ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for RPN2

Gene summary

Gene information	Gene symbol	RPN2
	Gene ID	6185
	Gene name	ribophorin II
	Synonyms	RIBIIR\|RPN-II\|RPNII\|SWP1
	Cytomap	20q11.23
	Type of gene	protein-coding
	Description	dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2dolichyl-diphosphooligosaccharide--protein glycosyltransferase 63 kDa subunitoligosaccharyltransferase complex subunit (non-catalytic)ribophorin-2
	Modification date	20180523
	UniProtAcc	P04844
	Context	PubMed: RPN2 [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 RPN2 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 RPN2

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 RPN2

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_351448	20	35807732:35807772:35812582:35812776:35826799:35826895	35812582:35812776	ENSG00000118705.12	ENST00000237530.6,ENST00000373632.4,ENST00000462163.1
exon_skip_351458	20	35812621:35812776:35826799:35826895:35827452:35827628	35826799:35826895	ENSG00000118705.12	ENST00000237530.6,ENST00000373632.4
exon_skip_351459	20	35812621:35812776:35826799:35826895:35832287:35832363	35826799:35826895	ENSG00000118705.12	ENST00000462163.1
exon_skip_351467	20	35812621:35812776:35827452:35827628:35832287:35832363	35827452:35827628	ENSG00000118705.12	ENST00000373622.5
exon_skip_351469	20	35812582:35812776:35832287:35832363:35833169:35833304	35832287:35832363	ENSG00000118705.12	ENST00000456102.1
exon_skip_351479	20	35826837:35826895:35827452:35827628:35832287:35832363	35827452:35827628	ENSG00000118705.12	ENST00000237530.6
exon_skip_351482	20	35827452:35827628:35828849:35828897:35832287:35832363	35828849:35828897	ENSG00000118705.12	ENST00000373632.4
exon_skip_351485	20	35833169:35833304:35835675:35835852:35838449:35838553	35835675:35835852	ENSG00000118705.12	ENST00000237530.6,ENST00000456102.1,ENST00000373632.4,ENST00000373622.5
exon_skip_351486	20	35835675:35835852:35838449:35838568:35842162:35842268	35838449:35838568	ENSG00000118705.12	ENST00000237530.6,ENST00000373622.5
exon_skip_351489	20	35838449:35838568:35842162:35842268:35852280:35852372	35842162:35842268	ENSG00000118705.12	ENST00000237530.6,ENST00000373622.5
exon_skip_351497	20	35852280:35852372:35854090:35854205:35856952:35857147	35854090:35854205	ENSG00000118705.12	ENST00000237530.6,ENST00000373622.5
exon_skip_351503	20	35857080:35857147:35858375:35858462:35860698:35860794	35858375:35858462	ENSG00000118705.12	ENST00000237530.6,ENST00000456400.1,ENST00000373622.5
exon_skip_351507	20	35858393:35858462:35860698:35860794:35862422:35862498	35860698:35860794	ENSG00000118705.12	ENST00000237530.6,ENST00000456400.1,ENST00000373622.5
exon_skip_351509	20	35858393:35858462:35862422:35862498:35864982:35865112	35862422:35862498	ENSG00000118705.12	ENST00000470352.1,ENST00000437329.1
exon_skip_351510	20	35860698:35860794:35862422:35862498:35864982:35865112	35862422:35862498	ENSG00000118705.12	ENST00000237530.6,ENST00000373622.5
exon_skip_351515	20	35862422:35862498:35864982:35865112:35866804:35866852	35864982:35865112	ENSG00000118705.12	ENST00000373622.5
exon_skip_351516	20	35862422:35862498:35864982:35865112:35869705:35869783	35864982:35865112	ENSG00000118705.12	ENST00000237530.6,ENST00000470352.1,ENST00000437329.1
exon_skip_351524	20	35865084:35865112:35866804:35866852:35869705:35869820	35866804:35866852	ENSG00000118705.12	ENST00000373622.5

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for RPN2

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_351448	20	35807732:35807772:35812582:35812776:35826799:35826895	35812582:35812776	ENSG00000118705.12	ENST00000237530.6,ENST00000373632.4,ENST00000462163.1
exon_skip_351458	20	35812621:35812776:35826799:35826895:35827452:35827628	35826799:35826895	ENSG00000118705.12	ENST00000237530.6,ENST00000373632.4
exon_skip_351459	20	35812621:35812776:35826799:35826895:35832287:35832363	35826799:35826895	ENSG00000118705.12	ENST00000462163.1
exon_skip_351467	20	35812621:35812776:35827452:35827628:35832287:35832363	35827452:35827628	ENSG00000118705.12	ENST00000373622.5
exon_skip_351469	20	35812582:35812776:35832287:35832363:35833169:35833304	35832287:35832363	ENSG00000118705.12	ENST00000456102.1
exon_skip_351479	20	35826837:35826895:35827452:35827628:35832287:35832363	35827452:35827628	ENSG00000118705.12	ENST00000237530.6
exon_skip_351482	20	35827452:35827628:35828849:35828897:35832287:35832363	35828849:35828897	ENSG00000118705.12	ENST00000373632.4
exon_skip_351485	20	35833169:35833304:35835675:35835852:35838449:35838553	35835675:35835852	ENSG00000118705.12	ENST00000456102.1,ENST00000237530.6,ENST00000373622.5,ENST00000373632.4
exon_skip_351486	20	35835675:35835852:35838449:35838568:35842162:35842268	35838449:35838568	ENSG00000118705.12	ENST00000237530.6,ENST00000373622.5
exon_skip_351489	20	35838449:35838568:35842162:35842268:35852280:35852372	35842162:35842268	ENSG00000118705.12	ENST00000237530.6,ENST00000373622.5
exon_skip_351497	20	35852280:35852372:35854090:35854205:35856952:35857147	35854090:35854205	ENSG00000118705.12	ENST00000237530.6,ENST00000373622.5
exon_skip_351503	20	35857080:35857147:35858375:35858462:35860698:35860794	35858375:35858462	ENSG00000118705.12	ENST00000237530.6,ENST00000373622.5,ENST00000456400.1
exon_skip_351507	20	35858393:35858462:35860698:35860794:35862422:35862498	35860698:35860794	ENSG00000118705.12	ENST00000237530.6,ENST00000373622.5,ENST00000456400.1
exon_skip_351509	20	35858393:35858462:35862422:35862498:35864982:35865112	35862422:35862498	ENSG00000118705.12	ENST00000437329.1,ENST00000470352.1
exon_skip_351510	20	35860698:35860794:35862422:35862498:35864982:35865112	35862422:35862498	ENSG00000118705.12	ENST00000237530.6,ENST00000373622.5
exon_skip_351515	20	35862422:35862498:35864982:35865112:35866804:35866852	35864982:35865112	ENSG00000118705.12	ENST00000373622.5
exon_skip_351516	20	35862422:35862498:35864982:35865112:35869705:35869783	35864982:35865112	ENSG00000118705.12	ENST00000237530.6,ENST00000437329.1,ENST00000470352.1
exon_skip_351524	20	35865084:35865112:35866804:35866852:35869705:35869820	35866804:35866852	ENSG00000118705.12	ENST00000373622.5

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 RPN2

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
ENST00000237530	35812582	35812776	Frame-shift
ENST00000237530	35827452	35827628	Frame-shift
ENST00000237530	35838449	35838568	Frame-shift
ENST00000237530	35842162	35842268	Frame-shift
ENST00000237530	35854090	35854205	Frame-shift
ENST00000237530	35862422	35862498	Frame-shift
ENST00000237530	35864982	35865112	Frame-shift
ENST00000237530	35826799	35826895	In-frame
ENST00000237530	35835675	35835852	In-frame
ENST00000237530	35858375	35858462	In-frame
ENST00000237530	35860698	35860794	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
ENST00000237530	35812582	35812776	Frame-shift
ENST00000237530	35827452	35827628	Frame-shift
ENST00000237530	35838449	35838568	Frame-shift
ENST00000237530	35842162	35842268	Frame-shift
ENST00000237530	35854090	35854205	Frame-shift
ENST00000237530	35862422	35862498	Frame-shift
ENST00000237530	35864982	35865112	Frame-shift
ENST00000237530	35826799	35826895	In-frame
ENST00000237530	35835675	35835852	In-frame
ENST00000237530	35858375	35858462	In-frame
ENST00000237530	35860698	35860794	In-frame

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Infer the effects of exon skipping event on protein functional features for RPN2

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
ENST00000237530	2528	631	35826799	35826895	519	614	69	101
ENST00000237530	2528	631	35835675	35835852	1002	1178	230	289
ENST00000237530	2528	631	35858375	35858462	1806	1892	498	527
ENST00000237530	2528	631	35860698	35860794	1893	1988	527	559

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
ENST00000237530	2528	631	35826799	35826895	519	614	69	101
ENST00000237530	2528	631	35835675	35835852	1002	1178	230	289
ENST00000237530	2528	631	35858375	35858462	1806	1892	498	527
ENST00000237530	2528	631	35860698	35860794	1893	1988	527	559

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
P04844	69	101	70	101	Alternative sequence	ID=VSP_043051;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
P04844	69	101	23	631	Chain	ID=PRO_0000022244;Note=Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2
P04844	69	101	23	540	Topological domain	Note=Lumenal;Ontology_term=ECO:0000255;evidence=ECO:0000255
P04844	230	289	23	631	Chain	ID=PRO_0000022244;Note=Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2
P04844	230	289	260	260	Sequence conflict	Note=A->S;Ontology_term=ECO:0000305;evidence=ECO:0000305
P04844	230	289	286	286	Sequence conflict	Note=A->S;Ontology_term=ECO:0000305;evidence=ECO:0000305
P04844	230	289	23	540	Topological domain	Note=Lumenal;Ontology_term=ECO:0000255;evidence=ECO:0000255
P04844	498	527	23	631	Chain	ID=PRO_0000022244;Note=Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2
P04844	498	527	23	540	Topological domain	Note=Lumenal;Ontology_term=ECO:0000255;evidence=ECO:0000255
P04844	527	559	23	631	Chain	ID=PRO_0000022244;Note=Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2
P04844	527	559	23	540	Topological domain	Note=Lumenal;Ontology_term=ECO:0000255;evidence=ECO:0000255
P04844	527	559	541	561	Transmembrane	Note=Helical;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
P04844	69	101	70	101	Alternative sequence	ID=VSP_043051;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
P04844	69	101	23	631	Chain	ID=PRO_0000022244;Note=Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2
P04844	69	101	23	540	Topological domain	Note=Lumenal;Ontology_term=ECO:0000255;evidence=ECO:0000255
P04844	230	289	23	631	Chain	ID=PRO_0000022244;Note=Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2
P04844	230	289	260	260	Sequence conflict	Note=A->S;Ontology_term=ECO:0000305;evidence=ECO:0000305
P04844	230	289	286	286	Sequence conflict	Note=A->S;Ontology_term=ECO:0000305;evidence=ECO:0000305
P04844	230	289	23	540	Topological domain	Note=Lumenal;Ontology_term=ECO:0000255;evidence=ECO:0000255
P04844	498	527	23	631	Chain	ID=PRO_0000022244;Note=Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2
P04844	498	527	23	540	Topological domain	Note=Lumenal;Ontology_term=ECO:0000255;evidence=ECO:0000255
P04844	527	559	23	631	Chain	ID=PRO_0000022244;Note=Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit 2
P04844	527	559	23	540	Topological domain	Note=Lumenal;Ontology_term=ECO:0000255;evidence=ECO:0000255
P04844	527	559	541	561	Transmembrane	Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255

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SNVs in the skipped exons for RPN2

- 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-4R-AA8I-01	exon_skip_351507	35860699	35860794	35860726	35860726	Frame_Shift_Del	C	-	p.R536fs
LIHC	TCGA-DD-A3A0-01	exon_skip_351509 exon_skip_351510	35862423	35862498	35862458	35862458	Frame_Shift_Del	T	-	p.T571fs
LIHC	TCGA-G3-A3CJ-01	exon_skip_351509 exon_skip_351510	35862423	35862498	35862480	35862480	Frame_Shift_Del	T	-	p.F579fs
LUAD	TCGA-44-2656-01	exon_skip_351507	35860699	35860794	35860725	35860726	Frame_Shift_Ins	-	C	p.R536fs
LUAD	TCGA-50-5933-01		35826800	35826895	35826893	35826893	Nonsense_Mutation	G	T	p.E101*
HNSC	TCGA-CV-7427-01	exon_skip_351479 exon_skip_351467	35827453	35827628	35827508	35827508	Nonsense_Mutation	C	A	p.S120*
SKCM	TCGA-FR-A44A-06	exon_skip_351485	35835676	35835852	35835688	35835688	Nonsense_Mutation	C	T	p.Q235*
SKCM	TCGA-FR-A44A-06	exon_skip_351485	35835676	35835852	35835688	35835688	Nonsense_Mutation	C	T	p.Q235X
BLCA	TCGA-ZF-A9R2-01	exon_skip_351507	35860699	35860794	35860769	35860769	Nonsense_Mutation	C	A	p.S551*

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

Depth of coverage in three exons	Mutation description
	Sample: TCGA-CV-7427-01
	Cancer type: HNSC
	ESID: exon_skip_351467
	Skipped exon start: 35827453
	Skipped exon end: 35827628
	Mutation start: 35827508
	Mutation end: 35827508
	Mutation type: Nonsense_Mutation
	Reference seq: C
	Mutation seq: A
	AAchange: p.S120*
exon_skip_351479_HNSC_TCGA-CV-7427-01.png
exon_skip_85043_HNSC_TCGA-CV-7427-01.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
PACADD137_PANCREAS	35862423	35862498	35862480	35862480	Frame_Shift_Del	T	-	p.F579fs
MFE319_ENDOMETRIUM	35812583	35812776	35812621	35812621	Missense_Mutation	G	A	p.A18T
SNU1040_LARGE_INTESTINE	35812583	35812776	35812640	35812640	Missense_Mutation	C	T	p.T24M
MN60_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	35812583	35812776	35812697	35812697	Missense_Mutation	G	A	p.R43H
SF295_CENTRAL_NERVOUS_SYSTEM	35812583	35812776	35812709	35812709	Missense_Mutation	A	C	p.N47T
ISHIKAWAHERAKLIO02ER_ENDOMETRIUM	35812583	35812776	35812756	35812756	Missense_Mutation	G	A	p.A63T
EB2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	35826800	35826895	35826858	35826858	Missense_Mutation	A	G	p.Y89C
EB1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	35826800	35826895	35826858	35826858	Missense_Mutation	A	G	p.Y89C
SW1116_LARGE_INTESTINE	35827453	35827628	35827472	35827472	Missense_Mutation	C	G	p.T108S
BCP1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	35827453	35827628	35827600	35827600	Missense_Mutation	C	T	p.R151C
SNU719_STOMACH	35832288	35832363	35832358	35832358	Missense_Mutation	A	C	p.I184L
FADU_UPPER_AERODIGESTIVE_TRACT	35835676	35835852	35835740	35835740	Missense_Mutation	C	T	p.A252V
NCIH650_LUNG	35835676	35835852	35835766	35835766	Missense_Mutation	G	C	p.V261L
NB69_AUTONOMIC_GANGLIA	35835676	35835852	35835773	35835773	Missense_Mutation	C	T	p.S263L
RAMOS2G64C10_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	35835676	35835852	35835811	35835811	Missense_Mutation	G	A	p.E276K
MOLT4_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	35835676	35835852	35835850	35835850	Missense_Mutation	C	T	p.R289W
MCC13_SKIN	35842163	35842268	35842187	35842187	Missense_Mutation	G	A	p.M337I
KARPAS45_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	35858376	35858462	35858406	35858406	Missense_Mutation	G	A	p.E509K
EN_ENDOMETRIUM	35860699	35860794	35860708	35860708	Missense_Mutation	C	T	p.R531C
KM12_LARGE_INTESTINE	35862423	35862498	35862472	35862472	Missense_Mutation	C	T	p.T576M
RAJI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	35862423	35862498	35862472	35862472	Missense_Mutation	C	T	p.T576M
LS411N_LARGE_INTESTINE	35858376	35858462	35858377	35858377	Splice_Site	C	T	p.A499V

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for RPN2

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 RPN2

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for RPN2

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RelatedDrugs for RPN2

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 RPN2

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
RPN2	C0033578	Prostatic 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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