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Center for Computational Systems Medicine
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Fusion Gene and Fusion Protein Summary

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Fusion Amino Acid Sequences (multiple BPs and multiple gene isoforms)

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Fusion Protein Breakpoint Sequences - (for the Screening of the FusionNeoAntigens)

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Potential FusionNeoAntigens in HLA I - (netMHCpan v4.1 + deepHLApan v1.1)

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Potential FusionNeoAntigens in HLA II - (netMHCIIpan v4.1)

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Fusion Breakpoint 14 AA Peptide Structure - (RoseTTAFold)

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D - (Glide)

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Vaccine Design for the FusionNeoAntigens (RNA/protein sequences)

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Potential target of CAR-T therapy development

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Information on the samples that have these potential fusion neoantigens

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Fusion Protein Targeting Drugs - (Manual Curation)

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Fusion Protein Related diseases - (Manual Curation)

Fusion Protein:ST7-EXOC4

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: ST7-EXOC4
FusionPDB ID: 87021
FusionGDB2.0 ID: 87021
HgeneTgene
Gene symbol

ST7

EXOC4

Gene ID

93655

60412

Gene nameST7 overlapping transcript 3exocyst complex component 4
SynonymsNCRNA00026|ST7|ST7OT3SEC8|SEC8L1|Sec8p
Cytomap

7q31.2

7q33

Type of genencRNAprotein-coding
DescriptionST7 overlapping transcript 3 (non-coding RNA)ST7 overlapping transcript 3 (non-protein coding)suppression of tumorigenicity 7exocyst complex component 4SEC8-like 1exocyst complex component Sec8
Modification date2020031320200320
UniProtAcc.

Q96A65

Main function of 5'-partner protein: FUNCTION: Component of the exocyst complex involved in the docking of exocytic vesicles with fusion sites on the plasma membrane. {ECO:0000250}.
Ensembl transtripts involved in fusion geneENST idsENST00000265437, ENST00000323984, 
ENST00000393446, ENST00000393449, 
ENST00000393451, ENST00000422922, 
ENST00000432298, ENST00000393443, 
ENST00000393444, ENST00000393447, 
ENST00000465133, ENST00000487459, 
ENST00000460346, ENST00000393161, 
ENST00000541309, ENST00000545148, 
ENST00000253861, ENST00000539845, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score17 X 11 X 9=168335 X 25 X 10=8750
# samples 2339
** MAII scorelog2(23/1683*10)=-2.87132941038557
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(39/8750*10)=-4.48773698785744
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: ST7 [Title/Abstract] AND EXOC4 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: ST7 [Title/Abstract] AND EXOC4 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)ST7(116655068)-EXOC4(133314798), # samples:1
ST7(116593745)-EXOC4(133314798), # samples:1
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


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/chr7:116655068/chr7:133314798)
- 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 buttonRetention analysis results 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, are available here.

check buttonFusion gene breakpoints across ST7 (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 EXOC4 (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 Amino Acid Sequences


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)
ENST00000432298ST7chr7116655068+ENST00000253861EXOC4chr7133314798+2866127631634523
ENST00000432298ST7chr7116655068+ENST00000539845EXOC4chr7133314798+1694127631634523
ENST00000422922ST7chr7116655068+ENST00000253861EXOC4chr7133314798+2866127631634523
ENST00000422922ST7chr7116655068+ENST00000539845EXOC4chr7133314798+1694127631634523
ENST00000393446ST7chr7116593745+ENST00000253861EXOC4chr7133314798+31934543031961552
ENST00000393446ST7chr7116593745+ENST00000539845EXOC4chr7133314798+20214543031961552
ENST00000265437ST7chr7116593745+ENST00000253861EXOC4chr7133314798+31043652141872552
ENST00000265437ST7chr7116593745+ENST00000539845EXOC4chr7133314798+19323652141872552
ENST00000393451ST7chr7116593745+ENST00000253861EXOC4chr7133314798+30893501991857552
ENST00000393451ST7chr7116593745+ENST00000539845EXOC4chr7133314798+19173501991857552
ENST00000393449ST7chr7116593745+ENST00000253861EXOC4chr7133314798+30523131621820552
ENST00000393449ST7chr7116593745+ENST00000539845EXOC4chr7133314798+18803131621820552
ENST00000323984ST7chr7116593745+ENST00000253861EXOC4chr7133314798+30523131621820552
ENST00000323984ST7chr7116593745+ENST00000539845EXOC4chr7133314798+18803131621820552

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
ENST00000432298ENST00000253861ST7chr7116655068+EXOC4chr7133314798+0.0009411380.9990589
ENST00000432298ENST00000539845ST7chr7116655068+EXOC4chr7133314798+0.0028133860.9971866
ENST00000422922ENST00000253861ST7chr7116655068+EXOC4chr7133314798+0.0009411380.9990589
ENST00000422922ENST00000539845ST7chr7116655068+EXOC4chr7133314798+0.0028133860.9971866
ENST00000393446ENST00000253861ST7chr7116593745+EXOC4chr7133314798+0.0012667070.99873334
ENST00000393446ENST00000539845ST7chr7116593745+EXOC4chr7133314798+0.0037826080.9962174
ENST00000265437ENST00000253861ST7chr7116593745+EXOC4chr7133314798+0.0013189590.998681
ENST00000265437ENST00000539845ST7chr7116593745+EXOC4chr7133314798+0.004070290.99592966
ENST00000393451ENST00000253861ST7chr7116593745+EXOC4chr7133314798+0.0012900310.9987099
ENST00000393451ENST00000539845ST7chr7116593745+EXOC4chr7133314798+0.0038783630.9961216
ENST00000393449ENST00000253861ST7chr7116593745+EXOC4chr7133314798+0.0012409540.99875903
ENST00000393449ENST00000539845ST7chr7116593745+EXOC4chr7133314798+0.0036700320.99632996
ENST00000323984ENST00000253861ST7chr7116593745+EXOC4chr7133314798+0.0012409540.99875903
ENST00000323984ENST00000539845ST7chr7116593745+EXOC4chr7133314798+0.0036700320.99632996

check button Predicted full-length fusion amino acid sequences. For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among all the predicted ones.

Get the fusion protein sequences from here.

Fusion protein sequence information is available in the fasta format.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

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Fusion Protein Breakpoint Sequences for ST7-EXOC4

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
ST7chr7116593745EXOC4chr713331479831350LRVPLKINDNLSTGGPDDNLIEGGGT
ST7chr7116593745EXOC4chr713331479835050LRVPLKINDNLSTGGPDDNLIEGGGT
ST7chr7116593745EXOC4chr713331479836550LRVPLKINDNLSTGGPDDNLIEGGGT
ST7chr7116593745EXOC4chr713331479845450LRVPLKINDNLSTGGPDDNLIEGGGT
ST7chr7116655068EXOC4chr713331479812721TQFPAYCFIMDYTGGPDDNLIEGGGT

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Potential FusionNeoAntigen Information of ST7-EXOC4 in HLA I

check button Multiple sequence alignments of the potential FusionNeoAntigens per fusion breakpoints. If the MSA is empty, then it means that there were predicted fusion neoantigens in this fusion breakpoint, but those predicted fusion neoantigens were not across the breakpoint, which is not fusion-specific.

check button Potential FusionNeoAntigen Information
* We used NetMHCpan v4.1 (%rank<0.5) and deepHLApan v1.1 (immunogenic score>0.5)
Fusion geneHchrHbpTgeneTchrTbpHLA IFusionNeoAntigen peptideBinding scoreImmunogenic scoreNeoantigen start (at BP 13)Neoantigen end (at BP 13)

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Potential FusionNeoAntigen Information of ST7-EXOC4 in HLA II

check button Multiple sequence alignments of the potential FusionNeoAntigens per fusion breakpoints. If the MSA is empty, then it means that there were predicted fusion neoantigens in this fusion breakpoint, but those predicted fusion neoantigens were not across the breakpoint, which is not fusion-specific.
ST7-EXOC4_116593745_133314798.msa

check button Potential FusionNeoAntigen Information
* We used NetMHCIIpan v4.1 (%rank<0.5).
Fusion geneHchrHbpTgeneTchrTbpHLA IIFusionNeoAntigen peptideNeoantigen start (at BP 13)Neoantigen end (at BP 13)
ST7-EXOC4chr7116593745chr7133314798365DRB1-0303RVPLKINDNLSTGGP116
ST7-EXOC4chr7116593745chr7133314798365DRB1-0324RVPLKINDNLSTGGP116
ST7-EXOC4chr7116593745chr7133314798365DRB1-0422RVPLKINDNLSTGGP116
ST7-EXOC4chr7116593745chr7133314798365DRB1-0434RVPLKINDNLSTGGP116
ST7-EXOC4chr7116593745chr7133314798365DRB1-0466RVPLKINDNLSTGGP116
ST7-EXOC4chr7116593745chr7133314798365DRB1-1336RVPLKINDNLSTGGP116
ST7-EXOC4chr7116593745chr7133314798365DRB1-1367RVPLKINDNLSTGGP116
ST7-EXOC4chr7116593745chr7133314798365DRB1-1396RVPLKINDNLSTGGP116
ST7-EXOC4chr7116593745chr7133314798365DRB1-1419RVPLKINDNLSTGGP116
ST7-EXOC4chr7116593745chr7133314798365DRB1-1424RVPLKINDNLSTGGP116
ST7-EXOC4chr7116593745chr7133314798365DRB1-1446RVPLKINDNLSTGGP116
ST7-EXOC4chr7116593745chr7133314798365DRB1-1447RVPLKINDNLSTGGP116
ST7-EXOC4chr7116593745chr7133314798365DRB1-1447LRVPLKINDNLSTGG015
ST7-EXOC4chr7116593745chr7133314798365DRB1-1525RVPLKINDNLSTGGP116
ST7-EXOC4chr7116593745chr7133314798365DRB3-0201RVPLKINDNLSTGGP116
ST7-EXOC4chr7116593745chr7133314798365DRB3-0201LRVPLKINDNLSTGG015
ST7-EXOC4chr7116593745chr7133314798365DRB3-0201VPLKINDNLSTGGPD217
ST7-EXOC4chr7116593745chr7133314798365DRB3-0202RVPLKINDNLSTGGP116
ST7-EXOC4chr7116593745chr7133314798365DRB3-0202LRVPLKINDNLSTGG015
ST7-EXOC4chr7116593745chr7133314798365DRB3-0202VPLKINDNLSTGGPD217
ST7-EXOC4chr7116593745chr7133314798365DRB3-0204RVPLKINDNLSTGGP116
ST7-EXOC4chr7116593745chr7133314798365DRB3-0204LRVPLKINDNLSTGG015
ST7-EXOC4chr7116593745chr7133314798365DRB3-0204VPLKINDNLSTGGPD217
ST7-EXOC4chr7116593745chr7133314798365DRB3-0205RVPLKINDNLSTGGP116
ST7-EXOC4chr7116593745chr7133314798365DRB3-0205LRVPLKINDNLSTGG015
ST7-EXOC4chr7116593745chr7133314798365DRB3-0205VPLKINDNLSTGGPD217
ST7-EXOC4chr7116593745chr7133314798365DRB3-0209RVPLKINDNLSTGGP116
ST7-EXOC4chr7116593745chr7133314798365DRB3-0210RVPLKINDNLSTGGP116
ST7-EXOC4chr7116593745chr7133314798365DRB3-0210LRVPLKINDNLSTGG015
ST7-EXOC4chr7116593745chr7133314798365DRB3-0210VPLKINDNLSTGGPD217
ST7-EXOC4chr7116593745chr7133314798365DRB3-0211RVPLKINDNLSTGGP116
ST7-EXOC4chr7116593745chr7133314798365DRB3-0211LRVPLKINDNLSTGG015
ST7-EXOC4chr7116593745chr7133314798365DRB3-0211VPLKINDNLSTGGPD217
ST7-EXOC4chr7116593745chr7133314798365DRB3-0212RVPLKINDNLSTGGP116
ST7-EXOC4chr7116593745chr7133314798365DRB3-0212LRVPLKINDNLSTGG015
ST7-EXOC4chr7116593745chr7133314798365DRB3-0212VPLKINDNLSTGGPD217
ST7-EXOC4chr7116593745chr7133314798365DRB3-0213RVPLKINDNLSTGGP116
ST7-EXOC4chr7116593745chr7133314798365DRB3-0213LRVPLKINDNLSTGG015
ST7-EXOC4chr7116593745chr7133314798365DRB3-0214RVPLKINDNLSTGGP116
ST7-EXOC4chr7116593745chr7133314798365DRB3-0214LRVPLKINDNLSTGG015
ST7-EXOC4chr7116593745chr7133314798365DRB3-0214VPLKINDNLSTGGPD217
ST7-EXOC4chr7116593745chr7133314798365DRB3-0215RVPLKINDNLSTGGP116
ST7-EXOC4chr7116593745chr7133314798365DRB3-0215LRVPLKINDNLSTGG015
ST7-EXOC4chr7116593745chr7133314798365DRB3-0215VPLKINDNLSTGGPD217
ST7-EXOC4chr7116593745chr7133314798365DRB3-0216RVPLKINDNLSTGGP116
ST7-EXOC4chr7116593745chr7133314798365DRB3-0216LRVPLKINDNLSTGG015
ST7-EXOC4chr7116593745chr7133314798365DRB3-0217RVPLKINDNLSTGGP116
ST7-EXOC4chr7116593745chr7133314798365DRB3-0217LRVPLKINDNLSTGG015
ST7-EXOC4chr7116593745chr7133314798365DRB3-0217VPLKINDNLSTGGPD217
ST7-EXOC4chr7116593745chr7133314798365DRB3-0218RVPLKINDNLSTGGP116
ST7-EXOC4chr7116593745chr7133314798365DRB3-0218LRVPLKINDNLSTGG015
ST7-EXOC4chr7116593745chr7133314798365DRB3-0218VPLKINDNLSTGGPD217
ST7-EXOC4chr7116593745chr7133314798365DRB3-0219RVPLKINDNLSTGGP116
ST7-EXOC4chr7116593745chr7133314798365DRB3-0219LRVPLKINDNLSTGG015
ST7-EXOC4chr7116593745chr7133314798365DRB3-0219VPLKINDNLSTGGPD217
ST7-EXOC4chr7116593745chr7133314798365DRB3-0220RVPLKINDNLSTGGP116
ST7-EXOC4chr7116593745chr7133314798365DRB3-0220LRVPLKINDNLSTGG015
ST7-EXOC4chr7116593745chr7133314798365DRB3-0220VPLKINDNLSTGGPD217
ST7-EXOC4chr7116593745chr7133314798365DRB3-0221RVPLKINDNLSTGGP116
ST7-EXOC4chr7116593745chr7133314798365DRB3-0222RVPLKINDNLSTGGP116
ST7-EXOC4chr7116593745chr7133314798365DRB3-0222LRVPLKINDNLSTGG015
ST7-EXOC4chr7116593745chr7133314798365DRB3-0222VPLKINDNLSTGGPD217
ST7-EXOC4chr7116593745chr7133314798365DRB3-0223RVPLKINDNLSTGGP116
ST7-EXOC4chr7116593745chr7133314798365DRB3-0223LRVPLKINDNLSTGG015
ST7-EXOC4chr7116593745chr7133314798365DRB3-0223VPLKINDNLSTGGPD217
ST7-EXOC4chr7116593745chr7133314798365DRB3-0224RVPLKINDNLSTGGP116
ST7-EXOC4chr7116593745chr7133314798365DRB3-0224LRVPLKINDNLSTGG015
ST7-EXOC4chr7116593745chr7133314798365DRB3-0224VPLKINDNLSTGGPD217
ST7-EXOC4chr7116593745chr7133314798365DRB3-0225RVPLKINDNLSTGGP116
ST7-EXOC4chr7116593745chr7133314798365DRB3-0225LRVPLKINDNLSTGG015
ST7-EXOC4chr7116593745chr7133314798365DRB3-0225VPLKINDNLSTGGPD217
ST7-EXOC4chr7116593745chr7133314798365DRB3-0301RVPLKINDNLSTGGP116
ST7-EXOC4chr7116593745chr7133314798365DRB3-0301LRVPLKINDNLSTGG015
ST7-EXOC4chr7116593745chr7133314798365DRB3-0301VPLKINDNLSTGGPD217
ST7-EXOC4chr7116593745chr7133314798365DRB3-0303RVPLKINDNLSTGGP116

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Fusion breakpoint peptide structures of ST7-EXOC4

check button3D structures of the fusion breakpoint peptide of 14AA sequence that have potential fusion neoantigens
* The minimum length of the amino acid sequence in RoseTTAFold is 14AA. Here, we predicted the 14AA fusion protein breakpoint sequence not the fusion neoantigen peptide, which is shorter than 14 AA.

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of ST7-EXOC4

check buttonVirtual screening between 25 HLAs (from PDB) and FusionNeoAntigens
* We used Glide to predict the interaction between HLAs and neoantigens.
HLA allelePDB IDFile nameBPseqDocking scoreGlide score

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Vaccine Design for the FusionNeoAntigens of ST7-EXOC4

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-Is.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptide sequenceFusionNeoAntigen RNA sequence

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
ST7-EXOC4chr7116593745chr7133314798015LRVPLKINDNLSTGGTGCGGGTGCCTTTGAAAATCAACGACAACTTGAGCACAGGGGGTC
ST7-EXOC4chr7116593745chr7133314798116RVPLKINDNLSTGGPGGGTGCCTTTGAAAATCAACGACAACTTGAGCACAGGGGGTCCTG
ST7-EXOC4chr7116593745chr7133314798217VPLKINDNLSTGGPDTGCCTTTGAAAATCAACGACAACTTGAGCACAGGGGGTCCTGATG

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Information of the samples that have these potential fusion neoantigens of ST7-EXOC4

check button These samples were reported as having these fusion breakpoints. For individual breakpoints, we checked the open reading frames considering multiple gene isoforms and chose the in-frame fusion genes only. Then, we made fusion protein sequences and predicted the fusion neoantigens. These fusion-positive samples may have these potential fusion neoantigens.
Cancer typeFusion geneHchrHbpHenstTchrTbpTenstSample

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Potential target of CAR-T therapy development for ST7-EXOC4

check button Predicted 3D structure. We used RoseTTAFold.

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, to provide the retention of the transmembrane domain, we only show the protein feature retention information of those transmembrane features


* Minus value of BPloci means that the break point is located before the CDS.
- In-frame and retained 'Transmembrane'.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneST7chr7:116593745chr7:133314798ENST00000265437+11615_3550586.0TransmembraneHelical
HgeneST7chr7:116593745chr7:133314798ENST00000393451+11515_3550555.0TransmembraneHelical

check button Subcellular localization prediction of the transmembrane domain retained fusion proteins
* We used DeepLoc 1.0. The order of the X-axis of the barplot is as follows: Entry_ID, Localization, Type, Nucleus, Cytoplasm, Extracellular, Mitochondrion, Cell_membrane, Endoplasmic_reticulum, Plastid, Golgi.apparatus, Lysosome.Vacuole, Peroxisome. Y-axis is the output score of DeepLoc. Clicking the image will open a new tab with a large image.
HgeneHchrHbpHenstTgeneTchrTbpTenstDeepLoc result

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Related Drugs to ST7-EXOC4

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 ST7-EXOC4

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