ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for KDSR

Gene summary

Gene information	Gene symbol	KDSR
	Gene ID	2531
	Gene name	3-ketodihydrosphingosine reductase
	Synonyms	DHSR\|EKVP4\|FVT1\|SDR35C1
	Cytomap	18q21.33
	Type of gene	protein-coding
	Description	3-ketodihydrosphingosine reductase3-dehydrosphinganine reductaseFVT-1KDS reductasefollicular lymphoma variant translocation 1follicular variant translocation protein 1short chain dehydrogenase/reductase family 35C member 1
	Modification date	20180523
	UniProtAcc	Q06136
	Context	PubMed: KDSR [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
KDSR	GO:0006666	3-keto-sphinganine metabolic process	15364918

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Exon skipping events across known transcript of Ensembl for KDSR 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 KDSR

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 KDSR

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_299626	18	60998883:60999134:61002489:61002591:61006032:61006116	61002489:61002591	ENSG00000119537.11	ENST00000589592.1,ENST00000326575.5,ENST00000406396.3,ENST00000586791.1
exon_skip_299629	18	60998883:60999134:61006032:61006116:61011642:61011726	61006032:61006116	ENSG00000119537.11	ENST00000591902.1
exon_skip_299632	18	61002489:61002591:61006032:61006116:61011642:61011726	61006032:61006116	ENSG00000119537.11	ENST00000589592.1,ENST00000326575.5,ENST00000406396.3,ENST00000586791.1
exon_skip_299636	18	61006032:61006116:61011642:61011726:61018120:61018310	61011642:61011726	ENSG00000119537.11	ENST00000406396.3,ENST00000591902.1
exon_skip_299638	18	61011642:61011726:61018120:61018310:61022436:61022532	61018120:61018310	ENSG00000119537.11	ENST00000585750.1
exon_skip_299639	18	61011642:61011726:61018120:61018312:61022436:61022532	61018120:61018312	ENSG00000119537.11	ENST00000406396.3,ENST00000591902.1
exon_skip_299642	18	61022451:61022532:61022730:61022796:61026968:61027025	61022730:61022796	ENSG00000119537.11	ENST00000326575.5,ENST00000406396.3,ENST00000592327.1
exon_skip_299645	18	61022730:61022796:61026968:61027025:61030011:61030101	61026968:61027025	ENSG00000119537.11	ENST00000326575.5,ENST00000406396.3,ENST00000589530.1,ENST00000592327.1
exon_skip_299647	18	61030075:61030101:61033194:61033541:61034243:61034439	61033194:61033541	ENSG00000119537.11	ENST00000587292.1

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for KDSR

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_299626	18	60998883:60999134:61002489:61002591:61006032:61006116	61002489:61002591	ENSG00000119537.11	ENST00000406396.3,ENST00000586791.1,ENST00000589592.1,ENST00000326575.5
exon_skip_299629	18	60998883:60999134:61006032:61006116:61011642:61011726	61006032:61006116	ENSG00000119537.11	ENST00000591902.1
exon_skip_299632	18	61002489:61002591:61006032:61006116:61011642:61011726	61006032:61006116	ENSG00000119537.11	ENST00000406396.3,ENST00000586791.1,ENST00000589592.1,ENST00000326575.5
exon_skip_299636	18	61006032:61006116:61011642:61011726:61018120:61018310	61011642:61011726	ENSG00000119537.11	ENST00000406396.3,ENST00000591902.1
exon_skip_299638	18	61011642:61011726:61018120:61018310:61022436:61022532	61018120:61018310	ENSG00000119537.11	ENST00000585750.1
exon_skip_299639	18	61011642:61011726:61018120:61018312:61022436:61022532	61018120:61018312	ENSG00000119537.11	ENST00000406396.3,ENST00000591902.1
exon_skip_299642	18	61022451:61022532:61022730:61022796:61026968:61027025	61022730:61022796	ENSG00000119537.11	ENST00000406396.3,ENST00000326575.5,ENST00000592327.1
exon_skip_299645	18	61022730:61022796:61026968:61027025:61030011:61030101	61026968:61027025	ENSG00000119537.11	ENST00000406396.3,ENST00000326575.5,ENST00000592327.1,ENST00000589530.1
exon_skip_299647	18	61030075:61030101:61033194:61033541:61034243:61034439	61033194:61033541	ENSG00000119537.11	ENST00000587292.1

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 KDSR

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
ENST00000406396	61002489	61002591	In-frame
ENST00000406396	61006032	61006116	In-frame
ENST00000406396	61011642	61011726	In-frame
ENST00000406396	61018120	61018312	In-frame
ENST00000406396	61022730	61022796	In-frame
ENST00000406396	61026968	61027025	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
ENST00000406396	61002489	61002591	In-frame
ENST00000406396	61006032	61006116	In-frame
ENST00000406396	61011642	61011726	In-frame
ENST00000406396	61018120	61018312	In-frame
ENST00000406396	61022730	61022796	In-frame
ENST00000406396	61026968	61027025	In-frame

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

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
ENST00000406396	5464	332	61026968	61027025	591	647	66	85
ENST00000406396	5464	332	61022730	61022796	648	713	85	107
ENST00000406396	5464	332	61018120	61018312	810	1001	139	203
ENST00000406396	5464	332	61011642	61011726	1002	1085	203	231
ENST00000406396	5464	332	61006032	61006116	1086	1169	231	259
ENST00000406396	5464	332	61002489	61002591	1170	1271	259	293

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
ENST00000406396	5464	332	61026968	61027025	591	647	66	85
ENST00000406396	5464	332	61022730	61022796	648	713	85	107
ENST00000406396	5464	332	61018120	61018312	810	1001	139	203
ENST00000406396	5464	332	61011642	61011726	1002	1085	203	231
ENST00000406396	5464	332	61006032	61006116	1086	1169	231	259
ENST00000406396	5464	332	61002489	61002591	1170	1271	259	293

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
Q06136	66	85	26	332	Chain	ID=PRO_0000031982;Note=3-ketodihydrosphingosine reductase
Q06136	66	85	26	270	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q06136	85	107	26	332	Chain	ID=PRO_0000031982;Note=3-ketodihydrosphingosine reductase
Q06136	85	107	86	107	Natural variant	ID=VAR_079186;Note=In EKVP4%3B loss of 3-dehydrosphinganine reductase activity. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:28575652;Dbxref=PMID:28575652
Q06136	85	107	26	270	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q06136	139	203	186	186	Active site	Note=Proton acceptor;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU10001
Q06136	139	203	190	190	Active site	Ontology_term=ECO:0000305;evidence=ECO:0000305
Q06136	139	203	139	202	Alternative sequence	ID=VSP_056641;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q06136	139	203	173	173	Binding site	Note=Substrate;Ontology_term=ECO:0000250;evidence=ECO:0000250
Q06136	139	203	26	332	Chain	ID=PRO_0000031982;Note=3-ketodihydrosphingosine reductase
Q06136	139	203	186	186	Natural variant	ID=VAR_079187;Note=In EKVP4. Y->F;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:28575652;Dbxref=dbSNP:rs1114167452,PMID:28575652
Q06136	139	203	26	270	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q06136	203	231	26	332	Chain	ID=PRO_0000031982;Note=3-ketodihydrosphingosine reductase
Q06136	203	231	26	270	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q06136	231	259	26	332	Chain	ID=PRO_0000031982;Note=3-ketodihydrosphingosine reductase
Q06136	231	259	26	270	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q06136	259	293	26	332	Chain	ID=PRO_0000031982;Note=3-ketodihydrosphingosine reductase
Q06136	259	293	260	293	Natural variant	ID=VAR_079188;Note=In EKVP4%3B loss of 3-dehydrosphinganine reductase activity. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:28575652;Dbxref=PMID:28575652
Q06136	259	293	26	270	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q06136	259	293	292	293	Topological domain	Note=Lumenal;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q06136	259	293	271	291	Transmembrane	Note=Helical;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
Q06136	66	85	26	332	Chain	ID=PRO_0000031982;Note=3-ketodihydrosphingosine reductase
Q06136	66	85	26	270	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q06136	85	107	26	332	Chain	ID=PRO_0000031982;Note=3-ketodihydrosphingosine reductase
Q06136	85	107	86	107	Natural variant	ID=VAR_079186;Note=In EKVP4%3B loss of 3-dehydrosphinganine reductase activity. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:28575652;Dbxref=PMID:28575652
Q06136	85	107	26	270	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q06136	139	203	186	186	Active site	Note=Proton acceptor;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU10001
Q06136	139	203	190	190	Active site	Ontology_term=ECO:0000305;evidence=ECO:0000305
Q06136	139	203	139	202	Alternative sequence	ID=VSP_056641;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:14702039;Dbxref=PMID:14702039
Q06136	139	203	173	173	Binding site	Note=Substrate;Ontology_term=ECO:0000250;evidence=ECO:0000250
Q06136	139	203	26	332	Chain	ID=PRO_0000031982;Note=3-ketodihydrosphingosine reductase
Q06136	139	203	186	186	Natural variant	ID=VAR_079187;Note=In EKVP4. Y->F;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:28575652;Dbxref=dbSNP:rs1114167452,PMID:28575652
Q06136	139	203	26	270	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q06136	203	231	26	332	Chain	ID=PRO_0000031982;Note=3-ketodihydrosphingosine reductase
Q06136	203	231	26	270	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q06136	231	259	26	332	Chain	ID=PRO_0000031982;Note=3-ketodihydrosphingosine reductase
Q06136	231	259	26	270	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q06136	259	293	26	332	Chain	ID=PRO_0000031982;Note=3-ketodihydrosphingosine reductase
Q06136	259	293	260	293	Natural variant	ID=VAR_079188;Note=In EKVP4%3B loss of 3-dehydrosphinganine reductase activity. Missing;Ontology_term=ECO:0000269;evidence=ECO:0000269\|PubMed:28575652;Dbxref=PMID:28575652
Q06136	259	293	26	270	Topological domain	Note=Cytoplasmic;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q06136	259	293	292	293	Topological domain	Note=Lumenal;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q06136	259	293	271	291	Transmembrane	Note=Helical;Ontology_term=ECO:0000255;evidence=ECO:0000255

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SNVs in the skipped exons for KDSR

- 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.

KDSR_UCS_exon_skip_299626_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-CV-A45W-01	exon_skip_299638	61018121	61018310	61018124	61018125	Frame_Shift_Ins	-	A	p.R202fs
HNSC	TCGA-CV-A45W-01	exon_skip_299639	61018121	61018312	61018124	61018125	Frame_Shift_Ins	-	A	p.R202fs
SKCM	TCGA-FS-A4FC-06	exon_skip_299638	61018121	61018310	61018162	61018163	Frame_Shift_Ins	-	G	p.K190fs
SKCM	TCGA-FS-A4FC-06	exon_skip_299638	61018121	61018310	61018162	61018163	Frame_Shift_Ins	-	G	p.V190fs
SKCM	TCGA-FS-A4FC-06	exon_skip_299639	61018121	61018312	61018162	61018163	Frame_Shift_Ins	-	G	p.K190fs
SKCM	TCGA-FS-A4FC-06	exon_skip_299639	61018121	61018312	61018162	61018163	Frame_Shift_Ins	-	G	p.V190fs
READ	TCGA-AG-A002-01	exon_skip_299645	61026969	61027025	61027001	61027001	Nonsense_Mutation	C	A	p.E75X
UCS	TCGA-ND-A4WC-01	exon_skip_299626	61002490	61002591	61002592	61002592	Splice_Site	C	T	.
SKCM	TCGA-DA-A1HV-06	exon_skip_299632 exon_skip_299629	61006033	61006116	61006117	61006117	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-DA-A1HV-06
	Cancer type: SKCM
	ESID: exon_skip_299629
	Skipped exon start: 61006033
	Skipped exon end: 61006116
	Mutation start: 61006117
	Mutation end: 61006117
	Mutation type: Splice_Site
	Reference seq: C
	Mutation seq: T
	AAchange: .
exon_skip_299629_SKCM_TCGA-DA-A1HV-06.png
exon_skip_299632_SKCM_TCGA-DA-A1HV-06.png
	Sample: TCGA-DA-A1HV-06
	Cancer type: SKCM
	ESID: exon_skip_299629
	Skipped exon start: 61006033
	Skipped exon end: 61006116
	Mutation start: 61006117
	Mutation end: 61006117
	Mutation type: Splice_Site
	Reference seq: C
	Mutation seq: T
	AAchange: .
exon_skip_299629_SKCM_TCGA-DA-A1HV-06.png
exon_skip_299632_SKCM_TCGA-DA-A1HV-06.png
	Sample: TCGA-ND-A4WC-01
	Cancer type: UCS
	ESID: exon_skip_299626
	Skipped exon start: 61002490
	Skipped exon end: 61002591
	Mutation start: 61002592
	Mutation end: 61002592
	Mutation type: Splice_Site
	Reference seq: C
	Mutation seq: T
	AAchange: .
exon_skip_149665_UCS_TCGA-ND-A4WC-01.png
exon_skip_299626_UCS_TCGA-ND-A4WC-01.png
exon_skip_344918_UCS_TCGA-ND-A4WC-01.png
exon_skip_360263_UCS_TCGA-ND-A4WC-01.png
exon_skip_382353_UCS_TCGA-ND-A4WC-01.png
exon_skip_385882_UCS_TCGA-ND-A4WC-01.png
exon_skip_443509_UCS_TCGA-ND-A4WC-01.png
exon_skip_45962_UCS_TCGA-ND-A4WC-01.png
exon_skip_48320_UCS_TCGA-ND-A4WC-01.png
exon_skip_484856_UCS_TCGA-ND-A4WC-01.png
exon_skip_59444_UCS_TCGA-ND-A4WC-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
NB1643_AUTONOMIC_GANGLIA	61026969	61027025	61027000	61027001	Frame_Shift_Del	TC	-	p.E75fs
DU145_PROSTATE	61002490	61002591	61002551	61002551	Missense_Mutation	A	G	p.M273T
SNU81_LARGE_INTESTINE	61006033	61006116	61006041	61006041	Missense_Mutation	C	A	p.D257Y
CORL47_LUNG	61006033	61006116	61006080	61006080	Missense_Mutation	C	G	p.V244L
KMM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	61018121	61018310	61018140	61018140	Missense_Mutation	G	A	p.A197V
KMM1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	61018121	61018312	61018140	61018140	Missense_Mutation	G	A	p.A197V
SNUC2A_LARGE_INTESTINE	61018121	61018310	61018291	61018291	Missense_Mutation	G	T	p.L147M
SNUC2A_LARGE_INTESTINE	61018121	61018312	61018291	61018291	Missense_Mutation	G	T	p.L147M
SNUC2B_LARGE_INTESTINE	61018121	61018310	61018291	61018291	Missense_Mutation	G	T	p.L147M
SNUC2B_LARGE_INTESTINE	61018121	61018312	61018291	61018291	Missense_Mutation	G	T	p.L147M
BICR18_UPPER_AERODIGESTIVE_TRACT	61026969	61027025	61026991	61026991	Missense_Mutation	A	T	p.M78K
HEPG2_LIVER	61006033	61006116	61006104	61006104	Nonsense_Mutation	G	A	p.R236*
C3A_LIVER	61006033	61006116	61006104	61006104	Nonsense_Mutation	G	A	p.R236*

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

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 KDSR

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

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RelatedDrugs for KDSR

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 KDSR

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
KDSR	C0024301	Lymphoma, Follicular	1	CTD_human

	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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