_CENTRAL_NERVOUS_SYSTEM	78298830	78298998	78298911	78298911	Missense_Mutation	T	C	p.S1036P
COLO668_LUNG	78298830	78298998	78298931	78298931	Missense_Mutation	C	A	p.D1042E
MKN1_STOMACH	78298830	78298998	78298963	78298963	Missense_Mutation	C	T	p.T1053M
NCIH510_LUNG	78298830	78298998	78298983	78298983	Missense_Mutation	G	A	p.V1060I
HEC59_ENDOMETRIUM	78313001	78314156	78313317	78313317	Missense_Mutation	G	A	p.R1717K
MOLT3_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	78313001	78314156	78313347	78313347	Missense_Mutation	C	T	p.T1727M
T3M10_LUNG	78313001	78314156	78313347	78313347	Missense_Mutation	C	T	p.T1727M
SW48_LARGE_INTESTINE	78313001	78314156	78313448	78313448	Missense_Mutation	A	G	p.M1761V
TE5_OESOPHAGUS	78313001	78314156	78313474	78313474	Missense_Mutation	A	T	p.L1769F
IGROV1_OVARY	78313001	78314156	78313510	78313510	Missense_Mutation	C	G	p.I1781M
LN464_CENTRAL_NERVOUS_SYSTEM	78313001	78314156	78313569	78313569	Missense_Mutation	C	T	p.T1801I
SNU869_BILIARY_TRACT	78313001	78314156	78313745	78313745	Missense_Mutation	G	A	p.D1860N
KCL22_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	78313001	78314156	78313749	78313749	Missense_Mutation	A	C	p.E1861A
RERFLCAD2_LUNG	78313001	78314156	78313764	78313764	Missense_Mutation	C	T	p.T1866I
SNU1076_UPPER_AERODIGESTIVE_TRACT	78313001	78314156	78313764	78313764	Missense_Mutation	C	T	p.T1866I
SNU878_LIVER	78313001	78314156	78313767	78313767	Missense_Mutation	C	T	p.P1867L
HPBALL_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	78313001	78314156	78313802	78313802	Missense_Mutation	C	T	p.R1879C
MRKNU1_BREAST	78313001	78314156	78313824	78313824	Missense_Mutation	C	T	p.S1886F
SNUC2A_LARGE_INTESTINE	78313001	78314156	78313946	78313946	Missense_Mutation	G	A	p.V1927I
SNUC2B_LARGE_INTESTINE	78313001	78314156	78313946	78313946	Missense_Mutation	G	A	p.V1927I
PECAPJ34CLONEC12_UPPER_AERODIGESTIVE_TRACT	78313001	78314156	78313946	78313946	Missense_Mutation	G	T	p.V1927F
HCT15_LARGE_INTESTINE	78313001	78314156	78314048	78314048	Missense_Mutation	G	T	p.A1961S
SNU869_BILIARY_TRACT	78313001	78314156	78314145	78314145	Missense_Mutation	G	A	p.R1993Q
COLO792_SKIN	78323570	78323706	78323642	78323642	Missense_Mutation	C	T	p.P3342S
COLO792_SKIN	78323570	78323706	78323642	78323643	Missense_Mutation	CC	TT	p.P3342L
ALLPO_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	78353420	78353514	78353493	78353493	Missense_Mutation	G	A	p.R4540Q
PANC0213_PANCREAS	78358839	78358971	78358905	78358905	Missense_Mutation	C	G	p.Q4797E
HMC18_BREAST	78363628	78363717	78363652	78363652	Missense_Mutation	C	A	p.H5074N
TGBC11TKB_STOMACH	78363628	78363717	78363707	78363707	Missense_Mutation	G	A	p.R5092Q
DU145_PROSTATE	78363812	78363996	78363821	78363821	Missense_Mutation	G	C	p.G5099R
SNU1079_BILIARY_TRACT	78363812	78363996	78363843	78363844	Missense_Mutation	AA	CG	p.K5106T
SNU1079_BILIARY_TRACT	78363812	78363996	78363843	78363843	Missense_Mutation	A	C	p.K5106T
RCCER_KIDNEY	78363812	78363996	78363871	78363871	Missense_Mutation	G	C	p.K5115N
SNU1040_LARGE_INTESTINE	78363812	78363996	78363977	78363977	Missense_Mutation	C	T	p.R5151C
JOPACA1_PANCREAS	78363812	78363996	78363982	78363982	Missense_Mutation	C	A	p.F5152L
NCIH1666_LUNG	78363812	78363996	78363993	78363993	Missense_Mutation	G	T	p.W5156L
SNU81_LARGE_INTESTINE	78237373	78237577	78237526	78237526	Nonsense_Mutation	A	T	p.K16*
HEC251_ENDOMETRIUM	78363628	78363717	78363717	78363717	Splice_Site	A	C	p.K5095N

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for RNF213

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_284257	17	78363627:78363717:78363811:78363996:78367144:78369053	78363811:78363996	ENST00000427003.3,ENST00000336301.6,ENST00000508628.2,ENST00000411702.3,ENST00000582970.1,ENST00000560083.1	LGG	rs3185057	chr17:78363847	G/A	1.24e-03
exon_skip_284257	17	78363627:78363717:78363811:78363996:78367144:78369053	78363811:78363996	ENST00000427003.3,ENST00000336301.6,ENST00000508628.2,ENST00000411702.3,ENST00000582970.1,ENST00000560083.1	THCA	rs3185057	chr17:78363847	G/A	4.47e-04
exon_skip_284257	17	78363627:78363717:78363811:78363996:78367144:78369053	78363811:78363996	ENST00000427003.3,ENST00000336301.6,ENST00000508628.2,ENST00000411702.3,ENST00000582970.1,ENST00000560083.1	THCA	rs3185057	chr17:78363847	G/A	1.19e-03

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for RNF213

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for RNF213

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RelatedDrugs for RNF213

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 RNF213

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
RNF213	C1846689	MOYAMOYA DISEASE 2	3	UNIPROT

	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 RNF213

Exon skipping events across known transcript of Ensembl for RNF213 from UCSC genome browser

Gene isoform structures and expression levels for RNF213

Exon skipping events with PSIs in TCGA for RNF213

Exon skipping events with PSIs in GTEx for RNF213

Open reading frame (ORF) annotation in the exon skipping event for RNF213

Infer the effects of exon skipping event on protein functional features for RNF213

SNVs in the skipped exons for RNF213

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for RNF213

Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for RNF213

Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for RNF213

RelatedDrugs for RNF213

RelatedDiseases for RNF213