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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:KLK3-MSMB (FusionGDB2 ID:43086)

Fusion Gene Summary for KLK3-MSMB

check button Fusion gene summary
Fusion gene informationFusion gene name: KLK3-MSMB
Fusion gene ID: 43086
HgeneTgene
Gene symbol

KLK3

MSMB

Gene ID

3818

4477

Gene namekallikrein B1microseminoprotein beta
SynonymsKLK3|PKK|PKKD|PPKHPC13|IGBF|MSP|MSPB|PN44|PRPS|PSP|PSP-94|PSP57|PSP94
Cytomap

4q35.2

10q11.22

Type of geneprotein-codingprotein-coding
Descriptionplasma kallikreinkallikrein B, plasma (Fletcher factor) 1kininogeninplasma prekallikreinbeta-microseminoproteinimmunoglobulin binding factorprostate secreted seminal plasma proteinprostate secretory protein of 94 amino acidsseminal plasma beta-inhibin
Modification date2020032020200313
UniProtAcc

P07288

P08118

Ensembl transtripts involved in fusion geneENST00000326003, ENST00000360617, 
ENST00000593997, ENST00000595952, 
ENST00000597483, 
ENST00000298239, 
ENST00000474170, ENST00000358559, 
Fusion gene scores* DoF score24 X 31 X 2=148818 X 7 X 6=756
# samples 3121
** MAII scorelog2(31/1488*10)=-2.26303440583379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(21/756*10)=-1.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: KLK3 [Title/Abstract] AND MSMB [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointKLK3(51361836)-MSMB(51562326), # samples:1
MSMB(51562517)-KLK3(51361285), # samples:2
Anticipated loss of major functional domain due to fusion event.MSMB-KLK3 seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF.
MSMB-KLK3 seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
* 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
HgeneKLK3

GO:0031639

plasminogen activation

89876

HgeneKLK3

GO:0051919

positive regulation of fibrinolysis

89876


check buttonFusion gene breakpoints across KLK3 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

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

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
ChimerDB4PRADTCGA-G9-6365KLK3chr19

51361836

+MSMBchr10

51562326

+


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Fusion Gene ORF analysis for KLK3-MSMB

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
5CDS-intronENST00000326003ENST00000298239KLK3chr19

51361836

+MSMBchr10

51562326

+
5CDS-intronENST00000326003ENST00000474170KLK3chr19

51361836

+MSMBchr10

51562326

+
5CDS-intronENST00000360617ENST00000298239KLK3chr19

51361836

+MSMBchr10

51562326

+
5CDS-intronENST00000360617ENST00000474170KLK3chr19

51361836

+MSMBchr10

51562326

+
5CDS-intronENST00000593997ENST00000298239KLK3chr19

51361836

+MSMBchr10

51562326

+
5CDS-intronENST00000593997ENST00000474170KLK3chr19

51361836

+MSMBchr10

51562326

+
5CDS-intronENST00000595952ENST00000298239KLK3chr19

51361836

+MSMBchr10

51562326

+
5CDS-intronENST00000595952ENST00000474170KLK3chr19

51361836

+MSMBchr10

51562326

+
5CDS-intronENST00000597483ENST00000298239KLK3chr19

51361836

+MSMBchr10

51562326

+
5CDS-intronENST00000597483ENST00000474170KLK3chr19

51361836

+MSMBchr10

51562326

+
In-frameENST00000326003ENST00000358559KLK3chr19

51361836

+MSMBchr10

51562326

+
In-frameENST00000360617ENST00000358559KLK3chr19

51361836

+MSMBchr10

51562326

+
In-frameENST00000593997ENST00000358559KLK3chr19

51361836

+MSMBchr10

51562326

+
In-frameENST00000595952ENST00000358559KLK3chr19

51361836

+MSMBchr10

51562326

+
In-frameENST00000597483ENST00000358559KLK3chr19

51361836

+MSMBchr10

51562326

+

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)
ENST00000326003KLK3chr1951361836+ENST00000358559MSMBchr1051562326+74054917535172
ENST00000597483KLK3chr1951361836+ENST00000358559MSMBchr1051562326+5964052391129
ENST00000593997KLK3chr1951361836+ENST00000358559MSMBchr1051562326+110491321515164
ENST00000595952KLK3chr1951361836+ENST00000358559MSMBchr1051562326+5773867372121
ENST00000360617KLK3chr1951361836+ENST00000358559MSMBchr1051562326+6995080494164

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
ENST00000326003ENST00000358559KLK3chr1951361836+MSMBchr1051562326+0.234590590.76540935
ENST00000597483ENST00000358559KLK3chr1951361836+MSMBchr1051562326+0.251006570.7489934
ENST00000593997ENST00000358559KLK3chr1951361836+MSMBchr1051562326+0.211170330.7888297
ENST00000595952ENST00000358559KLK3chr1951361836+MSMBchr1051562326+0.195315990.80468404
ENST00000360617ENST00000358559KLK3chr1951361836+MSMBchr1051562326+0.143869360.85613066

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Fusion Genomic Features for KLK3-MSMB


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.
genomic feature

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 KLK3-MSMB


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/chr19:51361836/chr10:51562326)
- 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
KLK3

P07288

MSMB

P08118

FUNCTION: Hydrolyzes semenogelin-1 thus leading to the liquefaction of the seminal coagulum.

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
HgeneKLK3chr19:51361836chr10:51562326ENST00000326003+1525_2580262.0DomainPeptidase S1
HgeneKLK3chr19:51361836chr10:51562326ENST00000360617+1525_2580239.0DomainPeptidase S1
HgeneKLK3chr19:51361836chr10:51562326ENST00000593997+1425_2580228.0DomainPeptidase S1
HgeneKLK3chr19:51361836chr10:51562326ENST00000595952+1525_2580219.0DomainPeptidase S1


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Fusion Gene Sequence for KLK3-MSMB


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.
>43086_43086_1_KLK3-MSMB_KLK3_chr19_51361836_ENST00000326003_MSMB_chr10_51562326_ENST00000358559_length(transcript)=740nt_BP=549nt
AGCCCCAAGCTTACCACCTGCACCCGGAGAGCTGTGTCACCATGTGGGTCCCGGTTGTCTTCCTCACCCTGTCCGTGACGTGGATTGGTG
CTGCACCCCTCATCCTGTCTCGGATTGTGGGAGGCTGGGAGTGCGAGAAGCATTCCCAACCCTGGCAGGTGCTTGTGGCCTCTCGTGGCA
GGGCAGTCTGCGGCGGTGTTCTGGTGCACCCCCAGTGGGTCCTCACAGCTGCCCACTGCATCAGGAACAAAAGCGTGATCTTGCTGGGTC
GGCACAGCCTGTTTCATCCTGAAGACACAGGCCAGGTATTTCAGGTCAGCCACAGCTTCCCACACCCGCTCTACGATATGAGCCTCCTGA
AGAATCGATTCCTCAGGCCAGGTGATGACTCCAGCCACGACCTCATGCTGCTCCGCCTGTCAGAGCCTGCCGAGCTCACGGATGCTGTGA
AGGTCATGGACCTGCCCACCCAGGAGCCAGCACTGGGGACCACCTGCTACGCCTCAGGCTGGGGCAGCATTGAACCAGAGGAGTAAAAGC
ACCTGCTCGAGGACTGCAAGTATATCGTGGTGGAGAAGAAGGACCCAAAAAAGACCTGTTCTGTCAGTGAATGGATAATCTAATGTGCTT
CTAGTAGGCACAGGGCTCCCAGGCCAGGCCTCATTCTCCTCTGGCCTCTAATAGTCAATGATTGTGTAGCCATGCCTATCAGTAAAAAGA

>43086_43086_1_KLK3-MSMB_KLK3_chr19_51361836_ENST00000326003_MSMB_chr10_51562326_ENST00000358559_length(amino acids)=172AA_BP=
MHPESCVTMWVPVVFLTLSVTWIGAAPLILSRIVGGWECEKHSQPWQVLVASRGRAVCGGVLVHPQWVLTAAHCIRNKSVILLGRHSLFH

--------------------------------------------------------------
>43086_43086_2_KLK3-MSMB_KLK3_chr19_51361836_ENST00000360617_MSMB_chr10_51562326_ENST00000358559_length(transcript)=699nt_BP=508nt
ATGTGGGTCCCGGTTGTCTTCCTCACCCTGTCCGTGACGTGGATTGGTGCTGCACCCCTCATCCTGTCTCGGATTGTGGGAGGCTGGGAG
TGCGAGAAGCATTCCCAACCCTGGCAGGTGCTTGTGGCCTCTCGTGGCAGGGCAGTCTGCGGCGGTGTTCTGGTGCACCCCCAGTGGGTC
CTCACAGCTGCCCACTGCATCAGGAACAAAAGCGTGATCTTGCTGGGTCGGCACAGCCTGTTTCATCCTGAAGACACAGGCCAGGTATTT
CAGGTCAGCCACAGCTTCCCACACCCGCTCTACGATATGAGCCTCCTGAAGAATCGATTCCTCAGGCCAGGTGATGACTCCAGCCACGAC
CTCATGCTGCTCCGCCTGTCAGAGCCTGCCGAGCTCACGGATGCTGTGAAGGTCATGGACCTGCCCACCCAGGAGCCAGCACTGGGGACC
ACCTGCTACGCCTCAGGCTGGGGCAGCATTGAACCAGAGGAGTAAAAGCACCTGCTCGAGGACTGCAAGTATATCGTGGTGGAGAAGAAG
GACCCAAAAAAGACCTGTTCTGTCAGTGAATGGATAATCTAATGTGCTTCTAGTAGGCACAGGGCTCCCAGGCCAGGCCTCATTCTCCTC

>43086_43086_2_KLK3-MSMB_KLK3_chr19_51361836_ENST00000360617_MSMB_chr10_51562326_ENST00000358559_length(amino acids)=164AA_BP=
MWVPVVFLTLSVTWIGAAPLILSRIVGGWECEKHSQPWQVLVASRGRAVCGGVLVHPQWVLTAAHCIRNKSVILLGRHSLFHPEDTGQVF

--------------------------------------------------------------
>43086_43086_3_KLK3-MSMB_KLK3_chr19_51361836_ENST00000593997_MSMB_chr10_51562326_ENST00000358559_length(transcript)=1104nt_BP=913nt
CACCCGGAGAGCTGTGTCACCATGTGGGTCCCGGTTGTCTTCCTCACCCTGTCCGTGACGTGGATTGGTGCTGCACCCCTCATCCTGTCT
CGGATTGTGGGAGGCTGGGAGTGCGAGAAGCATTCCCAACCCTGGCAGGTGCTTGTGGCCTCTCGTGGCAGGGCAGTCTGCGGCGGTGTT
CTGGTGCACCCCCAGTGGGTCCTCACAGCTGCCCACTGCATCAGGAACAAAAGCGTGATCTTGCTGGGTCGGCACAGCCTGTTTCATCCT
GAAGACACAGGCCAGGTATTTCAGGTCAGCCACAGCTTCCCACACCCGCTCTACGATATGAGCCTCCTGAAGAATCGATTCCTCAGGCCA
GGTGATGACTCCAGCCACGACCTCATGCTGCTCCGCCTGTCAGAGCCTGCCGAGCTCACGGATGCTGTGAAGGTCATGGACCTGCCCACC
CAGGAGCCAGCACTGGGGACCACCTGCTACGCCTCAGGCTGGGGCAGCATTGAACCAGAGGAGTAAAAGCACCTGCTCGGTGAGTCATCC
CTACTCCCAAGATCTTGAGGGGAAAGGTGAGTGGGGACCTTAATTCTGGGCTGGGGTCTAGAAGCCAACAAGGCGTCTGCCTCCCCTGCT
CCCCAGCTGTAGCCATGCCACCTCCCCGTGTCTCATCTCATTCCCTCCTTCCCTCTTCTTTGACTCCCTCAAGGCAATAGGTTATTCTTA
CAGCACAACTCATCTGTTCCTGCGTTCAGCACACGGTTACTAGGCACCTGCTATGCACCCAGCACTGCCCTAGAGCCTGGGACATAGCAG
TGAACAGACAGAGAGCAGCCCCTCCCTTCTGTAGCCCCCAAGCCAGTGAGGGGCACAGGCAGGAACAGGGACCACAACACAGAAAAGCTG
GAGGGTGTCAGGAAGGACTGCAAGTATATCGTGGTGGAGAAGAAGGACCCAAAAAAGACCTGTTCTGTCAGTGAATGGATAATCTAATGT
GCTTCTAGTAGGCACAGGGCTCCCAGGCCAGGCCTCATTCTCCTCTGGCCTCTAATAGTCAATGATTGTGTAGCCATGCCTATCAGTAAA

>43086_43086_3_KLK3-MSMB_KLK3_chr19_51361836_ENST00000593997_MSMB_chr10_51562326_ENST00000358559_length(amino acids)=164AA_BP=
MWVPVVFLTLSVTWIGAAPLILSRIVGGWECEKHSQPWQVLVASRGRAVCGGVLVHPQWVLTAAHCIRNKSVILLGRHSLFHPEDTGQVF

--------------------------------------------------------------
>43086_43086_4_KLK3-MSMB_KLK3_chr19_51361836_ENST00000595952_MSMB_chr10_51562326_ENST00000358559_length(transcript)=577nt_BP=386nt
TGTCACCATGTGGGTCCCGGTTGTCTTCCTCACCCTGTCCGTGACGTGGATTGGTGCTGCACCCCTCATCCTGTCTCGGATTGTGGGAGG
CTGGGAGTGCGAGAAGCATTCCCAACCCTGGCAGGTGCTTGTGGCCTCTCGTGGCAGGGCAGTCTGCGGCGGTGTTCTGGTGCACCCCCA
GTGGGTCCTCACAGCTGCCCACTGCATCAGGAAGCCAGGTGATGACTCCAGCCACGACCTCATGCTGCTCCGCCTGTCAGAGCCTGCCGA
GCTCACGGATGCTGTGAAGGTCATGGACCTGCCCACCCAGGAGCCAGCACTGGGGACCACCTGCTACGCCTCAGGCTGGGGCAGCATTGA
ACCAGAGGAGTAAAAGCACCTGCTCGAGGACTGCAAGTATATCGTGGTGGAGAAGAAGGACCCAAAAAAGACCTGTTCTGTCAGTGAATG
GATAATCTAATGTGCTTCTAGTAGGCACAGGGCTCCCAGGCCAGGCCTCATTCTCCTCTGGCCTCTAATAGTCAATGATTGTGTAGCCAT

>43086_43086_4_KLK3-MSMB_KLK3_chr19_51361836_ENST00000595952_MSMB_chr10_51562326_ENST00000358559_length(amino acids)=121AA_BP=
MWVPVVFLTLSVTWIGAAPLILSRIVGGWECEKHSQPWQVLVASRGRAVCGGVLVHPQWVLTAAHCIRKPGDDSSHDLMLLRLSEPAELT

--------------------------------------------------------------
>43086_43086_5_KLK3-MSMB_KLK3_chr19_51361836_ENST00000597483_MSMB_chr10_51562326_ENST00000358559_length(transcript)=596nt_BP=405nt
ACCTGCACCCGGAGAGCTGTGTCACCATGTGGGTCCCGGTTGTCTTCCTCACCCTGTCCGTGACGTGGATTGGTGCTGCACCCCTCATCC
TGTCTCGGATTGTGGGAGGCTGGGAGTGCGAGAAGCATTCCCAACCCTGGCAGGTGCTTGTGGCCTCTCGTGGCAGGGCAGTCTGCGGCG
GTGTTCTGGTGCACCCCCAGTGGGTCCTCACAGCTGCCCACTGCATCAGGAAGCCAGGTGATGACTCCAGCCACGACCTCATGCTGCTCC
GCCTGTCAGAGCCTGCCGAGCTCACGGATGCTGTGAAGGTCATGGACCTGCCCACCCAGGAGCCAGCACTGGGGACCACCTGCTACGCCT
CAGGCTGGGGCAGCATTGAACCAGAGGAGTAAAAGCACCTGCTCGAGGACTGCAAGTATATCGTGGTGGAGAAGAAGGACCCAAAAAAGA
CCTGTTCTGTCAGTGAATGGATAATCTAATGTGCTTCTAGTAGGCACAGGGCTCCCAGGCCAGGCCTCATTCTCCTCTGGCCTCTAATAG

>43086_43086_5_KLK3-MSMB_KLK3_chr19_51361836_ENST00000597483_MSMB_chr10_51562326_ENST00000358559_length(amino acids)=129AA_BP=
LHPESCVTMWVPVVFLTLSVTWIGAAPLILSRIVGGWECEKHSQPWQVLVASRGRAVCGGVLVHPQWVLTAAHCIRKPGDDSSHDLMLLR

--------------------------------------------------------------

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Fusion Gene PPI Analysis for KLK3-MSMB


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 KLK3-MSMB


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 KLK3-MSMB


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