ExonSkipDB Logo

Home

Download

Statistics

Landscape

Help

Contact
Center for Computational Systems Medicine
leaf

Gene summary

leaf

Gene structures and expression levels

leaf

Exon skipping events with PSIs in TCGA

leaf

Exon skipping events with PSIs in GTEx

leaf

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

leaf

Exon skipping events in the canonical protein sequence

leaf

SNVs in the skipped exons with depth of coverage

leaf

Splicing Quantitative Trait Loci (sQTLs) in the skipped exons

leaf

Splicing Quantitative Trait Methylation (sQTM) in the skipped exon

leaf

Related drugs with this gene

leaf

Related diseases with this gene

Gene summary for CTSS

check button Gene summary
Gene informationGene symbol

CTSS

Gene ID

1520

Gene namecathepsin S
Synonyms-
Cytomap

1q21.3

Type of geneprotein-coding
Descriptioncathepsin S
Modification date20180527
UniProtAcc

P25774

ContextPubMed: CTSS [Title/Abstract] AND exon [Title/Abstract] AND skip [Title/Abstract]
- Title (PMID)

check button Gene ontology of each this gene with evidence of Inferred from Direct Assay (IDA) from Entrez
GeneGO IDGO termPubMed ID
CTSS

GO:0006508

proteolysis

12788072|22864553

CTSS

GO:0010447

response to acidic pH

22864553

CTSS

GO:0016485

protein processing

22864553

CTSS

GO:0030574

collagen catabolic process

22952693

CTSS

GO:0034769

basement membrane disassembly

22952693

CTSS

GO:0048002

antigen processing and presentation of peptide antigen

8612130

CTSS

GO:0051603

proteolysis involved in cellular protein catabolic process

22952693

CTSS

GO:2001259

positive regulation of cation channel activity

22864553


Top

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

check buttonSkipped 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.
all structure

Top

Gene isoform structures and expression levels for CTSS

check button Expression levels of gene isoforms across TCGA.
gencode gene structure

check button Expression levels of gene isoforms across GTEx.
gencode gene structure


Top

Exon skipping events with PSIs in TCGA for CTSS

check button Information of exkip skipping event in TCGA.
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_303001150705390:150705621:150720252:150720355:150722481:150722567150720252:150720355ENSG00000163131.6ENST00000448301.2,ENST00000368985.3,ENST00000472977.2
exon_skip_303091150720271:150720355:150720640:150720761:150722481:150722567150720640:150720761ENSG00000163131.6ENST00000483930.1
exon_skip_303111150720271:150720355:150722481:150722647:150724256:150724310150722481:150722647ENSG00000163131.6ENST00000448301.2,ENST00000368985.3
exon_skip_303141150720271:150720355:150724256:150724484:150727476:150727626150724256:150724484ENSG00000163131.6ENST00000480760.1
exon_skip_303161150722481:150722647:150724256:150724484:150727476:150727626150724256:150724484ENSG00000163131.6ENST00000368985.3
exon_skip_303181150724256:150724484:150727476:150727626:150730333:150730456150727476:150727626ENSG00000163131.6ENST00000368985.3,ENST00000480760.1
exon_skip_303191150727476:150727626:150730333:150730456:150737113:150737178150730333:150730456ENSG00000163131.6ENST00000368985.3,ENST00000480760.1
exon_skip_303201150730333:150730456:150737113:150737240:150738173:150738268150737113:150737240ENSG00000163131.6ENST00000448301.2

check button PSI values of skipped exons in TCGA.
psi tcga

Top

Exon skipping events with PSIs in GTEx for CTSS

check button Information of exkip skipping event in GTEx
Exon skip IDchrExons involved in exon skippingSkipped exonENSGENSTs
exon_skip_303001150705390:150705621:150720252:150720355:150722481:150722567150720252:150720355ENSG00000163131.6ENST00000368985.3,ENST00000472977.2,ENST00000448301.2
exon_skip_303091150720271:150720355:150720640:150720761:150722481:150722567150720640:150720761ENSG00000163131.6ENST00000483930.1
exon_skip_303111150720271:150720355:150722481:150722647:150724256:150724310150722481:150722647ENSG00000163131.6ENST00000368985.3,ENST00000448301.2
exon_skip_303141150720271:150720355:150724256:150724484:150727476:150727626150724256:150724484ENSG00000163131.6ENST00000480760.1
exon_skip_303161150722481:150722647:150724256:150724484:150727476:150727626150724256:150724484ENSG00000163131.6ENST00000368985.3
exon_skip_303181150724256:150724484:150727476:150727626:150730333:150730456150727476:150727626ENSG00000163131.6ENST00000368985.3,ENST00000480760.1
exon_skip_303191150727476:150727626:150730333:150730456:150737113:150737178150730333:150730456ENSG00000163131.6ENST00000368985.3,ENST00000480760.1
exon_skip_303201150730333:150730456:150737113:150737240:150738173:150738268150737113:150737240ENSG00000163131.6ENST00000448301.2

check button PSI values of skipped exons in GTEx.
psi gtex

* Skipped exon sequences.

Top

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

check button Open reading frame (ORF) of individual exon skipping events in TCGA based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST00000368985150720252150720355Frame-shift
ENST00000368985150722481150722647Frame-shift
ENST00000368985150724256150724484In-frame
ENST00000368985150727476150727626In-frame
ENST00000368985150730333150730456In-frame

check button Open reading frame (ORF) of individual exon skipping events in GTEx based on the Ensembl gene structure combined from isoforms.
ENSTStart of skipped exonEnd of skipped exonORF
ENST00000368985150720252150720355Frame-shift
ENST00000368985150722481150722647Frame-shift
ENST00000368985150724256150724484In-frame
ENST00000368985150727476150727626In-frame
ENST00000368985150730333150730456In-frame

Top

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

check button Exon skipping at the protein sequence level and followed lost functional features.
* Click on the image to enlarge it in a new window.
prot feature distribution

check button Loci of skipped exons in TCGA across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end
ENST0000036898541243311507303331507304563885104283
ENST00000368985412433115072747615072762651166083133
ENST000003689854124331150724256150724484661888133209

check button Loci of skipped exons in GTEx across genomic, transcript, and protein sequence levels of In-frame cases.
ENSTLength of mRNALength of AA seq.Genomic startGenomic endmRNA startmRNA endAA startAA end
ENST0000036898541243311507303331507304563885104283
ENST00000368985412433115072747615072762651166083133
ENST000003689854124331150724256150724484661888133209

check button 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 featureDescription of feature
P2577442837275Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2C0Y
P2577442834467HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2C0Y
P2577442837982HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2C0Y
P25774428317114PropeptideID=PRO_0000026313;Note=Activation peptide
P257748313384133Alternative sequenceID=VSP_042712;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039
P2577483133115331ChainID=PRO_0000026314;Note=Cathepsin S
P2577483133126224Disulfide bondOntology_term=ECO:0000269;evidence=ECO:0000269|PubMed:17469812;Dbxref=PMID:17469812
P2577483133104104GlycosylationNote=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
P25774831338591HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2C0Y
P2577483133100102HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2C0Y
P2577483133121124HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3OVX
P2577483133113113Natural variantID=VAR_025385;Note=R->W;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:14702039,ECO:0000269|PubMed:15489334,ECO:0000269|Ref.5;Dbxref=dbSNP:rs2230061,PMID:14702039,PMID:15489334
P257748313317114PropeptideID=PRO_0000026313;Note=Activation peptide
P25774831339292Sequence conflictNote=M->T;Ontology_term=ECO:0000305;evidence=ECO:0000305
P25774831339292Sequence conflictNote=M->T;Ontology_term=ECO:0000305;evidence=ECO:0000305
P25774133209139139Active siteOntology_term=ECO:0000250;evidence=ECO:0000250
P2577413320984133Alternative sequenceID=VSP_042712;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039
P25774133209135137Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2HH5
P25774133209198200Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3OVX
P25774133209115331ChainID=PRO_0000026314;Note=Cathepsin S
P25774133209126224Disulfide bondOntology_term=ECO:0000269;evidence=ECO:0000269|PubMed:17469812;Dbxref=PMID:17469812
P25774133209136180Disulfide bondOntology_term=ECO:0000269;evidence=ECO:0000269|PubMed:17469812;Dbxref=PMID:17469812
P25774133209170213Disulfide bondOntology_term=ECO:0000269;evidence=ECO:0000269|PubMed:17469812;Dbxref=PMID:17469812
P25774133209139156HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3OVX
P25774133209164170HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3OVX
P25774133209173175HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3OVX
P25774133209179181HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3OVX
P25774133209185195HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3OVX
P25774133209161161Natural variantID=VAR_025386;Note=S->T;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:1373132,ECO:0000269|PubMed:8157683;Dbxref=dbSNP:rs1059604,PMID:1373132,PMID:8157683
P25774133209201203TurnOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3OVX


check button 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 featureDescription of feature
P2577442837275Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2C0Y
P2577442834467HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2C0Y
P2577442837982HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2C0Y
P25774428317114PropeptideID=PRO_0000026313;Note=Activation peptide
P257748313384133Alternative sequenceID=VSP_042712;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039
P2577483133115331ChainID=PRO_0000026314;Note=Cathepsin S
P2577483133126224Disulfide bondOntology_term=ECO:0000269;evidence=ECO:0000269|PubMed:17469812;Dbxref=PMID:17469812
P2577483133104104GlycosylationNote=N-linked (GlcNAc...) asparagine;Ontology_term=ECO:0000255;evidence=ECO:0000255
P25774831338591HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2C0Y
P2577483133100102HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2C0Y
P2577483133121124HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3OVX
P2577483133113113Natural variantID=VAR_025385;Note=R->W;Ontology_term=ECO:0000269,ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:14702039,ECO:0000269|PubMed:15489334,ECO:0000269|Ref.5;Dbxref=dbSNP:rs2230061,PMID:14702039,PMID:15489334
P257748313317114PropeptideID=PRO_0000026313;Note=Activation peptide
P25774831339292Sequence conflictNote=M->T;Ontology_term=ECO:0000305;evidence=ECO:0000305
P25774831339292Sequence conflictNote=M->T;Ontology_term=ECO:0000305;evidence=ECO:0000305
P25774133209139139Active siteOntology_term=ECO:0000250;evidence=ECO:0000250
P2577413320984133Alternative sequenceID=VSP_042712;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039
P25774133209135137Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2HH5
P25774133209198200Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3OVX
P25774133209115331ChainID=PRO_0000026314;Note=Cathepsin S
P25774133209126224Disulfide bondOntology_term=ECO:0000269;evidence=ECO:0000269|PubMed:17469812;Dbxref=PMID:17469812
P25774133209136180Disulfide bondOntology_term=ECO:0000269;evidence=ECO:0000269|PubMed:17469812;Dbxref=PMID:17469812
P25774133209170213Disulfide bondOntology_term=ECO:0000269;evidence=ECO:0000269|PubMed:17469812;Dbxref=PMID:17469812
P25774133209139156HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3OVX
P25774133209164170HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3OVX
P25774133209173175HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3OVX
P25774133209179181HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3OVX
P25774133209185195HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3OVX
P25774133209161161Natural variantID=VAR_025386;Note=S->T;Ontology_term=ECO:0000269,ECO:0000269;evidence=ECO:0000269|PubMed:1373132,ECO:0000269|PubMed:8157683;Dbxref=dbSNP:rs1059604,PMID:1373132,PMID:8157683
P25774133209201203TurnOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:3OVX


Top

SNVs in the skipped exons for CTSS

check button - Lollipop plot for presenting exon skipping associated SNVs.
* Click on the image to enlarge it in a new window.
lollipop

check button - Differential PSIs between mutated versus non-mutated samples.

check button - Non-synonymous mutations located in the skipped exons in TCGA.
Cancer typeSampleESIDSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
LIHCTCGA-DD-A39Y-01exon_skip_30311
150722482150722647150722598150722598Frame_Shift_DelT-p.K226fs
LIHCTCGA-G3-A3CJ-01exon_skip_30311
150722482150722647150722598150722598Frame_Shift_DelT-p.K226fs
LIHCTCGA-DD-A3A0-01exon_skip_30311
150722482150722647150722621150722621Frame_Shift_DelT-p.K218fs
LIHCTCGA-G3-A3CJ-01exon_skip_30320
150737114150737240150737129150737129Frame_Shift_DelT-p.K37fs
LIHCTCGA-DD-AACQ-01exon_skip_30311
150722482150722647150722488150722488Nonsense_MutationTAp.R263X

check button - Depth of coverage in the three exons composing exon skipping event
Depth of coverage in three exonsMutation description

check button - Non-synonymous mutations located in the skipped exons in CCLE.
SampleSkipped exon startSkipped exon endMutation startMutation endMutation typeReference seqMutation seqAAchange
HEC108_ENDOMETRIUM150720253150720355150720310150720310Missense_MutationAGp.V280A
CHLA258_BONE150722482150722647150722514150722514Missense_MutationGAp.A254V
NCIH1092_LUNG150722482150722647150722514150722514Missense_MutationGAp.A254V
NCIH1105_LUNG150722482150722647150722523150722523Missense_MutationCTp.G251D
ISTSL1_LUNG150722482150722647150722545150722545Missense_MutationTGp.N244H
HCC1569_BREAST150724257150724484150724307150724307Missense_MutationTCp.I193V
OCIMY7_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE150724257150724484150724406150724406Missense_MutationCTp.V160M
HS746T_STOMACH150724257150724484150724480150724480Missense_MutationGTp.S135Y
VMCUB1_URINARY_TRACT150727477150727626150727513150727513Missense_MutationCGp.W121C
KMH2_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE150727477150727626150727578150727578Missense_MutationGTp.Q100K
M14_SKIN150730334150730456150730434150730434Missense_MutationATp.L50H
MDAMB435S_SKIN150730334150730456150730434150730434Missense_MutationATp.L50H
SKCO1_LARGE_INTESTINE150730334150730456150730440150730440Missense_MutationCTp.R48Q
F36P_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE150737114150737240150737139150737139Missense_MutationGTp.T34N
SNU1040_LARGE_INTESTINE150737114150737240150737199150737199Missense_MutationGAp.A14V
SNUC4_LARGE_INTESTINE150737114150737240150737215150737215Missense_MutationACp.L9V
MFE296_ENDOMETRIUM150737114150737240150737123150737123Nonsense_MutationGCp.Y39*
HEC108_ENDOMETRIUM150720253150720355150720354150720354Splice_SiteAGp.G265G

Top

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

check button sQTL information located at the skipped exons.
Exon skip IDChromosomeThree exonsSkippped exonENSTCancer typeSNP idLocationDNA change (ref/var)P-value
exon_skip_303181150724256:150724484:150727476:150727626:150730333:150730456150727476:150727626ENST00000368985.3,ENST00000480760.1COADrs2230061chr1:150727539G/A1.64e-04
exon_skip_303181150724256:150724484:150727476:150727626:150730333:150730456150727476:150727626ENST00000368985.3,ENST00000480760.1HNSCrs2230061chr1:150727539G/A9.20e-04
exon_skip_303181150724256:150724484:150727476:150727626:150730333:150730456150727476:150727626ENST00000368985.3,ENST00000480760.1BRCArs2230061chr1:150727539G/A6.96e-07
exon_skip_303181150724256:150724484:150727476:150727626:150730333:150730456150727476:150727626ENST00000368985.3,ENST00000480760.1LGGrs2230061chr1:150727539G/A5.63e-04
exon_skip_303181150724256:150724484:150727476:150727626:150730333:150730456150727476:150727626ENST00000368985.3,ENST00000480760.1PAADrs2230061chr1:150727539G/A5.96e-04
exon_skip_303181150724256:150724484:150727476:150727626:150730333:150730456150727476:150727626ENST00000368985.3,ENST00000480760.1PRADrs2230061chr1:150727539G/A2.94e-04
exon_skip_303181150724256:150724484:150727476:150727626:150730333:150730456150727476:150727626ENST00000368985.3,ENST00000480760.1STADrs2230061chr1:150727539G/A1.19e-04
exon_skip_303181150724256:150724484:150727476:150727626:150730333:150730456150727476:150727626ENST00000368985.3,ENST00000480760.1THCArs2230061chr1:150727539G/A5.95e-06

Top

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


Top

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


Top

RelatedDrugs for CTSS

check button Approved drugs targeting this gene.
(DrugBank Version 5.1.0 2018-04-02)
GeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
P25774DB12010FostamatinibCathepsin Ssmall moleculeapproved|investigational

Top

RelatedDiseases for CTSS

check button Diseases associated with this gene.
(DisGeNet 4.0)
GeneDisease IDDisease name# pubmedsSource
CTSSC0011616Contact Dermatitis1CTD_human
CTSSC0023893Liver Cirrhosis, Experimental1CTD_human
CTSSC0027626Neoplasm Invasiveness1CTD_human
CTSSC0028754Obesity1CTD_human