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Center for Computational Systems Medicine level2
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein Structure

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pLDDT scores

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Ramachandran Plot of Fusion Protein Structure

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:PGA3-CTSE

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: PGA3-CTSE
FusionPDB ID: 64497
FusionGDB2.0 ID: 64497
HgeneTgene
Gene symbol

PGA3

CTSE

Gene ID

643834

1510

Gene namepepsinogen A3cathepsin E
Synonyms-CATE
Cytomap

11q12.2

1q32.1

Type of geneprotein-codingprotein-coding
Descriptionpepsin A-3pepsinogen 3, group I (pepsinogen A)pepsinogen-3cathepsin Eerythrocyte membrane aspartic proteinaseslow-moving proteinase
Modification date2020031320200313
UniProtAcc.

P14091

Ensembl transtripts involved in fusion geneENST idsENST00000325558, ENST00000538258, 
ENST00000543125, 		ENST00000468617, 
ENST00000358184, ENST00000360218, 
ENST00000361052, ENST00000432969, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score15 X 13 X 4=7803 X 3 X 2=18
# samples 163
** MAII scorelog2(16/780*10)=-2.28540221886225
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(3/18*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context (manual curation of fusion genes in FusionPDB)

PubMed: PGA3 [Title/Abstract] AND CTSE [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)PGA3(60971741)-CTSE(206319100), # samples:9
CTSE(206318467)-PGA3(60973981), # samples:3
Anticipated loss of major functional domain due to fusion event.CTSE-PGA3 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
CTSE-PGA3 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
PGA3-CTSE seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
PGA3-CTSE seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
PGA3-CTSE seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
PGA3-CTSE seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
PGA3-CTSE seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
PGA3-CTSE 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
TgeneCTSE

GO:0006508

proteolysis

16997486

TgeneCTSE

GO:0019886

antigen processing and presentation of exogenous peptide antigen via MHC class II

8765029


check buttonFusion gene breakpoints across PGA3 (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 CTSE (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
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
ChimerDB4Non-Cancer139NPGA3chr11

60971741

+CTSEchr1

206319100

+
ChimerDB4Non-Cancer203NPGA3chr11

60971741

+CTSEchr1

206319100

+
ChimerDB4Non-Cancer267NPGA3chr11

60971741

+CTSEchr1

206319100

+
ChimerDB4Non-Cancer43NPGA3chr11

60971741

+CTSEchr1

206319100

+
ChimerDB4Non-Cancer5263NPGA3chr11

60971741

+CTSEchr1

206319100

+
ChimerDB4Non-Cancer5357NPGA3chr11

60971741

+CTSEchr1

206319100

+
ChimerDB4Non-Cancer5381NPGA3chr11

60971741

+CTSEchr1

206319100

+
ChimerDB4Non-Cancer5759NPGA3chr11

60971741

+CTSEchr1

206319100

+
ChimerDB4Non-CancerTCGA-BR-8060-11APGA3chr11

60971741

+CTSEchr1

206319100

+
ChimerDB4Non-CancerTCGA-L5-A4OJ-11APGA3chr11

60978907

+CTSEchr1

206331020

+


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Fusion ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)
ENST00000325558PGA3chr1160971741+ENST00000361052CTSEchr1206319100+23044041311384417
ENST00000325558PGA3chr1160971741+ENST00000358184CTSEchr1206319100+22894041311369412
ENST00000325558PGA3chr1160971741+ENST00000360218CTSEchr1206319100+21464041311270379
ENST00000325558PGA3chr1160971741+ENST00000432969CTSEchr1206319100+16034041311270379

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
ENST00000325558ENST00000361052PGA3chr1160971741+CTSEchr1206319100+0.000660420.9993395
ENST00000325558ENST00000358184PGA3chr1160971741+CTSEchr1206319100+0.0006506870.9993493
ENST00000325558ENST00000360218PGA3chr1160971741+CTSEchr1206319100+0.0048851170.9951149
ENST00000325558ENST00000432969PGA3chr1160971741+CTSEchr1206319100+0.0090755760.9909244

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Fusion Amino Acid Sequences


check button For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>64497_64497_1_PGA3-CTSE_PGA3_chr11_60971741_ENST00000325558_CTSE_chr1_206319100_ENST00000358184_length(amino acids)=412AA_BP=89
MHLPPVLPSPSSWDPGRTMKWLLLLGLVALSECIMYKVPLIRKKSLRRTLSERGLLKDFLKKHNLNPARKYFPQWKAPTLVDEQPLENYL
DMEYFGTISIGSPPQNFTVIFDTGSSNLWVPSVYCTSPACKTHSRFQPSQSSTYSQPGQSFSIQYGTGSLSGIIGADQVSVEGLTVVGQQ
FGESVTEPGQTFVDAEFDGILGLGYPSLAVGGVTPVFDNMMAQNLVDLPMFSVYMSSNPEGGAGSELIFGGYDHSHFSGSLNWVPVTKQA
YWQIALDNIQVGGTVMFCSEGCQAIVDTGTSLITGPSDKIKQLQNAIGAAPVDGEYAVECANLNVMPDVTFTINGVPYTLSPTAYTLLDF

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

>64497_64497_2_PGA3-CTSE_PGA3_chr11_60971741_ENST00000325558_CTSE_chr1_206319100_ENST00000360218_length(amino acids)=379AA_BP=89
MHLPPVLPSPSSWDPGRTMKWLLLLGLVALSECIMYKVPLIRKKSLRRTLSERGLLKDFLKKHNLNPARKYFPQWKAPTLVDEQPLENYL
DMEYFGTISIGSPPQNFTVIFDTGSSNLWVPSVYCTSPACKTHSRFQPSQSSTYSQPGQSFSIQYGTGSLSGIIGADQVSVEGLTVVGQQ
FGESVTEPGQTFVDAEFDGILGLGYPSLAVGGVTPVFDNMMAQNLVDLPMFSVYMSSNPEGGAGSELIFGGYDHSHFSGSLNWVPVTKQA
YWQIALDNMLWSVPTLTSCRMSPSPLTESPIPSAQLPTPYWTSWMECSSAAVAFKDLTSTLQLGPSGSWGMSSFDSFTQSLTVGITVWDW

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

>64497_64497_3_PGA3-CTSE_PGA3_chr11_60971741_ENST00000325558_CTSE_chr1_206319100_ENST00000361052_length(amino acids)=417AA_BP=89
MHLPPVLPSPSSWDPGRTMKWLLLLGLVALSECIMYKVPLIRKKSLRRTLSERGLLKDFLKKHNLNPARKYFPQWKAPTLVDEQPLENYL
DMEYFGTISIGSPPQNFTVIFDTGSSNLWVPSVYCTSPACKTHSRFQPSQSSTYSQPGQSFSIQYGTGSLSGIIGADQVSAFSYQVEGLT
VVGQQFGESVTEPGQTFVDAEFDGILGLGYPSLAVGGVTPVFDNMMAQNLVDLPMFSVYMSSNPEGGAGSELIFGGYDHSHFSGSLNWVP
VTKQAYWQIALDNIQVGGTVMFCSEGCQAIVDTGTSLITGPSDKIKQLQNAIGAAPVDGEYAVECANLNVMPDVTFTINGVPYTLSPTAY

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

>64497_64497_4_PGA3-CTSE_PGA3_chr11_60971741_ENST00000325558_CTSE_chr1_206319100_ENST00000432969_length(amino acids)=379AA_BP=89
MHLPPVLPSPSSWDPGRTMKWLLLLGLVALSECIMYKVPLIRKKSLRRTLSERGLLKDFLKKHNLNPARKYFPQWKAPTLVDEQPLENYL
DMEYFGTISIGSPPQNFTVIFDTGSSNLWVPSVYCTSPACKTHSRFQPSQSSTYSQPGQSFSIQYGTGSLSGIIGADQVSVEGLTVVGQQ
FGESVTEPGQTFVDAEFDGILGLGYPSLAVGGVTPVFDNMMAQNLVDLPMFSVYMSSNPEGGAGSELIFGGYDHSHFSGSLNWVPVTKQA
YWQIALDNMLWSVPTLTSCRMSPSPLTESPIPSAQLPTPYWTSWMECSSAAVAFKDLTSTLQLGPSGSWGMSSFDSFTQSLTVGITVWDW

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

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Fusion Protein Functional Features


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/chr11:60971741/chr1:206319100)
- 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
.CTSE

P14091

FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.FUNCTION: May have a role in immune function. Probably involved in the processing of antigenic peptides during MHC class II-mediated antigen presentation. May play a role in activation-induced lymphocyte depletion in the thymus, and in neuronal degeneration and glial cell activation in the brain. {ECO:0000269|PubMed:8765029}.

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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
TgeneCTSEchr11:60971741chr1:206319100ENST000003581841978_39675.0397.0DomainPeptidase A1
TgeneCTSEchr11:60971741chr1:206319100ENST000003602181878_39675.0364.0DomainPeptidase A1

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgenePGA3chr11:60971741chr1:206319100ENST00000325558+2976_38573.0389.0DomainPeptidase A1


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Fusion Protein Structures

check button PDB and CIF files of the predicted fusion proteins
* Here we show the 3D structure of the fusion proteins using Mol*. AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100. Model confidence is shown from the pLDDT values per residue. pLDDT corresponds to the model’s prediction of its score on the local Distance Difference Test. It is a measure of local accuracy (from AlphfaFold website). To color code individual residues, we transformed individual PDB files into CIF format.
Fusion protein PDB link (fusion AA seq ID in FusionPDB)HgeneHchrHbpHstrandTgeneTchrTbpTstrandAA seqLen(AA seq)
PDB file >>>855_PGA3_60971741_CTSE_206319100_855_PGA3_60971741_CTSE_206319100_ranked_0.pdbPGA36097174160971741ENST00000432969CTSEchr1206319100+
MHLPPVLPSPSSWDPGRTMKWLLLLGLVALSECIMYKVPLIRKKSLRRTLSERGLLKDFLKKHNLNPARKYFPQWKAPTLVDEQPLENYL
DMEYFGTISIGSPPQNFTVIFDTGSSNLWVPSVYCTSPACKTHSRFQPSQSSTYSQPGQSFSIQYGTGSLSGIIGADQVSAFSYQVEGLT
VVGQQFGESVTEPGQTFVDAEFDGILGLGYPSLAVGGVTPVFDNMMAQNLVDLPMFSVYMSSNPEGGAGSELIFGGYDHSHFSGSLNWVP
VTKQAYWQIALDNIQVGGTVMFCSEGCQAIVDTGTSLITGPSDKIKQLQNAIGAAPVDGEYAVECANLNVMPDVTFTINGVPYTLSPTAY
417


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pLDDT score distribution

check button pLDDT score distribution of the predicted wild-type structures of two partner proteins from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.
PGA3_pLDDT.png
all structure
all structure
CTSE_pLDDT.png
all structure
all structure

check button pLDDT score distribution of the predicted fusion protein structures from AlphaFold2
* AlphaFold produces a per-residue confidence score (pLDDT) between 0 and 100.
all structure


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Ramachandran Plot of Fusion Protein Structure


check button Ramachandran plot of the torsional angles - phi (φ)and psi (ψ) - of the residues (amino acids) contained in this fusion protein peptide.
Fusion AA seq ID in FusionPDB and their Ramachandran plots

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Fusion Protein-Protein Interaction


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 from validated records (BIOGRID-3.4.160)
GenePPI interactors


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
PGA3
CTSE


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs to PGA3-CTSE


check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

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Related Diseases to PGA3-CTSE


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

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