ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for HSDL2

Gene summary

Gene information	Gene symbol	HSDL2
	Gene ID	84263
	Gene name	hydroxysteroid dehydrogenase like 2
	Synonyms	C9orf99\|SDR13C1
	Cytomap	9q32
	Type of gene	protein-coding
	Description	hydroxysteroid dehydrogenase-like protein 2short chain dehydrogenase/reductase family 13C member 1
	Modification date	20180519
	UniProtAcc	Q6YN16
	Context	PubMed: HSDL2 [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 HSDL2 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 HSDL2

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 HSDL2

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_498105	9	115142401:115142460:115166274:115166438:115167903:115168002	115166274:115166438	ENSG00000119471.10	ENST00000398803.1,ENST00000539114.1
exon_skip_498110	9	115142401:115142460:115167903:115168002:115171186:115171301	115167903:115168002	ENSG00000119471.10	ENST00000488101.1,ENST00000262542.7,ENST00000467434.1
exon_skip_498125	9	115166274:115166438:115167903:115168002:115171186:115171301	115167903:115168002	ENSG00000119471.10	ENST00000539114.1,ENST00000398805.3
exon_skip_498131	9	115167903:115168002:115171186:115171301:115179120:115179224	115171186:115171301	ENSG00000119471.10	ENST00000488101.1,ENST00000262542.7,ENST00000398805.3
exon_skip_498132	9	115167912:115168002:115171186:115171301:115181139:115181238	115171186:115171301	ENSG00000119471.10	ENST00000467434.1
exon_skip_498133	9	115167912:115168002:115171186:115171301:115200710:115200905	115171186:115171301	ENSG00000119471.10	ENST00000539114.1
exon_skip_498136	9	115167912:115168002:115181139:115181238:115200710:115200905	115181139:115181238	ENSG00000119471.10	ENST00000398803.1
exon_skip_498138	9	115171186:115171301:115179120:115179224:115181139:115181238	115179120:115179224	ENSG00000119471.10	ENST00000488101.1,ENST00000262542.7,ENST00000398805.3
exon_skip_498140	9	115171186:115171301:115181139:115181238:115200710:115200905	115181139:115181238	ENSG00000119471.10	ENST00000467434.1
exon_skip_498141	9	115179120:115179224:115181139:115181238:115200710:115200905	115181139:115181238	ENSG00000119471.10	ENST00000488101.1,ENST00000262542.7,ENST00000398805.3,ENST00000480881.1
exon_skip_498142	9	115181139:115181238:115200710:115200905:115203978:115204050	115200710:115200905	ENSG00000119471.10	ENST00000488101.1,ENST00000398803.1,ENST00000262542.7,ENST00000467434.1,ENST00000398805.3
exon_skip_498144	9	115200710:115200905:115201022:115201092:115203978:115204050	115201022:115201092	ENSG00000119471.10	ENST00000480881.1
exon_skip_498145	9	115203978:115204050:115216292:115216442:115221728:115221817	115216292:115216442	ENSG00000119471.10	ENST00000398803.1,ENST00000539114.1,ENST00000262542.7,ENST00000467434.1,ENST00000398805.3

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for HSDL2

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_498105	9	115142401:115142460:115166274:115166438:115167903:115168002	115166274:115166438	ENSG00000119471.10	ENST00000398803.1,ENST00000539114.1
exon_skip_498110	9	115142401:115142460:115167903:115168002:115171186:115171301	115167903:115168002	ENSG00000119471.10	ENST00000488101.1,ENST00000262542.7,ENST00000467434.1
exon_skip_498125	9	115166274:115166438:115167903:115168002:115171186:115171301	115167903:115168002	ENSG00000119471.10	ENST00000398805.3,ENST00000539114.1
exon_skip_498131	9	115167903:115168002:115171186:115171301:115179120:115179224	115171186:115171301	ENSG00000119471.10	ENST00000398805.3,ENST00000488101.1,ENST00000262542.7
exon_skip_498132	9	115167912:115168002:115171186:115171301:115181139:115181238	115171186:115171301	ENSG00000119471.10	ENST00000467434.1
exon_skip_498133	9	115167912:115168002:115171186:115171301:115200710:115200905	115171186:115171301	ENSG00000119471.10	ENST00000539114.1
exon_skip_498136	9	115167912:115168002:115181139:115181238:115200710:115200905	115181139:115181238	ENSG00000119471.10	ENST00000398803.1
exon_skip_498138	9	115171186:115171301:115179120:115179224:115181139:115181238	115179120:115179224	ENSG00000119471.10	ENST00000398805.3,ENST00000488101.1,ENST00000262542.7
exon_skip_498140	9	115171186:115171301:115181139:115181238:115200710:115200905	115181139:115181238	ENSG00000119471.10	ENST00000467434.1
exon_skip_498141	9	115179120:115179224:115181139:115181238:115200710:115200905	115181139:115181238	ENSG00000119471.10	ENST00000398805.3,ENST00000488101.1,ENST00000262542.7,ENST00000480881.1
exon_skip_498142	9	115181139:115181238:115200710:115200905:115203978:115204050	115200710:115200905	ENSG00000119471.10	ENST00000398805.3,ENST00000398803.1,ENST00000488101.1,ENST00000262542.7,ENST00000467434.1
exon_skip_498144	9	115200710:115200905:115201022:115201092:115203978:115204050	115201022:115201092	ENSG00000119471.10	ENST00000480881.1
exon_skip_498145	9	115203978:115204050:115216292:115216442:115221728:115221817	115216292:115216442	ENSG00000119471.10	ENST00000398805.3,ENST00000398803.1,ENST00000262542.7,ENST00000539114.1,ENST00000467434.1

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 HSDL2

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
ENST00000398805	115171186	115171301	Frame-shift
ENST00000398805	115179120	115179224	Frame-shift
ENST00000398805	115167903	115168002	In-frame
ENST00000398805	115181139	115181238	In-frame
ENST00000398805	115200710	115200905	In-frame
ENST00000398805	115216292	115216442	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
ENST00000398805	115171186	115171301	Frame-shift
ENST00000398805	115179120	115179224	Frame-shift
ENST00000398805	115167903	115168002	In-frame
ENST00000398805	115181139	115181238	In-frame
ENST00000398805	115200710	115200905	In-frame
ENST00000398805	115216292	115216442	In-frame

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Infer the effects of exon skipping event on protein functional features for HSDL2

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
ENST00000398805	3367	418	115167903	115168002	409	507	60	93
ENST00000398805	3367	418	115181139	115181238	727	825	166	199
ENST00000398805	3367	418	115200710	115200905	826	1020	199	264
ENST00000398805	3367	418	115216292	115216442	1093	1242	288	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
ENST00000398805	3367	418	115167903	115168002	409	507	60	93
ENST00000398805	3367	418	115181139	115181238	727	825	166	199
ENST00000398805	3367	418	115200710	115200905	826	1020	199	264
ENST00000398805	3367	418	115216292	115216442	1093	1242	288	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
Q6YN16	60	93	67	72	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KVO
Q6YN16	60	93	74	74	Binding site	Note=NADP;Ontology_term=ECO:0000269;evidence=ECO:0000269\|Ref.11
Q6YN16	60	93	1	418	Chain	ID=PRO_0000319888;Note=Hydroxysteroid dehydrogenase-like protein 2
Q6YN16	60	93	54	63	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KVO
Q6YN16	60	93	78	92	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KVO
Q6YN16	60	93	62	62	Sequence conflict	Note=E->G;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q6YN16	60	93	89	89	Sequence conflict	Note=I->V;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q6YN16	166	199	168	168	Active site	Note=Proton acceptor;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU10001
Q6YN16	166	199	94	166	Alternative sequence	ID=VSP_031529;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:14702039,ECO:0000303\|PubMed:15489334;Dbxref=PMID:14702039,PMID:15489334
Q6YN16	166	199	191	196	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KVO
Q6YN16	166	199	172	172	Binding site	Note=NADP;Ontology_term=ECO:0000269;evidence=ECO:0000269\|Ref.11
Q6YN16	166	199	1	418	Chain	ID=PRO_0000319888;Note=Hydroxysteroid dehydrogenase-like protein 2
Q6YN16	166	199	166	185	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KVO
Q6YN16	166	199	186	189	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KVO
Q6YN16	199	264	242	244	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KVO
Q6YN16	199	264	261	263	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KVO
Q6YN16	199	264	1	418	Chain	ID=PRO_0000319888;Note=Hydroxysteroid dehydrogenase-like protein 2
Q6YN16	199	264	204	209	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KVO
Q6YN16	199	264	215	217	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KVO
Q6YN16	199	264	222	232	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KVO
Q6YN16	199	264	245	251	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KVO
Q6YN16	199	264	257	260	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KVO
Q6YN16	288	338	1	418	Chain	ID=PRO_0000319888;Note=Hydroxysteroid dehydrogenase-like protein 2
Q6YN16	288	338	306	415	Domain	Note=SCP2
Q6YN16	288	338	318	318	Modified residue	Note=N6-succinyllysine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q2TPA8

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
Q6YN16	60	93	67	72	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KVO
Q6YN16	60	93	74	74	Binding site	Note=NADP;Ontology_term=ECO:0000269;evidence=ECO:0000269\|Ref.11
Q6YN16	60	93	1	418	Chain	ID=PRO_0000319888;Note=Hydroxysteroid dehydrogenase-like protein 2
Q6YN16	60	93	54	63	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KVO
Q6YN16	60	93	78	92	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KVO
Q6YN16	60	93	62	62	Sequence conflict	Note=E->G;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q6YN16	60	93	89	89	Sequence conflict	Note=I->V;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q6YN16	166	199	168	168	Active site	Note=Proton acceptor;Ontology_term=ECO:0000255;evidence=ECO:0000255\|PROSITE-ProRule:PRU10001
Q6YN16	166	199	94	166	Alternative sequence	ID=VSP_031529;Note=In isoform 2. Missing;Ontology_term=ECO:0000303,ECO:0000303;evidence=ECO:0000303\|PubMed:14702039,ECO:0000303\|PubMed:15489334;Dbxref=PMID:14702039,PMID:15489334
Q6YN16	166	199	191	196	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KVO
Q6YN16	166	199	172	172	Binding site	Note=NADP;Ontology_term=ECO:0000269;evidence=ECO:0000269\|Ref.11
Q6YN16	166	199	1	418	Chain	ID=PRO_0000319888;Note=Hydroxysteroid dehydrogenase-like protein 2
Q6YN16	166	199	166	185	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KVO
Q6YN16	166	199	186	189	Turn	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KVO
Q6YN16	199	264	242	244	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KVO
Q6YN16	199	264	261	263	Beta strand	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KVO
Q6YN16	199	264	1	418	Chain	ID=PRO_0000319888;Note=Hydroxysteroid dehydrogenase-like protein 2
Q6YN16	199	264	204	209	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KVO
Q6YN16	199	264	215	217	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KVO
Q6YN16	199	264	222	232	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KVO
Q6YN16	199	264	245	251	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KVO
Q6YN16	199	264	257	260	Helix	Ontology_term=ECO:0000244;evidence=ECO:0000244\|PDB:3KVO
Q6YN16	288	338	1	418	Chain	ID=PRO_0000319888;Note=Hydroxysteroid dehydrogenase-like protein 2
Q6YN16	288	338	306	415	Domain	Note=SCP2
Q6YN16	288	338	318	318	Modified residue	Note=N6-succinyllysine;Ontology_term=ECO:0000250;evidence=ECO:0000250\|UniProtKB:Q2TPA8

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SNVs in the skipped exons for HSDL2

- 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
GBM	TCGA-19-2629-01	exon_skip_498136 exon_skip_498141 exon_skip_498140	115181140	115181238	115181194	115181194	Frame_Shift_Del	A	-	p.E185fs
LUSC	TCGA-33-4583-01	exon_skip_498142	115200711	115200905	115200823	115200823	Frame_Shift_Del	T	-	p.S237fs
KIRP	TCGA-WN-AB4C-01	exon_skip_498138	115179121	115179224	115179215	115179215	Nonsense_Mutation	C	T	p.Q164X
UCEC	TCGA-AP-A0LM-01	exon_skip_498136 exon_skip_498141 exon_skip_498140	115181140	115181238	115181193	115181193	Nonsense_Mutation	G	T	p.E185*
BRCA	TCGA-EW-A1J6-01	exon_skip_498142	115200711	115200905	115200812	115200812	Nonsense_Mutation	A	T	p.K234*

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

Depth of coverage in three exons

Mutation description

- 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
JHUEM7_ENDOMETRIUM	115166275	115166438	115166342	115166342	Missense_Mutation	A	C	p.K29Q
LOXIMVI_SKIN	115166275	115166438	115166346	115166346	Missense_Mutation	C	T	p.A30V
HEC151_ENDOMETRIUM	115166275	115166438	115166364	115166364	Missense_Mutation	A	G	p.N36S
SNU1066_UPPER_AERODIGESTIVE_TRACT	115167904	115168002	115167918	115167918	Missense_Mutation	G	A	p.G66R
LS180_LARGE_INTESTINE	115167904	115168002	115167939	115167939	Missense_Mutation	G	A	p.V73I
C33A_CERVIX	115167904	115168002	115167997	115167997	Missense_Mutation	T	C	p.F92S
KOSC2_UPPER_AERODIGESTIVE_TRACT	115171187	115171301	115171252	115171252	Missense_Mutation	A	G	p.K116E
LNCAPCLONEFGC_PROSTATE	115200711	115200905	115200815	115200815	Missense_Mutation	C	T	p.P235S
DND41_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	115200711	115200905	115200894	115200894	Missense_Mutation	C	T	p.A261V
HCC2998_LARGE_INTESTINE	115216293	115216442	115216371	115216371	Missense_Mutation	G	T	p.R315I
DOHH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	115216293	115216442	115216421	115216421	Missense_Mutation	A	C	p.I332L

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for HSDL2

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 HSDL2

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for HSDL2

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RelatedDrugs for HSDL2

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 HSDL2

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
HSDL2	C0023903	Liver neoplasms	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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