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Center for Computational Systems Medicine
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FusionGeneSummary

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FusionProtFeature

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FusionGeneSequence

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FusionGenePPI

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RelatedDrugs

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RelatedDiseases

Fusion gene ID: 28866

FusionGeneSummary for PRPF3_CTSS

check button Fusion gene summary
Fusion gene informationFusion gene name: PRPF3_CTSS
Fusion gene ID: 28866
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 date2018052320180527
UniProtAcc

O43395

P25774

Ensembl transtripts involved in fusion geneENST00000324862, ENST00000543398, 
ENST00000414970, ENST00000467329, 
ENST00000368985, ENST00000448301, 
ENST00000480760, 
Fusion gene scores* DoF score4 X 4 X 4=6412 X 10 X 8=960
# samples 412
** MAII scorelog2(4/64*10)=-0.678071905112638
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(12/960*10)=-3
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]

Functional or gene categories assigned by FusionGDB annotation
* 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 button Fusion gene information from three resources
(ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018))
* 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.
Data typeSourceCancer typeSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
TCGARVLUADTCGA-86-8673-01APRPF3chr1

150294041

+CTSSchr1

150730456

-
TCGALDLUADTCGA-86-8673-01APRPF3chr1

150294041

+CTSSchr1

150738270

-
* LD: Li Ding group's fusion gene list
  RV: Roel Verhaak group's fusion gene list
  ChiTaRs fusion database

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-5UTRENST00000324862ENST00000480760PRPF3chr1

150294041

+CTSSchr1

150730456

-
5UTR-3CDSENST00000543398ENST00000368985PRPF3chr1

150294041

+CTSSchr1

150730456

-
5UTR-3CDSENST00000543398ENST00000448301PRPF3chr1

150294041

+CTSSchr1

150730456

-
5UTR-5UTRENST00000543398ENST00000480760PRPF3chr1

150294041

+CTSSchr1

150730456

-
5UTR-3CDSENST00000414970ENST00000368985PRPF3chr1

150294041

+CTSSchr1

150730456

-
5UTR-3CDSENST00000414970ENST00000448301PRPF3chr1

150294041

+CTSSchr1

150730456

-
5UTR-5UTRENST00000414970ENST00000480760PRPF3chr1

150294041

+CTSSchr1

150730456

-
intron-3CDSENST00000467329ENST00000368985PRPF3chr1

150294041

+CTSSchr1

150730456

-
intron-3CDSENST00000467329ENST00000448301PRPF3chr1

150294041

+CTSSchr1

150730456

-
intron-5UTRENST00000467329ENST00000480760PRPF3chr1

150294041

+CTSSchr1

150730456

-
5UTR-5UTRENST00000324862ENST00000368985PRPF3chr1

150294041

+CTSSchr1

150738270

-
5UTR-5UTRENST00000324862ENST00000448301PRPF3chr1

150294041

+CTSSchr1

150738270

-
5UTR-intronENST00000324862ENST00000480760PRPF3chr1

150294041

+CTSSchr1

150738270

-
5UTR-5UTRENST00000543398ENST00000368985PRPF3chr1

150294041

+CTSSchr1

150738270

-
5UTR-5UTRENST00000543398ENST00000448301PRPF3chr1

150294041

+CTSSchr1

150738270

-
5UTR-intronENST00000543398ENST00000480760PRPF3chr1

150294041

+CTSSchr1

150738270

-
5UTR-5UTRENST00000414970ENST00000368985PRPF3chr1

150294041

+CTSSchr1

150738270

-
5UTR-5UTRENST00000414970ENST00000448301PRPF3chr1

150294041

+CTSSchr1

150738270

-
5UTR-intronENST00000414970ENST00000480760PRPF3chr1

150294041

+CTSSchr1

150738270

-
intron-5UTRENST00000467329ENST00000368985PRPF3chr1

150294041

+CTSSchr1

150738270

-
intron-5UTRENST00000467329ENST00000448301PRPF3chr1

150294041

+CTSSchr1

150738270

-
intron-intronENST00000467329ENST00000480760PRPF3chr1

150294041

+CTSSchr1

150738270

-

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FusionProtFeatures for PRPF3_CTSS


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
PRPF3

O43395

CTSS

P25774

Participates in pre-mRNA splicing. Part of the U4/U5/U6tri-snRNP complex, one of the building blocks of the spliceosome.{ECO:0000269|PubMed:9328476, ECO:0000269|PubMed:9404889,ECO:0000303|PubMed:20595234}. Thiol protease. Key protease responsible for the removalof the invariant chain from MHC class II molecules. The bond-specificity of this proteinase is in part similar to thespecificities of cathepsin L.

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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FusionGeneSequence for PRPF3_CTSS


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences.
(nt: nucleotides, aa: amino acids)

* Fusion amino acid sequences.

* Fusion transcript sequences (only coding sequence (CDS) region).

* Fusion transcript sequences (Full-length transcript).

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FusionGenePPI 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
PRPF3CCDC85B, GTPBP3, DVL2, DPY30, DVL3, SART3, RNPS1, USP15, USP39, USP4, PRPF4, MEPCE, SRRM1, PRPF19, CDC5L, PRPF8, ELAVL1, SF3A2, SART1, NHP2L1, PPIH, PRPF3, PRPF31, PRPF6, U2AF2, SNRPD2, SF3A3, SRSF5, SNRPA1, BCAS2, SRRM2, SRSF7, RBM25, SF3A1, SNRPC, PABPC1, EIF4A3, LSM1, HNRNPM, SON, THRAP3, PATL1, RPS10, SEPT2, CDK13, NOP58, MPHOSPH6, SUPT16H, NNT, FBL, SEPT7, SF3B2, SMNDC1, RBM39, CTNNBL1, SNIP1, MFAP1, SLU7, FRA10AC1, PCBP1, NKAP, ZCCHC10, MMS19, TARDBP, WBP4, WWOX, LIN28A, AURKB, CEP250, TUBG1, TRIM39, FAM9B, BRCA1, OBSL1, DDX23, TRA2A, CCDC84, SNRNP40, CASQ2, CD2BP2, PLRG1, SF3B1, SF3B3, SNRPD3, TFIP11, XAB2, RBM26, SNRNP70, UTP20, NTRK1, KRAS, ZBTB8A, HIST1H3E, KIFAP3, RAB4B, POU5F1, ZNF131, ILKAP, TUT1, AKAP7, SNRNP27, LSM6, ZGPAT, SNRPF, SNRPN, SNRPE, LSM5, SNRPG, TMOD3, RBM42, LSM2, LSM4, SNRPB, LSM8, SNRPD1, SNRNP200, LSM3, FBXO11, TXNL4A, ALYREF, RPL26L1, OLA1, RPL32, RNH1, CHCHD2, FAU, NCL, FOXA1CTSSSERPINB3, CST5, IRF2


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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RelatedDrugs for PRPF3_CTSS


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for PRPF3_CTSS


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgenePRPF3C1832378Retinitis Pigmentosa 182CTD_human;UNIPROT
TgeneCTSSC0011616Contact Dermatitis1CTD_human
TgeneCTSSC0023893Liver Cirrhosis, Experimental1CTD_human
TgeneCTSSC0027626Neoplasm Invasiveness1CTD_human
TgeneCTSSC0028754Obesity1CTD_human