ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for UBE2A

Gene summary

Gene information	Gene symbol	UBE2A
	Gene ID	7319
	Gene name	ubiquitin conjugating enzyme E2 A
	Synonyms	HHR6A\|MRXS30\|MRXSN\|RAD6A\|UBC2
	Cytomap	Xq24
	Type of gene	protein-coding
	Description	ubiquitin-conjugating enzyme E2 AE2 ubiquitin-conjugating enzyme ARAD6 homolog Aubiquitin carrier protein Aubiquitin-conjugating enzyme E2Aubiquitin-protein ligase A
	Modification date	20180523
	UniProtAcc	P49459
	Context	PubMed: UBE2A [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
UBE2A	GO:0008284	positive regulation of cell proliferation	11953320
UBE2A	GO:0033522	histone H2A ubiquitination	11953320
UBE2A	GO:0051865	protein autoubiquitination	11953320
UBE2A	GO:0070936	protein K48-linked ubiquitination	20061386
UBE2A	GO:0070979	protein K11-linked ubiquitination	20061386

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Exon skipping events across known transcript of Ensembl for UBE2A 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 UBE2A

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 UBE2A

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_512207	X	118708863:118708944:118709337:118709363:118716550:118716639	118709337:118709363	ENSG00000077721.11	ENST00000346330.3
exon_skip_512208	X	118709337:118709363:118715469:118715559:118716550:118716639	118715469:118715559	ENSG00000077721.11	ENST00000371558.2
exon_skip_512212	X	118709337:118709363:118716550:118716639:118717089:118717426	118716550:118716639	ENSG00000077721.11	ENST00000346330.3

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for UBE2A

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_512207	X	118708863:118708944:118709337:118709363:118716550:118716639	118709337:118709363	ENSG00000077721.11	ENST00000346330.3
exon_skip_512208	X	118709337:118709363:118715469:118715559:118716550:118716639	118715469:118715559	ENSG00000077721.11	ENST00000371558.2
exon_skip_512212	X	118709337:118709363:118716550:118716639:118717089:118717426	118716550:118716639	ENSG00000077721.11	ENST00000346330.3

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 UBE2A

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
ENST00000371558	118715469	118715559	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
ENST00000371558	118715469	118715559	In-frame

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Infer the effects of exon skipping event on protein functional features for UBE2A

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
ENST00000371558	1813	152	118715469	118715559	326	415	50	80

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
ENST00000371558	1813	152	118715469	118715559	326	415	50	80

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
P49459	50	80	1	75	Alternative sequence	ID=VSP_043851;Note=In isoform 3. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
P49459	50	80	51	80	Alternative sequence	ID=VSP_043852;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
P49459	50	80	1	152	Chain	ID=PRO_0000082445;Note=Ubiquitin-conjugating enzyme E2 A

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
P49459	50	80	1	75	Alternative sequence	ID=VSP_043851;Note=In isoform 3. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
P49459	50	80	51	80	Alternative sequence	ID=VSP_043852;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
P49459	50	80	1	152	Chain	ID=PRO_0000082445;Note=Ubiquitin-conjugating enzyme E2 A

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SNVs in the skipped exons for UBE2A

- 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.

UBE2A_BRCA_exon_skip_512208_psi_boxplot.png
boxplot

UBE2A_DLBC_exon_skip_512208_psi_boxplot.png
boxplot

UBE2A_LIHC_exon_skip_512208_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
BRCA	TCGA-B6-A0WV-01	exon_skip_512208	118715470	118715559	118715485	118715485	Frame_Shift_Del	C	-	p.T56fs
LIHC	TCGA-DD-A39Y-01	exon_skip_512208	118715470	118715559	118715555	118715555	Frame_Shift_Del	A	-	p.P4fs
DLBC	TCGA-FF-8041-01	exon_skip_512208	118715470	118715559	118715490	118715490	Nonsense_Mutation	G	T	p.E58X

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

Depth of coverage in three exons	Mutation description
	Sample: TCGA-FF-8041-01
	Cancer type: DLBC
	ESID: exon_skip_512208
	Skipped exon start: 118715470
	Skipped exon end: 118715559
	Mutation start: 118715490
	Mutation end: 118715490
	Mutation type: Nonsense_Mutation
	Reference seq: G
	Mutation seq: T
	AAchange: p.E58X
exon_skip_491406_DLBC_TCGA-FF-8041-01.png
exon_skip_512208_DLBC_TCGA-FF-8041-01.png
	Sample: TCGA-B6-A0WV-01
	Cancer type: BRCA
	ESID: exon_skip_512208
	Skipped exon start: 118715470
	Skipped exon end: 118715559
	Mutation start: 118715485
	Mutation end: 118715485
	Mutation type: Frame_Shift_Del
	Reference seq: C
	Mutation seq: -
	AAchange: p.T56fs
exon_skip_512208_BRCA_TCGA-B6-A0WV-01.png
	Sample: TCGA-DD-A39Y-01
	Cancer type: LIHC
	ESID: exon_skip_512208
	Skipped exon start: 118715470
	Skipped exon end: 118715559
	Mutation start: 118715555
	Mutation end: 118715555
	Mutation type: Frame_Shift_Del
	Reference seq: A
	Mutation seq: -
	AAchange: p.P4fs
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- 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

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for UBE2A

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 UBE2A

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for UBE2A

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RelatedDrugs for UBE2A

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 UBE2A

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
UBE2A	C3275464	MENTAL RETARDATION, X-LINKED, SYNDROMIC, NASCIMENTO TYPE	1	ORPHANET;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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