ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for UBE2D3

Gene summary

Gene information	Gene symbol	UBE2D3
	Gene ID	7323
	Gene name	ubiquitin conjugating enzyme E2 D3
	Synonyms	E2(17)KB3\|UBC4/5\|UBCH5C
	Cytomap	4q24
	Type of gene	protein-coding
	Description	ubiquitin-conjugating enzyme E2 D3(E3-independent) E2 ubiquitin-conjugating enzyme D3E2 ubiquitin-conjugating enzyme D3ubiquitin carrier protein D3ubiquitin conjugating enzyme E2D 3ubiquitin-conjugating enzyme E2(17)KB 3ubiquitin-conjugating enzyme
	Modification date	20180523
	UniProtAcc	P61077
	Context	PubMed: UBE2D3 [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
UBE2D3	GO:0000209	protein polyubiquitination	14765125\|16522193
UBE2D3	GO:0006513	protein monoubiquitination	20347421
UBE2D3	GO:0016567	protein ubiquitination	9990509\|21532592
UBE2D3	GO:0043161	proteasome-mediated ubiquitin-dependent protein catabolic process	20347421
UBE2D3	GO:0051865	protein autoubiquitination	21068390
UBE2D3	GO:0070936	protein K48-linked ubiquitination	20061386
UBE2D3	GO:0070979	protein K11-linked ubiquitination	20061386

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Exon skipping events across known transcript of Ensembl for UBE2D3 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 UBE2D3

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 UBE2D3

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_431476	4	103718559:103718617:103720084:103720134:103720563:103720657	103720084:103720134	ENSG00000109332.15	ENST00000343106.5
exon_skip_431479	4	103720623:103720657:103722610:103722716:103723717:103723795	103722610:103722716	ENSG00000109332.15	ENST00000505009.1,ENST00000502404.1,ENST00000508474.1,ENST00000504211.1,ENST00000338145.3,ENST00000505307.1,ENST00000343106.5,ENST00000507845.1,ENST00000505207.1,ENST00000394803.5,ENST00000510129.1,ENST00000508635.1,ENST00000349311.8,ENST00000394801.4,ENS
exon_skip_431485	4	103723768:103723795:103730224:103730316:103730828:103730860	103730224:103730316	ENSG00000109332.15	ENST00000514755.1,ENST00000505307.1,ENST00000503418.1,ENST00000508635.1
exon_skip_431486	4	103723768:103723795:103730224:103730341:103730828:103730860	103730224:103730341	ENSG00000109332.15	ENST00000508974.1
exon_skip_431492	4	103730828:103730860:103730948:103731012:103747641:103747776	103730948:103731012	ENSG00000109332.15	ENST00000514755.1,ENST00000508238.1,ENST00000508974.1,ENST00000338145.3,ENST00000505307.1,ENST00000343106.5,ENST00000513098.1,ENST00000502690.1,ENST00000394803.5,ENST00000503418.1,ENST00000503282.1,ENST00000349311.8,ENST00000394801.4,ENST00000453744.2,ENS
exon_skip_431499	4	103730948:103731012:103746395:103746474:103746878:103746937	103746395:103746474	ENSG00000109332.15	ENST00000502404.1
exon_skip_431500	4	103730948:103731012:103746395:103746474:103746894:103746942	103746395:103746474	ENSG00000109332.15	ENST00000507845.1
exon_skip_431505	4	103730948:103731012:103747641:103747776:103789871:103790018	103747641:103747776	ENSG00000109332.15	ENST00000508238.1
exon_skip_431507	4	103730948:103731012:103747641:103747793:103789871:103790018	103747641:103747793	ENSG00000109332.15	ENST00000338145.3
exon_skip_431517	4	103747641:103747793:103748748:103748898:103749100:103749167	103748748:103748898	ENSG00000109332.15	ENST00000502690.1

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for UBE2D3

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_431476	4	103718559:103718617:103720084:103720134:103720563:103720657	103720084:103720134	ENSG00000109332.15	ENST00000343106.5
exon_skip_431479	4	103720623:103720657:103722610:103722716:103723717:103723795	103722610:103722716	ENSG00000109332.15	ENST00000453744.2,ENST00000394801.4,ENST00000394803.5,ENST00000394804.2,ENST00000508474.1,ENST00000343106.5,ENST00000321805.7,ENST00000350435.7,ENST00000338145.3,ENST00000349311.8,ENST00000504211.1,ENST00000505009.1,ENST00000357194.6,ENST00000505207.1,ENS
exon_skip_431485	4	103723768:103723795:103730224:103730316:103730828:103730860	103730224:103730316	ENSG00000109332.15	ENST00000508635.1,ENST00000505307.1,ENST00000514755.1,ENST00000503418.1
exon_skip_431486	4	103723768:103723795:103730224:103730341:103730828:103730860	103730224:103730341	ENSG00000109332.15	ENST00000508974.1
exon_skip_431492	4	103730828:103730860:103730948:103731012:103747641:103747776	103730948:103731012	ENSG00000109332.15	ENST00000453744.2,ENST00000394801.4,ENST00000394803.5,ENST00000394804.2,ENST00000343106.5,ENST00000503742.1,ENST00000321805.7,ENST00000338145.3,ENST00000349311.8,ENST00000505307.1,ENST00000508238.1,ENST00000514755.1,ENST00000508974.1,ENST00000502690.1,ENS
exon_skip_431499	4	103730948:103731012:103746395:103746474:103746878:103746937	103746395:103746474	ENSG00000109332.15	ENST00000502404.1
exon_skip_431500	4	103730948:103731012:103746395:103746474:103746894:103746942	103746395:103746474	ENSG00000109332.15	ENST00000507845.1
exon_skip_431505	4	103730948:103731012:103747641:103747776:103789871:103790018	103747641:103747776	ENSG00000109332.15	ENST00000508238.1
exon_skip_431507	4	103730948:103731012:103747641:103747793:103789871:103790018	103747641:103747793	ENSG00000109332.15	ENST00000338145.3
exon_skip_431517	4	103747641:103747793:103748748:103748898:103749100:103749167	103748748:103748898	ENSG00000109332.15	ENST00000502690.1

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 UBE2D3

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
ENST00000338145	103747641	103747793	3UTR-3CDS
ENST00000321805	103722610	103722716	Frame-shift
ENST00000338145	103722610	103722716	Frame-shift
ENST00000349311	103722610	103722716	Frame-shift
ENST00000394801	103722610	103722716	Frame-shift
ENST00000394803	103722610	103722716	Frame-shift
ENST00000394804	103722610	103722716	Frame-shift
ENST00000453744	103722610	103722716	Frame-shift
ENST00000321805	103730948	103731012	Frame-shift
ENST00000338145	103730948	103731012	Frame-shift
ENST00000349311	103730948	103731012	Frame-shift
ENST00000394801	103730948	103731012	Frame-shift
ENST00000394803	103730948	103731012	Frame-shift
ENST00000394804	103730948	103731012	Frame-shift
ENST00000453744	103730948	103731012	Frame-shift

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
ENST00000338145	103747641	103747793	3UTR-3CDS
ENST00000321805	103722610	103722716	Frame-shift
ENST00000338145	103722610	103722716	Frame-shift
ENST00000349311	103722610	103722716	Frame-shift
ENST00000394801	103722610	103722716	Frame-shift
ENST00000394803	103722610	103722716	Frame-shift
ENST00000394804	103722610	103722716	Frame-shift
ENST00000453744	103722610	103722716	Frame-shift
ENST00000321805	103730948	103731012	Frame-shift
ENST00000338145	103730948	103731012	Frame-shift
ENST00000349311	103730948	103731012	Frame-shift
ENST00000394801	103730948	103731012	Frame-shift
ENST00000394803	103730948	103731012	Frame-shift
ENST00000394804	103730948	103731012	Frame-shift
ENST00000453744	103730948	103731012	Frame-shift

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Infer the effects of exon skipping event on protein functional features for UBE2D3

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 UBE2D3

- 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.

UBE2D3_LIHC_exon_skip_431479_psi_boxplot.png
boxplot

UBE2D3_LUAD_exon_skip_431479_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
LUAD	TCGA-05-4420-01	exon_skip_431479	103722611	103722716	103722680	103722681	Frame_Shift_Ins	-	A	p.I78fs
LUAD	TCGA-05-4420-01	exon_skip_431479	103722611	103722716	103722680	103722681	Frame_Shift_Ins	-	A	p.Q79fs
LIHC	TCGA-CC-5259-01	exon_skip_431479	103722611	103722716	103722609	103722609	Splice_Site	A	C	.

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

Depth of coverage in three exons	Mutation description
	Sample: TCGA-CC-5259-01
	Cancer type: LIHC
	ESID: exon_skip_431479
	Skipped exon start: 103722611
	Skipped exon end: 103722716
	Mutation start: 103722609
	Mutation end: 103722609
	Mutation type: Splice_Site
	Reference seq: A
	Mutation seq: C
	AAchange: .
exon_skip_431479_LIHC_TCGA-CC-5259-01.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
HEC251_ENDOMETRIUM	103722611	103722716	103722616	103722616	Missense_Mutation	G	T	p.S100Y
KARPAS45_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	103730949	103731012	103730993	103730993	Missense_Mutation	C	T	p.R15H
RKO_LARGE_INTESTINE	103730949	103731012	103730996	103730996	Missense_Mutation	G	A	p.A14V

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for UBE2D3

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_431517	4	103747641:103747793:103748748:103748898:103749100:103749167	103748748:103748898	ENST00000502690.1	GBM	rs223390	chr4:103748797	A/G	2.79e-05
exon_skip_431517	4	103747641:103747793:103748748:103748898:103749100:103749167	103748748:103748898	ENST00000502690.1	CESC	rs223390	chr4:103748797	A/G	1.98e-05
exon_skip_431517	4	103747641:103747793:103748748:103748898:103749100:103749167	103748748:103748898	ENST00000502690.1	CESC	rs223390	chr4:103748797	A/G	4.79e-04
exon_skip_431517	4	103747641:103747793:103748748:103748898:103749100:103749167	103748748:103748898	ENST00000502690.1	COAD	rs223390	chr4:103748797	A/G	5.27e-08
exon_skip_431517	4	103747641:103747793:103748748:103748898:103749100:103749167	103748748:103748898	ENST00000502690.1	COAD	rs223390	chr4:103748797	A/G	1.06e-05
exon_skip_431517	4	103747641:103747793:103748748:103748898:103749100:103749167	103748748:103748898	ENST00000502690.1	COAD	rs223390	chr4:103748797	A/G	5.32e-04
exon_skip_431517	4	103747641:103747793:103748748:103748898:103749100:103749167	103748748:103748898	ENST00000502690.1	COAD	rs223390	chr4:103748797	A/G	8.19e-04
exon_skip_431517	4	103747641:103747793:103748748:103748898:103749100:103749167	103748748:103748898	ENST00000502690.1	COAD	rs223390	chr4:103748797	A/G	1.95e-03
exon_skip_431517	4	103747641:103747793:103748748:103748898:103749100:103749167	103748748:103748898	ENST00000502690.1	BLCA	rs223390	chr4:103748797	A/G	3.40e-04
exon_skip_431517	4	103747641:103747793:103748748:103748898:103749100:103749167	103748748:103748898	ENST00000502690.1	ESCA	rs223390	chr4:103748797	A/G	1.72e-04
exon_skip_431517	4	103747641:103747793:103748748:103748898:103749100:103749167	103748748:103748898	ENST00000502690.1	HNSC	rs223390	chr4:103748797	A/G	2.59e-09
exon_skip_431517	4	103747641:103747793:103748748:103748898:103749100:103749167	103748748:103748898	ENST00000502690.1	HNSC	rs223390	chr4:103748797	A/G	8.23e-07
exon_skip_431517	4	103747641:103747793:103748748:103748898:103749100:103749167	103748748:103748898	ENST00000502690.1	HNSC	rs223390	chr4:103748797	A/G	6.53e-06
exon_skip_431517	4	103747641:103747793:103748748:103748898:103749100:103749167	103748748:103748898	ENST00000502690.1	HNSC	rs223390	chr4:103748797	A/G	1.10e-04
exon_skip_431517	4	103747641:103747793:103748748:103748898:103749100:103749167	103748748:103748898	ENST00000502690.1	BRCA	rs223390	chr4:103748797	A/G	5.06e-15
exon_skip_431517	4	103747641:103747793:103748748:103748898:103749100:103749167	103748748:103748898	ENST00000502690.1	BRCA	rs223390	chr4:103748797	A/G	1.46e-11
exon_skip_431517	4	103747641:103747793:103748748:103748898:103749100:103749167	103748748:103748898	ENST00000502690.1	BRCA	rs223390	chr4:103748797	A/G	4.98e-11
exon_skip_431517	4	103747641:103747793:103748748:103748898:103749100:103749167	103748748:103748898	ENST00000502690.1	BRCA	rs223390	chr4:103748797	A/G	3.86e-05
exon_skip_431517	4	103747641:103747793:103748748:103748898:103749100:103749167	103748748:103748898	ENST00000502690.1	BRCA	rs223390	chr4:103748797	A/G	1.67e-03
exon_skip_431517	4	103747641:103747793:103748748:103748898:103749100:103749167	103748748:103748898	ENST00000502690.1	LGG	rs223390	chr4:103748797	A/G	3.91e-08
exon_skip_431517	4	103747641:103747793:103748748:103748898:103749100:103749167	103748748:103748898	ENST00000502690.1	LGG	rs223390	chr4:103748797	A/G	1.20e-04
exon_skip_431517	4	103747641:103747793:103748748:103748898:103749100:103749167	103748748:103748898	ENST00000502690.1	KIRC	rs223390	chr4:103748797	A/G	1.53e-06
exon_skip_431517	4	103747641:103747793:103748748:103748898:103749100:103749167	103748748:103748898	ENST00000502690.1	KIRC	rs223390	chr4:103748797	A/G	2.48e-04
exon_skip_431517	4	103747641:103747793:103748748:103748898:103749100:103749167	103748748:103748898	ENST00000502690.1	KIRC	rs223390	chr4:103748797	A/G	3.75e-04
exon_skip_431517	4	103747641:103747793:103748748:103748898:103749100:103749167	103748748:103748898	ENST00000502690.1	LUAD	rs223390	chr4:103748797	A/G	1.85e-05
exon_skip_431517	4	103747641:103747793:103748748:103748898:103749100:103749167	103748748:103748898	ENST00000502690.1	LUAD	rs223390	chr4:103748797	A/G	2.03e-04
exon_skip_431517	4	103747641:103747793:103748748:103748898:103749100:103749167	103748748:103748898	ENST00000502690.1	LUAD	rs223390	chr4:103748797	A/G	1.92e-03
exon_skip_431517	4	103747641:103747793:103748748:103748898:103749100:103749167	103748748:103748898	ENST00000502690.1	LIHC	rs223390	chr4:103748797	A/G	4.69e-04
exon_skip_431517	4	103747641:103747793:103748748:103748898:103749100:103749167	103748748:103748898	ENST00000502690.1	LUSC	rs223390	chr4:103748797	A/G	1.07e-06
exon_skip_431517	4	103747641:103747793:103748748:103748898:103749100:103749167	103748748:103748898	ENST00000502690.1	LUSC	rs223390	chr4:103748797	A/G	2.56e-06
exon_skip_431517	4	103747641:103747793:103748748:103748898:103749100:103749167	103748748:103748898	ENST00000502690.1	LUSC	rs223390	chr4:103748797	A/G	1.19e-05
exon_skip_431517	4	103747641:103747793:103748748:103748898:103749100:103749167	103748748:103748898	ENST00000502690.1	PAAD	rs223390	chr4:103748797	A/G	4.19e-04
exon_skip_431517	4	103747641:103747793:103748748:103748898:103749100:103749167	103748748:103748898	ENST00000502690.1	PRAD	rs223390	chr4:103748797	A/G	7.01e-06
exon_skip_431517	4	103747641:103747793:103748748:103748898:103749100:103749167	103748748:103748898	ENST00000502690.1	SARC	rs223390	chr4:103748797	A/G	7.49e-06
exon_skip_431517	4	103747641:103747793:103748748:103748898:103749100:103749167	103748748:103748898	ENST00000502690.1	TGCT	rs223390	chr4:103748797	A/G	1.26e-05
exon_skip_431517	4	103747641:103747793:103748748:103748898:103749100:103749167	103748748:103748898	ENST00000502690.1	STAD	rs223390	chr4:103748797	A/G	7.62e-13
exon_skip_431517	4	103747641:103747793:103748748:103748898:103749100:103749167	103748748:103748898	ENST00000502690.1	STAD	rs223390	chr4:103748797	A/G	2.96e-10
exon_skip_431517	4	103747641:103747793:103748748:103748898:103749100:103749167	103748748:103748898	ENST00000502690.1	STAD	rs223390	chr4:103748797	A/G	9.80e-05
exon_skip_431517	4	103747641:103747793:103748748:103748898:103749100:103749167	103748748:103748898	ENST00000502690.1	THCA	rs223390	chr4:103748797	A/G	1.97e-08
exon_skip_431517	4	103747641:103747793:103748748:103748898:103749100:103749167	103748748:103748898	ENST00000502690.1	THCA	rs223390	chr4:103748797	A/G	4.66e-05
exon_skip_431517	4	103747641:103747793:103748748:103748898:103749100:103749167	103748748:103748898	ENST00000502690.1	UCEC	rs223390	chr4:103748797	A/G	7.14e-05

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for UBE2D3

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for UBE2D3

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RelatedDrugs for UBE2D3

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 UBE2D3

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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