ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for DHPS

Gene summary

Gene information	Gene symbol	DHPS
	Gene ID	1725
	Gene name	deoxyhypusine synthase
	Synonyms	DHS\|DS\|MIG13
	Cytomap	19p13.13
	Type of gene	protein-coding
	Description	deoxyhypusine synthasemigration-inducing gene 13
	Modification date	20180523
	UniProtAcc	P49366
	Context	PubMed: DHPS [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
DHPS	GO:0008216	spermidine metabolic process	23525104
DHPS	GO:0008612	peptidyl-lysine modification to peptidyl-hypusine	23525104

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Exon skipping events across known transcript of Ensembl for DHPS 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 DHPS

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 DHPS

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_315435	19	12786575:12786747:12786830:12786892:12787921:12788025	12786830:12786892	ENSG00000095059.11	ENST00000598246.1
exon_skip_315436	19	12786575:12786747:12786830:12786892:12788104:12788210	12786830:12786892	ENSG00000095059.11	ENST00000600864.1
exon_skip_315441	19	12786575:12786747:12786830:12786919:12788104:12788210	12786830:12786919	ENSG00000095059.11	ENST00000351660.5
exon_skip_315447	19	12786575:12786747:12786830:12786956:12787921:12788025	12786830:12786956	ENSG00000095059.11	ENST00000210060.7,ENST00000594424.1,ENST00000601639.1
exon_skip_315448	19	12786575:12786747:12786830:12786956:12788104:12788210	12786830:12786956	ENSG00000095059.11	ENST00000601537.1
exon_skip_315458	19	12786830:12786892:12787921:12788025:12788104:12788210	12787921:12788025	ENSG00000095059.11	ENST00000598246.1
exon_skip_315460	19	12786830:12786892:12788104:12788210:12790270:12790334	12788104:12788210	ENSG00000095059.11	ENST00000600864.1
exon_skip_315465	19	12786830:12786919:12788104:12788210:12790270:12790334	12788104:12788210	ENSG00000095059.11	ENST00000351660.5
exon_skip_315468	19	12786830:12786956:12787921:12788025:12788104:12788210	12787921:12788025	ENSG00000095059.11	ENST00000210060.7,ENST00000594424.1,ENST00000601639.1
exon_skip_315470	19	12786830:12786956:12788104:12788210:12790270:12790334	12788104:12788210	ENSG00000095059.11	ENST00000601537.1
exon_skip_315474	19	12788141:12788210:12790270:12790357:12790436:12790533	12790270:12790357	ENSG00000095059.11	ENST00000210060.7,ENST00000594424.1,ENST00000595844.1,ENST00000351660.5,ENST00000595912.1,ENST00000596162.1,ENST00000601639.1,ENST00000597152.1,ENST00000598850.1,ENST00000601537.1
exon_skip_315475	19	12790507:12790533:12790614:12790736:12790963:12791139	12790614:12790736	ENSG00000095059.11	ENST00000595100.1,ENST00000593423.1
exon_skip_315476	19	12790507:12790533:12790614:12790736:12790974:12791034	12790614:12790736	ENSG00000095059.11	ENST00000210060.7,ENST00000594424.1,ENST00000595844.1,ENST00000351660.5,ENST00000596162.1,ENST00000597152.1,ENST00000601537.1
exon_skip_315479	19	12790507:12790533:12790614:12790844:12790974:12791034	12790614:12790844	ENSG00000095059.11	ENST00000598850.1

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for DHPS

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_315435	19	12786575:12786747:12786830:12786892:12787921:12788025	12786830:12786892	ENSG00000095059.11	ENST00000598246.1
exon_skip_315436	19	12786575:12786747:12786830:12786892:12788104:12788210	12786830:12786892	ENSG00000095059.11	ENST00000600864.1
exon_skip_315441	19	12786575:12786747:12786830:12786919:12788104:12788210	12786830:12786919	ENSG00000095059.11	ENST00000351660.5
exon_skip_315447	19	12786575:12786747:12786830:12786956:12787921:12788025	12786830:12786956	ENSG00000095059.11	ENST00000210060.7,ENST00000601639.1,ENST00000594424.1
exon_skip_315448	19	12786575:12786747:12786830:12786956:12788104:12788210	12786830:12786956	ENSG00000095059.11	ENST00000601537.1
exon_skip_315458	19	12786830:12786892:12787921:12788025:12788104:12788210	12787921:12788025	ENSG00000095059.11	ENST00000598246.1
exon_skip_315460	19	12786830:12786892:12788104:12788210:12790270:12790334	12788104:12788210	ENSG00000095059.11	ENST00000600864.1
exon_skip_315465	19	12786830:12786919:12788104:12788210:12790270:12790334	12788104:12788210	ENSG00000095059.11	ENST00000351660.5
exon_skip_315468	19	12786830:12786956:12787921:12788025:12788104:12788210	12787921:12788025	ENSG00000095059.11	ENST00000210060.7,ENST00000601639.1,ENST00000594424.1
exon_skip_315470	19	12786830:12786956:12788104:12788210:12790270:12790334	12788104:12788210	ENSG00000095059.11	ENST00000601537.1
exon_skip_315474	19	12788141:12788210:12790270:12790357:12790436:12790533	12790270:12790357	ENSG00000095059.11	ENST00000210060.7,ENST00000351660.5,ENST00000601639.1,ENST00000594424.1,ENST00000601537.1,ENST00000595844.1,ENST00000595912.1,ENST00000597152.1,ENST00000598850.1,ENST00000596162.1
exon_skip_315475	19	12790507:12790533:12790614:12790736:12790963:12791139	12790614:12790736	ENSG00000095059.11	ENST00000593423.1,ENST00000595100.1
exon_skip_315476	19	12790507:12790533:12790614:12790736:12790974:12791034	12790614:12790736	ENSG00000095059.11	ENST00000210060.7,ENST00000351660.5,ENST00000594424.1,ENST00000601537.1,ENST00000595844.1,ENST00000597152.1,ENST00000596162.1
exon_skip_315479	19	12790507:12790533:12790614:12790844:12790974:12791034	12790614:12790844	ENSG00000095059.11	ENST00000598850.1

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 DHPS

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
ENST00000210060	12787921	12788025	Frame-shift
ENST00000210060	12790614	12790736	Frame-shift
ENST00000210060	12786830	12786956	In-frame
ENST00000210060	12790270	12790357	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
ENST00000210060	12787921	12788025	Frame-shift
ENST00000210060	12790614	12790736	Frame-shift
ENST00000210060	12786830	12786956	In-frame
ENST00000210060	12790270	12790357	In-frame

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

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
ENST00000210060	1380	369	12790270	12790357	728	814	197	226
ENST00000210060	1380	369	12786830	12786956	1025	1150	296	338

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
ENST00000210060	1380	369	12790270	12790357	728	814	197	226
ENST00000210060	1380	369	12786830	12786956	1025	1150	296	338

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
P49366	197	226	1	369	Chain	ID=PRO_0000134469;Note=Deoxyhypusine synthase
P49366	197	226	203	214	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1RLZ
P49366	197	226	220	226	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1RLZ
P49366	197	226	199	199	Sequence conflict	Note=V->A;Ontology_term=ECO:0000305;evidence=ECO:0000305
P49366	197	226	199	199	Sequence conflict	Note=V->A;Ontology_term=ECO:0000305;evidence=ECO:0000305
P49366	197	226	220	220	Sequence conflict	Note=V->A;Ontology_term=ECO:0000305;evidence=ECO:0000305
P49366	197	226	220	220	Sequence conflict	Note=V->A;Ontology_term=ECO:0000305;evidence=ECO:0000305
P49366	296	338	329	329	Active site	Note=Nucleophile;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:9405486;Dbxref=PMID:9405486
P49366	296	338	262	308	Alternative sequence	ID=VSP_001351;Note=In isoform Short. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:8615810;Dbxref=PMID:8615810
P49366	296	338	299	307	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1RLZ
P49366	296	338	337	341	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1RLZ
P49366	296	338	1	369	Chain	ID=PRO_0000134469;Note=Deoxyhypusine synthase
P49366	296	338	321	327	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1RLZ
P49366	296	338	305	305	Mutagenesis	Note=Strongly reduced NAD binding. No effect on enzyme activity. Y->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:11311149;Dbxref=PMID:11311149
P49366	296	338	313	313	Mutagenesis	Note=Strongly reduced NAD binding. D->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:11311149;Dbxref=PMID:11311149
P49366	296	338	316	316	Mutagenesis	Note=Reduces spermidine binding by 98%25. Loss of covalent intermediate formation and deoxyhypusine synthesis. D->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:11311149;Dbxref=PMID:11311149
P49366	296	338	317	317	Mutagenesis	Note=Strongly reduced NAD binding. No effect on enzyme activity. S->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:11311149;Dbxref=PMID:11311149
P49366	296	338	323	323	Mutagenesis	Note=Reduces spermidine binding by 98%25. Strongly reduced formation of covalent intermediate. E->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:11311149;Dbxref=PMID:11311149
P49366	296	338	327	327	Mutagenesis	Note=Reduces spermidine binding by 98%25. Loss of covalent intermediate formation and deoxyhypusine synthesis. W->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:11311149;Dbxref=PMID:11311149
P49366	296	338	329	329	Mutagenesis	Note=Loss of covalent intermediate formation and deoxyhypusine synthesis. K->A%2CR;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:9405486;Dbxref=PMID:9405486
P49366	296	338	308	309	Nucleotide binding	Note=NAD;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:9493264;Dbxref=PMID:9493264
P49366	296	338	314	316	Region	Note=Spermidine binding;Ontology_term=ECO:0000305;evidence=ECO:0000305
P49366	296	338	323	329	Region	Note=Spermidine binding;Ontology_term=ECO:0000305;evidence=ECO:0000305
P49366	296	338	296	297	Sequence conflict	Note=MR->SG;Ontology_term=ECO:0000305;evidence=ECO:0000305
P49366	296	338	311	311	Sequence conflict	Note=E->EE;Ontology_term=ECO:0000305;evidence=ECO:0000305
P49366	296	338	296	298	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1RLZ

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
P49366	197	226	1	369	Chain	ID=PRO_0000134469;Note=Deoxyhypusine synthase
P49366	197	226	203	214	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1RLZ
P49366	197	226	220	226	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1RLZ
P49366	197	226	199	199	Sequence conflict	Note=V->A;Ontology_term=ECO:0000305;evidence=ECO:0000305
P49366	197	226	199	199	Sequence conflict	Note=V->A;Ontology_term=ECO:0000305;evidence=ECO:0000305
P49366	197	226	220	220	Sequence conflict	Note=V->A;Ontology_term=ECO:0000305;evidence=ECO:0000305
P49366	197	226	220	220	Sequence conflict	Note=V->A;Ontology_term=ECO:0000305;evidence=ECO:0000305
P49366	296	338	329	329	Active site	Note=Nucleophile;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:9405486;Dbxref=PMID:9405486
P49366	296	338	262	308	Alternative sequence	ID=VSP_001351;Note=In isoform Short. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:8615810;Dbxref=PMID:8615810
P49366	296	338	299	307	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1RLZ
P49366	296	338	337	341	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1RLZ
P49366	296	338	1	369	Chain	ID=PRO_0000134469;Note=Deoxyhypusine synthase
P49366	296	338	321	327	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1RLZ
P49366	296	338	305	305	Mutagenesis	Note=Strongly reduced NAD binding. No effect on enzyme activity. Y->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:11311149;Dbxref=PMID:11311149
P49366	296	338	313	313	Mutagenesis	Note=Strongly reduced NAD binding. D->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:11311149;Dbxref=PMID:11311149
P49366	296	338	316	316	Mutagenesis	Note=Reduces spermidine binding by 98%25. Loss of covalent intermediate formation and deoxyhypusine synthesis. D->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:11311149;Dbxref=PMID:11311149
P49366	296	338	317	317	Mutagenesis	Note=Strongly reduced NAD binding. No effect on enzyme activity. S->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:11311149;Dbxref=PMID:11311149
P49366	296	338	323	323	Mutagenesis	Note=Reduces spermidine binding by 98%25. Strongly reduced formation of covalent intermediate. E->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:11311149;Dbxref=PMID:11311149
P49366	296	338	327	327	Mutagenesis	Note=Reduces spermidine binding by 98%25. Loss of covalent intermediate formation and deoxyhypusine synthesis. W->A;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:11311149;Dbxref=PMID:11311149
P49366	296	338	329	329	Mutagenesis	Note=Loss of covalent intermediate formation and deoxyhypusine synthesis. K->A%2CR;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:9405486;Dbxref=PMID:9405486
P49366	296	338	308	309	Nucleotide binding	Note=NAD;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:9493264;Dbxref=PMID:9493264
P49366	296	338	314	316	Region	Note=Spermidine binding;Ontology_term=ECO:0000305;evidence=ECO:0000305
P49366	296	338	323	329	Region	Note=Spermidine binding;Ontology_term=ECO:0000305;evidence=ECO:0000305
P49366	296	338	296	297	Sequence conflict	Note=MR->SG;Ontology_term=ECO:0000305;evidence=ECO:0000305
P49366	296	338	311	311	Sequence conflict	Note=E->EE;Ontology_term=ECO:0000305;evidence=ECO:0000305
P49366	296	338	296	298	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:1RLZ

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SNVs in the skipped exons for DHPS

- 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
KIRC	TCGA-CJ-6030-01	exon_skip_315474	12790271	12790357	12790293	12790302	Frame_Shift_Del	GACTCTGGGT	-	p.216_219del
KIRC	TCGA-CJ-6030-01	exon_skip_315474	12790271	12790357	12790293	12790302	Frame_Shift_Del	GACTCTGGGT	-	p.NPES216fs
COAD	TCGA-CK-5914-01	exon_skip_315441	12786831	12786919	12786914	12786914	Nonsense_Mutation	C	A	p.E311X
COAD	TCGA-CK-5914-01	exon_skip_315448 exon_skip_315447	12786831	12786956	12786914	12786914	Nonsense_Mutation	C	A	p.E311X
HNSC	TCGA-CV-7414-01	exon_skip_315474	12790271	12790357	12790281	12790281	Nonsense_Mutation	C	T	p.W223*
PAAD	TCGA-IB-7651-01	exon_skip_315474	12790271	12790357	12790297	12790297	Nonsense_Mutation	C	A	p.E218*
PAAD	TCGA-IB-7651-01	exon_skip_315474	12790271	12790357	12790297	12790297	Nonsense_Mutation	C	A	p.E218X
LUSC	TCGA-85-6561-01	exon_skip_315476 exon_skip_315475	12790615	12790736	12790661	12790661	Nonsense_Mutation	C	A	p.E150*
LUSC	TCGA-85-6561-01	exon_skip_315479	12790615	12790844	12790661	12790661	Nonsense_Mutation	C	A	p.E150*

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

Depth of coverage in three exons	Mutation description
	Sample: TCGA-85-6561-01
	Cancer type: LUSC
	ESID: exon_skip_315479
	Skipped exon start: 12790615
	Skipped exon end: 12790844
	Mutation start: 12790661
	Mutation end: 12790661
	Mutation type: Nonsense_Mutation
	Reference seq: C
	Mutation seq: A
	AAchange: p.E150*
	Sample: TCGA-85-6561-01
	Cancer type: LUSC
	ESID: exon_skip_315475
	Skipped exon start: 12790615
	Skipped exon end: 12790736
	Mutation start: 12790661
	Mutation end: 12790661
	Mutation type: Nonsense_Mutation
	Reference seq: C
	Mutation seq: A
	AAchange: p.E150*
exon_skip_104683_LUSC_TCGA-85-6561-01.png
exon_skip_315479_LUSC_TCGA-85-6561-01.png
exon_skip_344069_LUSC_TCGA-85-6561-01.png
exon_skip_354387_LUSC_TCGA-85-6561-01.png
exon_skip_367235_LUSC_TCGA-85-6561-01.png
exon_skip_371719_LUSC_TCGA-85-6561-01.png
exon_skip_91283_LUSC_TCGA-85-6561-01.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
COLO684_ENDOMETRIUM	12790615	12790844	12790648	12790649	Frame_Shift_Del	CT	-	p.R154fs
COLO684_ENDOMETRIUM	12790615	12790736	12790648	12790649	Frame_Shift_Del	CT	-	p.R154fs
CORL279_LUNG	12788105	12788210	12788179	12788180	Frame_Shift_Ins	-	T	p.T237fs
HCC1569_BREAST	12787922	12788025	12787956	12787956	Missense_Mutation	A	G	p.V285A
ISHIKAWAHERAKLIO02ER_ENDOMETRIUM	12787922	12788025	12787986	12787986	Missense_Mutation	C	T	p.C275Y
SNU175_LARGE_INTESTINE	12788105	12788210	12788186	12788186	Missense_Mutation	C	T	p.A235T
HT115_LARGE_INTESTINE	12788105	12788210	12788186	12788186	Missense_Mutation	C	T	p.A235T
SNU1040_LARGE_INTESTINE	12788105	12788210	12788186	12788186	Missense_Mutation	C	T	p.A235T
SKLU1_LUNG	12788105	12788210	12788108	12788108	Nonsense_Mutation	C	A	p.E261*
PCI30_UPPER_AERODIGESTIVE_TRACT	12788105	12788210	12788105	12788105	Splice_Site	C	T	p.D262N

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

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 DHPS

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

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RelatedDrugs for DHPS

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 DHPS

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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