ExonSkipDB: functional annotation of exon skipping event in human

Gene summary for HPSE2

Gene summary

Gene information	Gene symbol	HPSE2
	Gene ID	60495
	Gene name	heparanase 2 (inactive)
	Synonyms	HPA2\|HPR2\|UFS\|UFS1
	Cytomap	10q24.2
	Type of gene	protein-coding
	Description	inactive heparanase-2heparanase 3heparanase-like protein
	Modification date	20180523
	UniProtAcc	Q8WWQ2
	Context	PubMed: HPSE2 [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 HPSE2 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 HPSE2

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 HPSE2

Information of exkip skipping event in TCGA.

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_52902	10	100219330:100219496:100221506:100221576:100242392:100242539	100221506:100221576	ENSG00000172987.8	ENST00000370546.1
exon_skip_52903	10	100219330:100219496:100242392:100242539:100249807:100249953	100242392:100242539	ENSG00000172987.8	ENST00000370549.1,ENST00000404542.1,ENST00000370552.3
exon_skip_52904	10	100374660:100374775:100380358:100380465:100401603:100401697	100380358:100380465	ENSG00000172987.8	ENST00000370549.1,ENST00000404542.1,ENST00000370552.3,ENST00000370546.1
exon_skip_52909	10	100380358:100380465:100401603:100401697:100453656:100453704	100401603:100401697	ENSG00000172987.8	ENST00000370549.1,ENST00000404542.1,ENST00000370552.3,ENST00000370546.1
exon_skip_52910	10	100453656:100453704:100481413:100481585:100503639:100503809	100481413:100481585	ENSG00000172987.8	ENST00000370552.3,ENST00000370546.1
exon_skip_52913	10	100481413:100481585:100503639:100503813:100903994:100904156	100503639:100503813	ENSG00000172987.8	ENST00000370552.3,ENST00000370546.1
exon_skip_52915	10	100481413:100481585:100903994:100904156:100992104:100992262	100903994:100904156	ENSG00000172987.8	ENST00000370549.1
exon_skip_52917	10	100503639:100503813:100903994:100904156:100992104:100992262	100903994:100904156	ENSG00000172987.8	ENST00000370552.3,ENST00000370546.1

PSI values of skipped exons in TCGA.

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Exon skipping events with PSIs in GTEx for HPSE2

Information of exkip skipping event in GTEx

Exon skip ID	chr	Exons involved in exon skipping	Skipped exon	ENSG	ENSTs
exon_skip_52902	10	100219330:100219496:100221506:100221576:100242392:100242539	100221506:100221576	ENSG00000172987.8	ENST00000370546.1
exon_skip_52903	10	100219330:100219496:100242392:100242539:100249807:100249953	100242392:100242539	ENSG00000172987.8	ENST00000370552.3,ENST00000370549.1,ENST00000404542.1
exon_skip_52904	10	100374660:100374775:100380358:100380465:100401603:100401697	100380358:100380465	ENSG00000172987.8	ENST00000370552.3,ENST00000370549.1,ENST00000370546.1,ENST00000404542.1
exon_skip_52909	10	100380358:100380465:100401603:100401697:100453656:100453704	100401603:100401697	ENSG00000172987.8	ENST00000370552.3,ENST00000370549.1,ENST00000370546.1,ENST00000404542.1
exon_skip_52910	10	100453656:100453704:100481413:100481585:100503639:100503809	100481413:100481585	ENSG00000172987.8	ENST00000370552.3,ENST00000370546.1
exon_skip_52913	10	100481413:100481585:100503639:100503813:100903994:100904156	100503639:100503813	ENSG00000172987.8	ENST00000370552.3,ENST00000370546.1
exon_skip_52915	10	100481413:100481585:100903994:100904156:100992104:100992262	100903994:100904156	ENSG00000172987.8	ENST00000370549.1
exon_skip_52917	10	100503639:100503813:100903994:100904156:100992104:100992262	100903994:100904156	ENSG00000172987.8	ENST00000370552.3,ENST00000370546.1

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 HPSE2

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
ENST00000370552	100380358	100380465	Frame-shift
ENST00000370552	100401603	100401697	Frame-shift
ENST00000370552	100481413	100481585	Frame-shift
ENST00000370552	100242392	100242539	In-frame
ENST00000370552	100503639	100503813	In-frame
ENST00000370552	100903994	100904156	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
ENST00000370552	100380358	100380465	Frame-shift
ENST00000370552	100401603	100401697	Frame-shift
ENST00000370552	100481413	100481585	Frame-shift
ENST00000370552	100242392	100242539	In-frame
ENST00000370552	100503639	100503813	In-frame
ENST00000370552	100903994	100904156	In-frame

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Infer the effects of exon skipping event on protein functional features for HPSE2

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
ENST00000370552	2312	592	100903994	100904156	509	670	149	203
ENST00000370552	2312	592	100503639	100503813	671	844	203	261
ENST00000370552	2312	592	100242392	100242539	1527	1673	489	537

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
ENST00000370552	2312	592	100903994	100904156	509	670	149	203
ENST00000370552	2312	592	100503639	100503813	671	844	203	261
ENST00000370552	2312	592	100242392	100242539	1527	1673	489	537

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
Q8WWQ2	149	203	150	261	Alternative sequence	ID=VSP_015850;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11027606;Dbxref=PMID:11027606
Q8WWQ2	149	203	42	592	Chain	ID=PRO_0000068140;Note=Inactive heparanase-2
Q8WWQ2	203	261	150	261	Alternative sequence	ID=VSP_015850;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11027606;Dbxref=PMID:11027606
Q8WWQ2	203	261	204	261	Alternative sequence	ID=VSP_015851;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11027606;Dbxref=PMID:11027606
Q8WWQ2	203	261	42	592	Chain	ID=PRO_0000068140;Note=Inactive heparanase-2
Q8WWQ2	203	261	254	254	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8WWQ2	203	261	213	213	Sequence conflict	Note=F->S;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q8WWQ2	203	261	213	213	Sequence conflict	Note=F->S;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q8WWQ2	489	537	42	592	Chain	ID=PRO_0000068140;Note=Inactive heparanase-2

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
Q8WWQ2	149	203	150	261	Alternative sequence	ID=VSP_015850;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11027606;Dbxref=PMID:11027606
Q8WWQ2	149	203	42	592	Chain	ID=PRO_0000068140;Note=Inactive heparanase-2
Q8WWQ2	203	261	150	261	Alternative sequence	ID=VSP_015850;Note=In isoform 4. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11027606;Dbxref=PMID:11027606
Q8WWQ2	203	261	204	261	Alternative sequence	ID=VSP_015851;Note=In isoform 3. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303\|PubMed:11027606;Dbxref=PMID:11027606
Q8WWQ2	203	261	42	592	Chain	ID=PRO_0000068140;Note=Inactive heparanase-2
Q8WWQ2	203	261	254	254	Glycosylation	Note=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
Q8WWQ2	203	261	213	213	Sequence conflict	Note=F->S;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q8WWQ2	203	261	213	213	Sequence conflict	Note=F->S;Ontology_term=ECO:0000305;evidence=ECO:0000305
Q8WWQ2	489	537	42	592	Chain	ID=PRO_0000068140;Note=Inactive heparanase-2

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SNVs in the skipped exons for HPSE2

- 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
STAD	TCGA-BR-6452-01	exon_skip_52909	100401604	100401697	100401612	100401612	Frame_Shift_Del	T	-	p.I364fs
HNSC	TCGA-CN-6021-01	exon_skip_52910	100481414	100481585	100481543	100481543	Frame_Shift_Del	C	-	p.G276fs
PAAD	TCGA-FB-AAQ3-01	exon_skip_52913	100503640	100503813	100503755	100503755	Frame_Shift_Del	A	-	p.A224fs
PAAD	TCGA-FB-AAQ3-01	exon_skip_52913	100503640	100503813	100503755	100503755	Frame_Shift_Del	A	-	p.F223fs
BLCA	TCGA-FD-A3B3-01	exon_skip_52903	100242393	100242539	100242424	100242424	Nonsense_Mutation	G	A	p.Q528*
UCEC	TCGA-AX-A05Z-01	exon_skip_52903	100242393	100242539	100242490	100242490	Nonsense_Mutation	G	A	p.R506*
SARC	TCGA-DX-A3U9-01	exon_skip_52910	100481414	100481585	100481499	100481499	Nonsense_Mutation	G	A	p.Q291*
SKCM	TCGA-EE-A2MR-06	exon_skip_52915 exon_skip_52917	100903995	100904156	100904148	100904148	Nonsense_Mutation	G	A	p.R153*

- 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
HT115_LARGE_INTESTINE	100242393	100242539	100242526	100242526	Missense_Mutation	G	A	p.R494C
BL70_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	100242393	100242539	100242531	100242531	Missense_Mutation	T	C	p.Y492C
KYSE410_OESOPHAGUS	100380359	100380465	100380363	100380363	Missense_Mutation	A	T	p.F401I
RMGI_OVARY	100380359	100380465	100380381	100380381	Missense_Mutation	C	A	p.D395Y
NCIH1975_LUNG	100380359	100380465	100380396	100380396	Missense_Mutation	T	C	p.T390A
NCIH2172_LUNG	100380359	100380465	100380449	100380449	Missense_Mutation	G	A	p.T372I
HUH7_LIVER	100401604	100401697	100401639	100401639	Missense_Mutation	C	T	p.D355N
HEC1_ENDOMETRIUM	100401604	100401697	100401648	100401648	Missense_Mutation	G	A	p.R352C
OCIAML5_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	100401604	100401697	100401650	100401650	Missense_Mutation	G	A	p.T351I
H2369_PLEURA	100481414	100481585	100481441	100481441	Missense_Mutation	C	A	p.R310M
NCIH510_LUNG	100481414	100481585	100481467	100481467	Missense_Mutation	T	A	p.L301F
ONS76_CENTRAL_NERVOUS_SYSTEM	100481414	100481585	100481481	100481481	Missense_Mutation	A	T	p.S297T
MIAPACA2_PANCREAS	100481414	100481585	100481489	100481489	Missense_Mutation	C	T	p.R294Q
SHP77_LUNG	100481414	100481585	100481509	100481509	Missense_Mutation	C	A	p.K287N
BICR18_UPPER_AERODIGESTIVE_TRACT	100481414	100481585	100481563	100481563	Missense_Mutation	C	G	p.M269I
DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	100481414	100481585	100481563	100481563	Missense_Mutation	C	G	p.M269I
BICR18_UPPER_AERODIGESTIVE_TRACT	100481414	100481585	100481567	100481567	Missense_Mutation	G	C	p.T268S
DAUDI_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	100481414	100481585	100481567	100481567	Missense_Mutation	G	C	p.T268S
OCILY7_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE	100503640	100503813	100503659	100503659	Missense_Mutation	A	C	p.I255M
DU145_PROSTATE	100503640	100503813	100503679	100503679	Missense_Mutation	C	T	p.A249T
NCIH661_LUNG	100503640	100503813	100503735	100503735	Missense_Mutation	C	T	p.R230H
HEC108_ENDOMETRIUM	100503640	100503813	100503751	100503751	Missense_Mutation	G	T	p.L225I
HCC2998_LARGE_INTESTINE	100503640	100503813	100503807	100503807	Missense_Mutation	G	T	p.S206Y
HMY1_SKIN	100903995	100904156	100904063	100904064	Missense_Mutation	GC	AT	p.A181I
HOP62_LUNG	100903995	100904156	100904072	100904072	Missense_Mutation	C	G	p.R178T
A427_LUNG	100903995	100904156	100904086	100904086	Missense_Mutation	C	A	p.M173I
SCC4_UPPER_AERODIGESTIVE_TRACT	100903995	100904156	100904151	100904151	Missense_Mutation	C	A	p.V152F
HCC44_LUNG	100903995	100904156	100904014	100904014	Nonsense_Mutation	G	T	p.Y197*

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Splicing Quantitative Trait Loci (sQTL) in the exon skipping event for HPSE2

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 HPSE2

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Survival analysis of Splicing Quantitative Trait Methylation (sQTM) in the skipped exon for HPSE2

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RelatedDrugs for HPSE2

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 HPSE2

Diseases associated with this gene.
(DisGeNet 4.0)

Gene	Disease ID	Disease name	# pubmeds	Source
HPSE2	C0403555	Ochoa syndrome	1	CTD_human;ORPHANET

	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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