ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for WRAP53

Gene summary

Gene information	Gene symbol	WRAP53
	Gene ID	55135
	Gene name	WD repeat containing antisense to TP53
	Synonyms	DKCB3\|TCAB1\|WDR79
	Cytomap	17p13.1
	Type of gene	protein-coding
	Description	telomerase Cajal body protein 1WD repeat-containing protein 79WD repeat-containing protein WRAP53WD40 protein Wrap53WD40 repeat-containing protein antisense to TP53WD40 repeat-containing protein encoding RNA antisense to p53
	Modification date	20180519
	UniProtAcc	Q9BUR4
	Context	PubMed: WRAP53 [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
WRAP53	GO:0007004	telomere maintenance via telomerase	23685356
WRAP53	GO:0051973	positive regulation of telomerase activity	19179534\|23685356

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Exon skipping events across known transcript of Ensembl for WRAP53 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 WRAP53

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 WRAP53

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_148878	17	7591965:7592397:7592541:7592640:7592907:7593019	7592541:7592640	ENSG00000141499.12	ENST00000431639.2,ENST00000498311.1,ENST00000396463.2,ENST00000467699.1,ENST00000316024.5,ENST00000457584.2
exon_skip_148879	17	7592907:7593019:7604058:7604147:7604744:7604867	7604058:7604147	ENSG00000141499.12	ENST00000498311.1,ENST00000467699.1
exon_skip_148880	17	7604058:7604147:7604744:7604867:7604974:7605107	7604744:7604867	ENSG00000141499.12	ENST00000498311.1,ENST00000467699.1
exon_skip_148882	17	7604058:7604147:7604776:7604867:7604974:7605107	7604776:7604867	ENSG00000141499.12	ENST00000534050.1,ENST00000431639.2,ENST00000396463.2,ENST00000316024.5,ENST00000457584.2
exon_skip_148884	17	7604974:7605107:7605661:7605870:7606060:7606164	7605661:7605870	ENSG00000141499.12	ENST00000534050.1,ENST00000431639.2,ENST00000498311.1,ENST00000396463.2,ENST00000316024.5,ENST00000457584.2
exon_skip_148885	17	7606060:7606164:7606310:7606445:7606560:7606692	7606310:7606445	ENSG00000141499.12	ENST00000534050.1,ENST00000431639.2,ENST00000498311.1,ENST00000463804.2,ENST00000396463.2,ENST00000467699.1,ENST00000316024.5,ENST00000457584.2

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for WRAP53

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_148878	17	7591965:7592397:7592541:7592640:7592907:7593019	7592541:7592640	ENSG00000141499.12	ENST00000431639.2,ENST00000316024.5,ENST00000457584.2,ENST00000498311.1,ENST00000396463.2,ENST00000467699.1
exon_skip_148879	17	7592907:7593019:7604058:7604147:7604744:7604867	7604058:7604147	ENSG00000141499.12	ENST00000498311.1,ENST00000467699.1
exon_skip_148880	17	7604058:7604147:7604744:7604867:7604974:7605107	7604744:7604867	ENSG00000141499.12	ENST00000498311.1,ENST00000467699.1
exon_skip_148882	17	7604058:7604147:7604776:7604867:7604974:7605107	7604776:7604867	ENSG00000141499.12	ENST00000431639.2,ENST00000316024.5,ENST00000457584.2,ENST00000396463.2,ENST00000534050.1
exon_skip_148884	17	7604974:7605107:7605661:7605870:7606060:7606164	7605661:7605870	ENSG00000141499.12	ENST00000431639.2,ENST00000316024.5,ENST00000457584.2,ENST00000498311.1,ENST00000396463.2,ENST00000534050.1
exon_skip_148885	17	7606060:7606164:7606310:7606445:7606560:7606692	7606310:7606445	ENSG00000141499.12	ENST00000431639.2,ENST00000316024.5,ENST00000457584.2,ENST00000498311.1,ENST00000396463.2,ENST00000467699.1,ENST00000534050.1,ENST00000463804.2

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 WRAP53

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
ENST00000316024	7604776	7604867	Frame-shift
ENST00000396463	7604776	7604867	Frame-shift
ENST00000431639	7604776	7604867	Frame-shift
ENST00000457584	7604776	7604867	Frame-shift
ENST00000316024	7605661	7605870	Frame-shift
ENST00000396463	7605661	7605870	Frame-shift
ENST00000431639	7605661	7605870	Frame-shift
ENST00000457584	7605661	7605870	Frame-shift
ENST00000316024	7592541	7592640	In-frame
ENST00000396463	7592541	7592640	In-frame
ENST00000431639	7592541	7592640	In-frame
ENST00000457584	7592541	7592640	In-frame
ENST00000316024	7606310	7606445	In-frame
ENST00000396463	7606310	7606445	In-frame
ENST00000431639	7606310	7606445	In-frame
ENST00000457584	7606310	7606445	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
ENST00000316024	7604776	7604867	Frame-shift
ENST00000396463	7604776	7604867	Frame-shift
ENST00000431639	7604776	7604867	Frame-shift
ENST00000457584	7604776	7604867	Frame-shift
ENST00000316024	7605661	7605870	Frame-shift
ENST00000396463	7605661	7605870	Frame-shift
ENST00000431639	7605661	7605870	Frame-shift
ENST00000457584	7605661	7605870	Frame-shift
ENST00000316024	7592541	7592640	In-frame
ENST00000396463	7592541	7592640	In-frame
ENST00000431639	7592541	7592640	In-frame
ENST00000457584	7592541	7592640	In-frame
ENST00000316024	7606310	7606445	In-frame
ENST00000396463	7606310	7606445	In-frame
ENST00000431639	7606310	7606445	In-frame
ENST00000457584	7606310	7606445	In-frame

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Infer the effects of exon skipping event on protein functional features for WRAP53

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
ENST00000316024	4028	548	7592541	7592640	2780	2878	144	176
ENST00000396463	1922	548	7592541	7592640	674	772	144	176
ENST00000431639	1835	548	7592541	7592640	587	685	144	176
ENST00000457584	1845	548	7592541	7592640	597	695	144	176
ENST00000316024	4028	548	7606310	7606445	3617	3751	423	467
ENST00000396463	1922	548	7606310	7606445	1511	1645	423	467
ENST00000431639	1835	548	7606310	7606445	1424	1558	423	467
ENST00000457584	1845	548	7606310	7606445	1434	1568	423	467

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
ENST00000316024	4028	548	7592541	7592640	2780	2878	144	176
ENST00000396463	1922	548	7592541	7592640	674	772	144	176
ENST00000431639	1835	548	7592541	7592640	587	685	144	176
ENST00000457584	1845	548	7592541	7592640	597	695	144	176
ENST00000316024	4028	548	7606310	7606445	3617	3751	423	467
ENST00000396463	1922	548	7606310	7606445	1511	1645	423	467
ENST00000431639	1835	548	7606310	7606445	1424	1558	423	467
ENST00000457584	1845	548	7606310	7606445	1434	1568	423	467

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
Q9BUR4	144	176	1	548	Chain	ID=PRO_0000242696;Note=Telomerase Cajal body protein 1
Q9BUR4	144	176	1	548	Chain	ID=PRO_0000242696;Note=Telomerase Cajal body protein 1
Q9BUR4	144	176	1	548	Chain	ID=PRO_0000242696;Note=Telomerase Cajal body protein 1
Q9BUR4	144	176	1	548	Chain	ID=PRO_0000242696;Note=Telomerase Cajal body protein 1
Q9BUR4	144	176	164	164	Natural variant	ID=VAR_065873;Note=In DKCB3%3B disrupts telomerase localization to Cajal bodies resulting in misdirection of telomerase RNA to nucleoli. F->L;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21205863;Dbxref=dbSNP:rs281865547,PMID:21205863
Q9BUR4	144	176	164	164	Natural variant	ID=VAR_065873;Note=In DKCB3%3B disrupts telomerase localization to Cajal bodies resulting in misdirection of telomerase RNA to nucleoli. F->L;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21205863;Dbxref=dbSNP:rs281865547,PMID:21205863
Q9BUR4	144	176	164	164	Natural variant	ID=VAR_065873;Note=In DKCB3%3B disrupts telomerase localization to Cajal bodies resulting in misdirection of telomerase RNA to nucleoli. F->L;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21205863;Dbxref=dbSNP:rs281865547,PMID:21205863
Q9BUR4	144	176	164	164	Natural variant	ID=VAR_065873;Note=In DKCB3%3B disrupts telomerase localization to Cajal bodies resulting in misdirection of telomerase RNA to nucleoli. F->L;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21205863;Dbxref=dbSNP:rs281865547,PMID:21205863
Q9BUR4	144	176	167	206	Repeat	Note=WD 1;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BUR4	144	176	167	206	Repeat	Note=WD 1;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BUR4	144	176	167	206	Repeat	Note=WD 1;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BUR4	144	176	167	206	Repeat	Note=WD 1;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BUR4	423	467	1	548	Chain	ID=PRO_0000242696;Note=Telomerase Cajal body protein 1
Q9BUR4	423	467	1	548	Chain	ID=PRO_0000242696;Note=Telomerase Cajal body protein 1
Q9BUR4	423	467	1	548	Chain	ID=PRO_0000242696;Note=Telomerase Cajal body protein 1
Q9BUR4	423	467	1	548	Chain	ID=PRO_0000242696;Note=Telomerase Cajal body protein 1
Q9BUR4	423	467	435	435	Natural variant	ID=VAR_065876;Note=In DKCB3%3B shortened telomeres%3B disrupts telomerase localization to Cajal bodies resulting in misdirection of telomerase RNA to nucleoli. G->R;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:21205863,ECO:0000269\|Pub
Q9BUR4	423	467	435	435	Natural variant	ID=VAR_065876;Note=In DKCB3%3B shortened telomeres%3B disrupts telomerase localization to Cajal bodies resulting in misdirection of telomerase RNA to nucleoli. G->R;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:21205863,ECO:0000269\|Pub
Q9BUR4	423	467	435	435	Natural variant	ID=VAR_065876;Note=In DKCB3%3B shortened telomeres%3B disrupts telomerase localization to Cajal bodies resulting in misdirection of telomerase RNA to nucleoli. G->R;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:21205863,ECO:0000269\|Pub
Q9BUR4	423	467	435	435	Natural variant	ID=VAR_065876;Note=In DKCB3%3B shortened telomeres%3B disrupts telomerase localization to Cajal bodies resulting in misdirection of telomerase RNA to nucleoli. G->R;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:21205863,ECO:0000269\|Pub
Q9BUR4	423	467	411	450	Repeat	Note=WD 6;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BUR4	423	467	411	450	Repeat	Note=WD 6;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BUR4	423	467	411	450	Repeat	Note=WD 6;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BUR4	423	467	411	450	Repeat	Note=WD 6;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
Q9BUR4	144	176	1	548	Chain	ID=PRO_0000242696;Note=Telomerase Cajal body protein 1
Q9BUR4	144	176	1	548	Chain	ID=PRO_0000242696;Note=Telomerase Cajal body protein 1
Q9BUR4	144	176	1	548	Chain	ID=PRO_0000242696;Note=Telomerase Cajal body protein 1
Q9BUR4	144	176	1	548	Chain	ID=PRO_0000242696;Note=Telomerase Cajal body protein 1
Q9BUR4	144	176	164	164	Natural variant	ID=VAR_065873;Note=In DKCB3%3B disrupts telomerase localization to Cajal bodies resulting in misdirection of telomerase RNA to nucleoli. F->L;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21205863;Dbxref=dbSNP:rs281865547,PMID:21205863
Q9BUR4	144	176	164	164	Natural variant	ID=VAR_065873;Note=In DKCB3%3B disrupts telomerase localization to Cajal bodies resulting in misdirection of telomerase RNA to nucleoli. F->L;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21205863;Dbxref=dbSNP:rs281865547,PMID:21205863
Q9BUR4	144	176	164	164	Natural variant	ID=VAR_065873;Note=In DKCB3%3B disrupts telomerase localization to Cajal bodies resulting in misdirection of telomerase RNA to nucleoli. F->L;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21205863;Dbxref=dbSNP:rs281865547,PMID:21205863
Q9BUR4	144	176	164	164	Natural variant	ID=VAR_065873;Note=In DKCB3%3B disrupts telomerase localization to Cajal bodies resulting in misdirection of telomerase RNA to nucleoli. F->L;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:21205863;Dbxref=dbSNP:rs281865547,PMID:21205863
Q9BUR4	144	176	167	206	Repeat	Note=WD 1;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BUR4	144	176	167	206	Repeat	Note=WD 1;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BUR4	144	176	167	206	Repeat	Note=WD 1;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BUR4	144	176	167	206	Repeat	Note=WD 1;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BUR4	423	467	1	548	Chain	ID=PRO_0000242696;Note=Telomerase Cajal body protein 1
Q9BUR4	423	467	1	548	Chain	ID=PRO_0000242696;Note=Telomerase Cajal body protein 1
Q9BUR4	423	467	1	548	Chain	ID=PRO_0000242696;Note=Telomerase Cajal body protein 1
Q9BUR4	423	467	1	548	Chain	ID=PRO_0000242696;Note=Telomerase Cajal body protein 1
Q9BUR4	423	467	435	435	Natural variant	ID=VAR_065876;Note=In DKCB3%3B shortened telomeres%3B disrupts telomerase localization to Cajal bodies resulting in misdirection of telomerase RNA to nucleoli. G->R;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:21205863,ECO:0000269\|Pub
Q9BUR4	423	467	435	435	Natural variant	ID=VAR_065876;Note=In DKCB3%3B shortened telomeres%3B disrupts telomerase localization to Cajal bodies resulting in misdirection of telomerase RNA to nucleoli. G->R;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:21205863,ECO:0000269\|Pub
Q9BUR4	423	467	435	435	Natural variant	ID=VAR_065876;Note=In DKCB3%3B shortened telomeres%3B disrupts telomerase localization to Cajal bodies resulting in misdirection of telomerase RNA to nucleoli. G->R;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:21205863,ECO:0000269\|Pub
Q9BUR4	423	467	435	435	Natural variant	ID=VAR_065876;Note=In DKCB3%3B shortened telomeres%3B disrupts telomerase localization to Cajal bodies resulting in misdirection of telomerase RNA to nucleoli. G->R;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269\|PubMed:21205863,ECO:0000269\|Pub
Q9BUR4	423	467	411	450	Repeat	Note=WD 6;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BUR4	423	467	411	450	Repeat	Note=WD 6;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BUR4	423	467	411	450	Repeat	Note=WD 6;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q9BUR4	423	467	411	450	Repeat	Note=WD 6;Ontology_term=ECO:0000255;evidence=ECO:0000255

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SNVs in the skipped exons for WRAP53

- 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
SKCM	TCGA-EE-A2MS-06	exon_skip_148879	7604059	7604147	7604071	7604071	Nonsense_Mutation	C	T	p.R219*
SKCM	TCGA-EE-A2MS-06	exon_skip_148879	7604059	7604147	7604071	7604071	Nonsense_Mutation	C	T	p.R219X
CESC	TCGA-EA-A411-01	exon_skip_148879	7604059	7604147	7604112	7604112	Nonsense_Mutation	T	A	p.Y232*

- 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
MM127_SKIN	7592542	7592640	7592612	7592613	Missense_Mutation	CC	TT	p.P168F
HCC1833_LUNG	7604059	7604147	7604062	7604062	Missense_Mutation	C	T	p.P216S
TE11_OESOPHAGUS	7604059	7604147	7604068	7604068	Missense_Mutation	C	T	p.L218F
MCC13_SKIN	7604777	7604867	7604808	7604808	Missense_Mutation	C	T	p.H255Y
MCC13_SKIN	7604745	7604867	7604808	7604808	Missense_Mutation	C	T	p.H255Y
GRST_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	7604777	7604867	7604820	7604820	Missense_Mutation	G	A	p.A259T
GRST_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	7604745	7604867	7604820	7604820	Missense_Mutation	G	A	p.A259T
LIM1215_LARGE_INTESTINE	7604777	7604867	7604820	7604820	Missense_Mutation	G	A	p.A259T
LIM1215_LARGE_INTESTINE	7604745	7604867	7604820	7604820	Missense_Mutation	G	A	p.A259T
CAPAN2_PANCREAS	7604777	7604867	7604845	7604845	Missense_Mutation	C	A	p.S267Y
CAPAN2_PANCREAS	7604745	7604867	7604845	7604845	Missense_Mutation	C	A	p.S267Y
LNCAPCLONEFGC_PROSTATE	7605662	7605870	7605823	7605823	Missense_Mutation	C	A	p.L373I
T84_LARGE_INTESTINE	7605662	7605870	7605842	7605842	Missense_Mutation	G	C	p.G379A
HCT116_LARGE_INTESTINE	7606311	7606445	7606439	7606439	Missense_Mutation	G	A	p.G466D
C8166_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	7605662	7605870	7605741	7605741	Nonsense_Mutation	C	A	p.Y345*

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for WRAP53

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_148878	17	7591965:7592397:7592541:7592640:7592907:7593019	7592541:7592640	ENST00000431639.2,ENST00000498311.1,ENST00000396463.2,ENST00000467699.1,ENST00000316024.5,ENST00000457584.2	PAAD	rs2287498	chr17:7592560	C/T	1.09e-04

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for WRAP53

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for WRAP53

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RelatedDrugs for WRAP53

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 WRAP53

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
WRAP53	C3151442	DYSKERATOSIS CONGENITA, AUTOSOMAL RECESSIVE, 3	1	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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