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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:PRPF3-CTSS (FusionGDB2 ID:69032)

Fusion Gene Summary for PRPF3-CTSS

check button Fusion gene summary
Fusion gene informationFusion gene name: PRPF3-CTSS
Fusion gene ID: 69032
HgeneTgene
Gene symbol

PRPF3

CTSS

Gene ID

9129

1520

Gene namepre-mRNA processing factor 3cathepsin S
SynonymsHPRP3|HPRP3P|PRP3|Prp3p|RP18|SNRNP90-
Cytomap

1q21.2

1q21.3

Type of geneprotein-codingprotein-coding
DescriptionU4/U6 small nuclear ribonucleoprotein Prp3PRP3 pre-mRNA processing factor 3 homologU4/U6 snRNP 90 kDa proteinU4/U6-associated RNA splicing factorpre-mRNA-splicing factor 3cathepsin S
Modification date2020031320200329
UniProtAcc.

P25774

Ensembl transtripts involved in fusion geneENST00000324862, ENST00000414970, 
ENST00000543398, ENST00000467329, 
ENST00000368985, ENST00000448301, 
ENST00000480760, 
Fusion gene scores* DoF score7 X 7 X 6=29414 X 15 X 9=1890
# samples 719
** MAII scorelog2(7/294*10)=-2.0703893278914
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(19/1890*10)=-3.31431491077749
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: PRPF3 [Title/Abstract] AND CTSS [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPRPF3(150294041)-CTSS(150738270), # samples:2
PRPF3(150294041)-CTSS(150730456), # samples:2
Anticipated loss of major functional domain due to fusion event.
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgenePRPF3

GO:0000244

spliceosomal tri-snRNP complex assembly

20595234

HgenePRPF3

GO:0000398

mRNA splicing, via spliceosome

28781166

TgeneCTSS

GO:0006508

proteolysis

12788072|22864553

TgeneCTSS

GO:0010447

response to acidic pH

22864553

TgeneCTSS

GO:0016485

protein processing

22864553

TgeneCTSS

GO:0030574

collagen catabolic process

22952693

TgeneCTSS

GO:0034769

basement membrane disassembly

22952693

TgeneCTSS

GO:0048002

antigen processing and presentation of peptide antigen

8612130

TgeneCTSS

GO:0051603

proteolysis involved in cellular protein catabolic process

22952693

TgeneCTSS

GO:2001259

positive regulation of cation channel activity

22864553


check buttonFusion gene breakpoints across PRPF3 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across CTSS (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check button Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* All genome coordinats were lifted-over on hg19.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChimerDB4LUADTCGA-86-8673-01APRPF3chr1

150294041

-CTSSchr1

150730456

-
ChimerDB4LUADTCGA-86-8673-01APRPF3chr1

150294041

+CTSSchr1

150730456

-
ChimerDB4LUADTCGA-86-8673-01APRPF3chr1

150294041

+CTSSchr1

150738270

-


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Fusion Gene ORF analysis for PRPF3-CTSS

check button Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
5UTR-3CDSENST00000324862ENST00000368985PRPF3chr1

150294041

+CTSSchr1

150730456

-
5UTR-3CDSENST00000324862ENST00000448301PRPF3chr1

150294041

+CTSSchr1

150730456

-
5UTR-3CDSENST00000414970ENST00000368985PRPF3chr1

150294041

+CTSSchr1

150730456

-
5UTR-3CDSENST00000414970ENST00000448301PRPF3chr1

150294041

+CTSSchr1

150730456

-
5UTR-3CDSENST00000543398ENST00000368985PRPF3chr1

150294041

+CTSSchr1

150730456

-
5UTR-3CDSENST00000543398ENST00000448301PRPF3chr1

150294041

+CTSSchr1

150730456

-
5UTR-5UTRENST00000324862ENST00000368985PRPF3chr1

150294041

+CTSSchr1

150738270

-
5UTR-5UTRENST00000324862ENST00000448301PRPF3chr1

150294041

+CTSSchr1

150738270

-
5UTR-5UTRENST00000324862ENST00000480760PRPF3chr1

150294041

+CTSSchr1

150730456

-
5UTR-5UTRENST00000414970ENST00000368985PRPF3chr1

150294041

+CTSSchr1

150738270

-
5UTR-5UTRENST00000414970ENST00000448301PRPF3chr1

150294041

+CTSSchr1

150738270

-
5UTR-5UTRENST00000414970ENST00000480760PRPF3chr1

150294041

+CTSSchr1

150730456

-
5UTR-5UTRENST00000543398ENST00000368985PRPF3chr1

150294041

+CTSSchr1

150738270

-
5UTR-5UTRENST00000543398ENST00000448301PRPF3chr1

150294041

+CTSSchr1

150738270

-
5UTR-5UTRENST00000543398ENST00000480760PRPF3chr1

150294041

+CTSSchr1

150730456

-
5UTR-intronENST00000324862ENST00000480760PRPF3chr1

150294041

+CTSSchr1

150738270

-
5UTR-intronENST00000414970ENST00000480760PRPF3chr1

150294041

+CTSSchr1

150738270

-
5UTR-intronENST00000543398ENST00000480760PRPF3chr1

150294041

+CTSSchr1

150738270

-
intron-3CDSENST00000467329ENST00000368985PRPF3chr1

150294041

+CTSSchr1

150730456

-
intron-3CDSENST00000467329ENST00000448301PRPF3chr1

150294041

+CTSSchr1

150730456

-
intron-5UTRENST00000467329ENST00000368985PRPF3chr1

150294041

+CTSSchr1

150738270

-
intron-5UTRENST00000467329ENST00000448301PRPF3chr1

150294041

+CTSSchr1

150738270

-
intron-5UTRENST00000467329ENST00000480760PRPF3chr1

150294041

+CTSSchr1

150730456

-
intron-intronENST00000467329ENST00000480760PRPF3chr1

150294041

+CTSSchr1

150738270

-

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)

check buttonDeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score

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Fusion Genomic Features for PRPF3-CTSS


check buttonFusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.

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Fusion Protein Features for PRPF3-CTSS


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:150294041/:150738270)
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
- How to search
1. Put your fusion gene symbol.
2. Press the tab key until there will be shown the breakpoint information filled.
4. Go down and press 'Search' tab twice.
4. Go down to have the hyperlink of the search result.
5. Click the hyperlink.
6. See the FGviewer result for your fusion gene.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
.CTSS

P25774

FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.FUNCTION: Thiol protease. Key protease responsible for the removal of the invariant chain from MHC class II molecules and MHC class II antigen presentation (PubMed:30612035). The bond-specificity of this proteinase is in part similar to the specificities of cathepsin L. {ECO:0000269|PubMed:30612035}.

check buttonRetention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at

download page


* Minus value of BPloci means that the break pointn is located before the CDS.
- In-frame and retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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Fusion Gene Sequence for PRPF3-CTSS


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.

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Fusion Gene PPI Analysis for PRPF3-CTSS


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page.


check button Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs for PRPF3-CTSS


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for PRPF3-CTSS


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource