ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for NT5DC2

Gene summary

Gene information	Gene symbol	NT5DC2
	Gene ID	64943
	Gene name	5'-nucleotidase domain containing 2
	Synonyms	-
	Cytomap	3p21.1
	Type of gene	protein-coding
	Description	5'-nucleotidase domain-containing protein 2
	Modification date	20180523
	UniProtAcc	Q9H857
	Context	PubMed: NT5DC2 [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 NT5DC2 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 NT5DC2

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 NT5DC2

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_384842	3	52558402:52558627:52558832:52558897:52558978:52559119	52558832:52558897	ENSG00000168268.6	ENST00000479024.1,ENST00000463947.1
exon_skip_384850	3	52559075:52559119:52559224:52559311:52561309:52561382	52559224:52559311	ENSG00000168268.6	ENST00000307092.4,ENST00000307076.4,ENST00000422318.2,ENST00000492555.1,ENST00000478091.1,ENST00000466112.1,ENST00000459839.1,ENST00000463947.1
exon_skip_384853	3	52561309:52561391:52561632:52561734:52561844:52561947	52561632:52561734	ENSG00000168268.6	ENST00000307092.4,ENST00000489316.1,ENST00000307076.4,ENST00000422318.2,ENST00000492555.1,ENST00000459839.1
exon_skip_384857	3	52561309:52561391:52561632:52561947:52562028:52562089	52561632:52561947	ENSG00000168268.6	ENST00000478091.1
exon_skip_384862	3	52561632:52561734:52561844:52561947:52562028:52562089	52561844:52561947	ENSG00000168268.6	ENST00000307092.4,ENST00000489316.1,ENST00000307076.4,ENST00000422318.2,ENST00000492555.1,ENST00000459839.1
exon_skip_384869	3	52562207:52562327:52562461:52562555:52562652:52562708	52562461:52562555	ENSG00000168268.6	ENST00000307092.4,ENST00000307076.4,ENST00000422318.2,ENST00000486792.1,ENST00000459839.1
exon_skip_384870	3	52562207:52562327:52562527:52562555:52562652:52562708	52562527:52562555	ENSG00000168268.6	ENST00000489316.1,ENST00000471522.1
exon_skip_384872	3	52562652:52562708:52562876:52562951:52563165:52563350	52562876:52562951	ENSG00000168268.6	ENST00000307076.4,ENST00000422318.2,ENST00000492555.1,ENST00000487779.1,ENST00000471522.1

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for NT5DC2

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_384842	3	52558402:52558627:52558832:52558897:52558978:52559119	52558832:52558897	ENSG00000168268.6	ENST00000463947.1,ENST00000479024.1
exon_skip_384850	3	52559075:52559119:52559224:52559311:52561309:52561382	52559224:52559311	ENSG00000168268.6	ENST00000307092.4,ENST00000463947.1,ENST00000307076.4,ENST00000422318.2,ENST00000459839.1,ENST00000492555.1,ENST00000466112.1,ENST00000478091.1
exon_skip_384853	3	52561309:52561391:52561632:52561734:52561844:52561947	52561632:52561734	ENSG00000168268.6	ENST00000307092.4,ENST00000307076.4,ENST00000422318.2,ENST00000459839.1,ENST00000492555.1,ENST00000489316.1
exon_skip_384857	3	52561309:52561391:52561632:52561947:52562028:52562089	52561632:52561947	ENSG00000168268.6	ENST00000478091.1
exon_skip_384862	3	52561632:52561734:52561844:52561947:52562028:52562089	52561844:52561947	ENSG00000168268.6	ENST00000307092.4,ENST00000307076.4,ENST00000422318.2,ENST00000459839.1,ENST00000492555.1,ENST00000489316.1
exon_skip_384869	3	52562207:52562327:52562461:52562555:52562652:52562708	52562461:52562555	ENSG00000168268.6	ENST00000307092.4,ENST00000307076.4,ENST00000422318.2,ENST00000459839.1,ENST00000486792.1
exon_skip_384870	3	52562207:52562327:52562527:52562555:52562652:52562708	52562527:52562555	ENSG00000168268.6	ENST00000489316.1,ENST00000471522.1
exon_skip_384872	3	52562652:52562708:52562876:52562951:52563165:52563350	52562876:52562951	ENSG00000168268.6	ENST00000307076.4,ENST00000422318.2,ENST00000492555.1,ENST00000471522.1,ENST00000487779.1

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 NT5DC2

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
ENST00000307076	52561844	52561947	Frame-shift
ENST00000307076	52562461	52562555	Frame-shift
ENST00000307076	52559224	52559311	In-frame
ENST00000307076	52561632	52561734	In-frame
ENST00000307076	52562876	52562951	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
ENST00000307076	52561844	52561947	Frame-shift
ENST00000307076	52562461	52562555	Frame-shift
ENST00000307076	52559224	52559311	In-frame
ENST00000307076	52561632	52561734	In-frame
ENST00000307076	52562876	52562951	In-frame

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Infer the effects of exon skipping event on protein functional features for NT5DC2

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
ENST00000307076	2064	520	52562876	52562951	708	782	102	127
ENST00000307076	2064	520	52561632	52561734	1226	1327	275	308
ENST00000307076	2064	520	52559224	52559311	1410	1496	336	365

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
ENST00000307076	2064	520	52562876	52562951	708	782	102	127
ENST00000307076	2064	520	52561632	52561734	1226	1327	275	308
ENST00000307076	2064	520	52559224	52559311	1410	1496	336	365

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
Q9H857	102	127	1	130	Alternative sequence	ID=VSP_019951;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.1
Q9H857	102	127	103	127	Alternative sequence	ID=VSP_019953;Note=In isoform 3. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9H857	102	127	1	520	Chain	ID=PRO_0000247224;Note=5'-nucleotidase domain-containing protein 2
Q9H857	275	308	1	520	Chain	ID=PRO_0000247224;Note=5'-nucleotidase domain-containing protein 2
Q9H857	336	365	1	520	Chain	ID=PRO_0000247224;Note=5'-nucleotidase domain-containing protein 2
Q9H857	336	365	358	358	Metal binding	Note=Magnesium;Ontology_term=ECO:0000250;evidence=ECO:0000250

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
Q9H857	102	127	1	130	Alternative sequence	ID=VSP_019951;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|Ref.1
Q9H857	102	127	103	127	Alternative sequence	ID=VSP_019953;Note=In isoform 3. Missing;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q9H857	102	127	1	520	Chain	ID=PRO_0000247224;Note=5'-nucleotidase domain-containing protein 2
Q9H857	275	308	1	520	Chain	ID=PRO_0000247224;Note=5'-nucleotidase domain-containing protein 2
Q9H857	336	365	1	520	Chain	ID=PRO_0000247224;Note=5'-nucleotidase domain-containing protein 2
Q9H857	336	365	358	358	Metal binding	Note=Magnesium;Ontology_term=ECO:0000250;evidence=ECO:0000250

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SNVs in the skipped exons for NT5DC2

- 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.

NT5DC2_COAD_exon_skip_384850_psi_boxplot.png
boxplot

NT5DC2_HNSC_exon_skip_384850_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
HNSC	TCGA-QK-A6VB-01	exon_skip_384850	52559225	52559311	52559266	52559266	Frame_Shift_Del	G	-	p.R352fs
LIHC	TCGA-DD-A3A0-01	exon_skip_384850	52559225	52559311	52559300	52559300	Frame_Shift_Del	A	-	p.F340fs
LIHC	TCGA-DD-A39Y-01	exon_skip_384853	52561633	52561734	52561679	52561679	Frame_Shift_Del	C	-	p.V294fs
LIHC	TCGA-DD-A39Y-01	exon_skip_384857	52561633	52561947	52561679	52561679	Frame_Shift_Del	C	-	p.V294fs
LIHC	TCGA-DD-A39Y-01	exon_skip_384869	52562462	52562555	52562508	52562508	Frame_Shift_Del	C	-	p.G162fs
LIHC	TCGA-DD-A39Y-01	exon_skip_384869	52562462	52562555	52562508	52562508	Frame_Shift_Del	C	-	p.G199fs
LIHC	TCGA-DD-A3A0-01	exon_skip_384869	52562462	52562555	52562508	52562508	Frame_Shift_Del	C	-	p.G162fs
COAD	TCGA-G4-6309-01	exon_skip_384850	52559225	52559311	52559312	52559312	Splice_Site	C	A	.
SKCM	TCGA-D3-A51T-06	exon_skip_384869	52562462	52562555	52562556	52562556	Splice_Site	C	T	.
SKCM	TCGA-D3-A51T-06	exon_skip_384870	52562528	52562555	52562556	52562556	Splice_Site	C	T	.

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

Depth of coverage in three exons	Mutation description
	Sample: TCGA-G4-6309-01
	Cancer type: COAD
	ESID: exon_skip_384850
	Skipped exon start: 52559225
	Skipped exon end: 52559311
	Mutation start: 52559312
	Mutation end: 52559312
	Mutation type: Splice_Site
	Reference seq: C
	Mutation seq: A
	AAchange: .
exon_skip_143553_COAD_TCGA-G4-6309-01.png
exon_skip_350036_COAD_TCGA-G4-6309-01.png
exon_skip_384850_COAD_TCGA-G4-6309-01.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
HCC2279_LUNG	52558833	52558897	52558846	52558846	Missense_Mutation	G	A	p.R430W
TOV21G_OVARY	52558833	52558897	52558856	52558856	Missense_Mutation	C	A	p.W426C
LU99_LUNG	52559225	52559311	52559251	52559251	Missense_Mutation	C	T	p.G357R
OVK18_OVARY	52561633	52561947	52561640	52561640	Missense_Mutation	G	A	p.R307W
OVK18_OVARY	52561633	52561734	52561640	52561640	Missense_Mutation	G	A	p.R307W
HEC108_ENDOMETRIUM	52561633	52561947	52561697	52561697	Missense_Mutation	G	A	p.R288C
HEC108_ENDOMETRIUM	52561633	52561734	52561697	52561697	Missense_Mutation	G	A	p.R288C
ISTMES2_PLEURA	52561633	52561947	52561721	52561721	Missense_Mutation	G	A	p.R280W
ISTMES2_PLEURA	52561633	52561734	52561721	52561721	Missense_Mutation	G	A	p.R280W
NCIH1155_LUNG	52561633	52561947	52561721	52561721	Missense_Mutation	G	A	p.R280W
NCIH1155_LUNG	52561633	52561734	52561721	52561721	Missense_Mutation	G	A	p.R280W
HEC50B_ENDOMETRIUM	52561845	52561947	52561927	52561927	Missense_Mutation	C	G	p.D248H
HEC50B_ENDOMETRIUM	52561633	52561947	52561927	52561927	Missense_Mutation	C	G	p.D248H
HCC2218_BREAST	52562877	52562951	52562905	52562905	Missense_Mutation	A	G	p.I118T
HCC2218_MATCHED_NORMAL_TISSUE	52562877	52562951	52562905	52562905	Missense_Mutation	A	G	p.I118T
NCIBL209_MATCHED_NORMAL_TISSUE	52562877	52562951	52562905	52562905	Missense_Mutation	A	G	p.I118T
NCIH2286_LUNG	52559225	52559311	52559225	52559225	Splice_Site	C	T	p.A365A
EFO27_OVARY	52559225	52559311	52559226	52559226	Splice_Site	G	A	p.A365V

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for NT5DC2

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_384857	3	52561309:52561391:52561632:52561947:52562028:52562089	52561632:52561947	ENST00000478091.1	GBM	rs11711421	chr3:52561779	C/T	6.17e-07
exon_skip_384857	3	52561309:52561391:52561632:52561947:52562028:52562089	52561632:52561947	ENST00000478091.1	GBM	rs11711421	chr3:52561779	C/T	6.17e-07
exon_skip_384857	3	52561309:52561391:52561632:52561947:52562028:52562089	52561632:52561947	ENST00000478091.1	CESC	rs11711421	chr3:52561779	C/T	1.04e-06
exon_skip_384857	3	52561309:52561391:52561632:52561947:52562028:52562089	52561632:52561947	ENST00000478091.1	CESC	rs11711421	chr3:52561779	C/T	1.51e-06
exon_skip_384857	3	52561309:52561391:52561632:52561947:52562028:52562089	52561632:52561947	ENST00000478091.1	BLCA	rs11711421	chr3:52561779	C/T	1.68e-05
exon_skip_384857	3	52561309:52561391:52561632:52561947:52562028:52562089	52561632:52561947	ENST00000478091.1	BLCA	rs11711421	chr3:52561779	C/T	1.68e-05
exon_skip_384857	3	52561309:52561391:52561632:52561947:52562028:52562089	52561632:52561947	ENST00000478091.1	HNSC	rs11711421	chr3:52561779	C/T	1.17e-06
exon_skip_384857	3	52561309:52561391:52561632:52561947:52562028:52562089	52561632:52561947	ENST00000478091.1	HNSC	rs11711421	chr3:52561779	C/T	3.94e-06
exon_skip_384857	3	52561309:52561391:52561632:52561947:52562028:52562089	52561632:52561947	ENST00000478091.1	BRCA	rs11711421	chr3:52561779	C/T	1.85e-13
exon_skip_384857	3	52561309:52561391:52561632:52561947:52562028:52562089	52561632:52561947	ENST00000478091.1	BRCA	rs11711421	chr3:52561779	C/T	2.55e-13
exon_skip_384857	3	52561309:52561391:52561632:52561947:52562028:52562089	52561632:52561947	ENST00000478091.1	LGG	rs11711421	chr3:52561779	C/T	1.34e-04
exon_skip_384857	3	52561309:52561391:52561632:52561947:52562028:52562089	52561632:52561947	ENST00000478091.1	LGG	rs11711421	chr3:52561779	C/T	1.34e-04
exon_skip_384857	3	52561309:52561391:52561632:52561947:52562028:52562089	52561632:52561947	ENST00000478091.1	KIRC	rs11711421	chr3:52561779	C/T	2.90e-09
exon_skip_384857	3	52561309:52561391:52561632:52561947:52562028:52562089	52561632:52561947	ENST00000478091.1	KIRC	rs11711421	chr3:52561779	C/T	3.53e-09
exon_skip_384857	3	52561309:52561391:52561632:52561947:52562028:52562089	52561632:52561947	ENST00000478091.1	LUAD	rs11711421	chr3:52561779	C/T	1.84e-08
exon_skip_384857	3	52561309:52561391:52561632:52561947:52562028:52562089	52561632:52561947	ENST00000478091.1	LUAD	rs11711421	chr3:52561779	C/T	5.17e-08
exon_skip_384857	3	52561309:52561391:52561632:52561947:52562028:52562089	52561632:52561947	ENST00000478091.1	LUSC	rs11711421	chr3:52561779	C/T	8.39e-05
exon_skip_384857	3	52561309:52561391:52561632:52561947:52562028:52562089	52561632:52561947	ENST00000478091.1	LUSC	rs11711421	chr3:52561779	C/T	4.62e-04
exon_skip_384857	3	52561309:52561391:52561632:52561947:52562028:52562089	52561632:52561947	ENST00000478091.1	OV	rs11711421	chr3:52561779	C/T	8.97e-05
exon_skip_384857	3	52561309:52561391:52561632:52561947:52562028:52562089	52561632:52561947	ENST00000478091.1	OV	rs11711421	chr3:52561779	C/T	8.97e-05
exon_skip_384857	3	52561309:52561391:52561632:52561947:52562028:52562089	52561632:52561947	ENST00000478091.1	READ	rs11711421	chr3:52561779	C/T	6.86e-05
exon_skip_384857	3	52561309:52561391:52561632:52561947:52562028:52562089	52561632:52561947	ENST00000478091.1	READ	rs11711421	chr3:52561779	C/T	6.86e-05
exon_skip_384857	3	52561309:52561391:52561632:52561947:52562028:52562089	52561632:52561947	ENST00000478091.1	PCPG	rs11711421	chr3:52561779	C/T	2.60e-04
exon_skip_384857	3	52561309:52561391:52561632:52561947:52562028:52562089	52561632:52561947	ENST00000478091.1	PCPG	rs11711421	chr3:52561779	C/T	2.60e-04
exon_skip_384857	3	52561309:52561391:52561632:52561947:52562028:52562089	52561632:52561947	ENST00000478091.1	PAAD	rs11711421	chr3:52561779	C/T	8.72e-10
exon_skip_384857	3	52561309:52561391:52561632:52561947:52562028:52562089	52561632:52561947	ENST00000478091.1	PAAD	rs11711421	chr3:52561779	C/T	8.72e-10
exon_skip_384857	3	52561309:52561391:52561632:52561947:52562028:52562089	52561632:52561947	ENST00000478091.1	PRAD	rs11711421	chr3:52561779	C/T	1.94e-11
exon_skip_384857	3	52561309:52561391:52561632:52561947:52562028:52562089	52561632:52561947	ENST00000478091.1	PRAD	rs11711421	chr3:52561779	C/T	1.94e-11
exon_skip_384857	3	52561309:52561391:52561632:52561947:52562028:52562089	52561632:52561947	ENST00000478091.1	STAD	rs11711421	chr3:52561779	C/T	6.38e-09
exon_skip_384857	3	52561309:52561391:52561632:52561947:52562028:52562089	52561632:52561947	ENST00000478091.1	STAD	rs11711421	chr3:52561779	C/T	6.38e-09

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Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for NT5DC2

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for NT5DC2

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RelatedDrugs for NT5DC2

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 NT5DC2

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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Gene summary for NT5DC2

Exon skipping events across known transcript of Ensembl for NT5DC2 from UCSC genome browser

Gene isoform structures and expression levels for NT5DC2

Exon skipping events with PSIs in TCGA for NT5DC2

Exon skipping events with PSIs in GTEx for NT5DC2

Open reading frame (ORF) annotation in the exon skipping event for NT5DC2

Infer the effects of exon skipping event on protein functional features for NT5DC2

SNVs in the skipped exons for NT5DC2

Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for NT5DC2

Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for NT5DC2

Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for NT5DC2

RelatedDrugs for NT5DC2

RelatedDiseases for NT5DC2