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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:MSI2-PCTP

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: MSI2-PCTP
FusionPDB ID: 55324
FusionGDB2.0 ID: 55324
HgeneTgene
Gene symbol

MSI2

PCTP

Gene ID

124540

58488

Gene namemusashi RNA binding protein 2phosphatidylcholine transfer protein
SynonymsMSI2HPC-TP|STARD2
Cytomap

17q22

17q22

Type of geneprotein-codingprotein-coding
DescriptionRNA-binding protein Musashi homolog 2musashi homolog 2musashi-2phosphatidylcholine transfer proteinSTART domain-containing protein 2StAR-related lipid transfer (START) domain containing 2stAR-related lipid transfer protein 2
Modification date2020031320200313
UniProtAcc

Q96DH6

Main function of 5'-partner protein: FUNCTION: RNA binding protein that regulates the expression of target mRNAs at the translation level. May play a role in the proliferation and maintenance of stem cells in the central nervous system (By similarity). {ECO:0000250}.		.
Ensembl transtripts involved in fusion geneENST idsENST00000284073, ENST00000322684, 
ENST00000416426, ENST00000442934, 
ENST00000579180, ENST00000579505, 
ENST00000325214, ENST00000268896, 
ENST00000576183, ENST00000576221, 
ENST00000573500, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score40 X 16 X 16=102409 X 7 X 5=315
# samples 4514
** MAII scorelog2(45/10240*10)=-4.50814690367033
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(14/315*10)=-1.16992500144231
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: MSI2 [Title/Abstract] AND PCTP [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: MSI2 [Title/Abstract] AND PCTP [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)MSI2(55339553)-PCTP(53844696), # samples:2
Anticipated loss of major functional domain due to fusion event.MSI2-PCTP 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.
MSI2-PCTP 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.
MSI2-PCTP 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.
MSI2-PCTP 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.
* 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
TgenePCTP

GO:0015914

phospholipid transport

12055623



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/chr17:55339553/chr17:53844696)
- 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 MSI2 (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 PCTP (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)
ENST00000416426MSI2chr1755339553+ENST00000573500PCTPchr1753844696+114938193899268
ENST00000284073MSI2chr1755339553+ENST00000573500PCTPchr1753844696+12895211791039286
ENST00000322684MSI2chr1755339553+ENST00000573500PCTPchr1753844696+110333535853272
ENST00000416426MSI2chr1755339553+ENST00000573500PCTPchr1753844695+114938193899268
ENST00000284073MSI2chr1755339553+ENST00000573500PCTPchr1753844695+12895211791039286
ENST00000322684MSI2chr1755339553+ENST00000573500PCTPchr1753844695+110333535853272
ENST00000416426MSI2chr1755339552+ENST00000573500PCTPchr1753844695+114938193899268
ENST00000284073MSI2chr1755339552+ENST00000573500PCTPchr1753844695+12895211791039286
ENST00000322684MSI2chr1755339552+ENST00000573500PCTPchr1753844695+110333535853272

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
ENST00000416426ENST00000573500MSI2chr1755339553+PCTPchr1753844696+0.0036356570.9963644
ENST00000284073ENST00000573500MSI2chr1755339553+PCTPchr1753844696+0.0061710480.99382895
ENST00000322684ENST00000573500MSI2chr1755339553+PCTPchr1753844696+0.0024788590.9975211
ENST00000416426ENST00000573500MSI2chr1755339553+PCTPchr1753844695+0.0036356570.9963644
ENST00000284073ENST00000573500MSI2chr1755339553+PCTPchr1753844695+0.0061710480.99382895
ENST00000322684ENST00000573500MSI2chr1755339553+PCTPchr1753844695+0.0024788590.9975211
ENST00000416426ENST00000573500MSI2chr1755339552+PCTPchr1753844695+0.0036356570.9963644
ENST00000284073ENST00000573500MSI2chr1755339552+PCTPchr1753844695+0.0061710480.99382895
ENST00000322684ENST00000573500MSI2chr1755339552+PCTPchr1753844695+0.0024788590.9975211

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 MSI2-PCTP

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
MSI2chr1755339552PCTPchr1753844695335100DPKVAFPRRAQPKKTGLYEYKVFGVL
MSI2chr1755339552PCTPchr175384469538196DPKVAFPRRAQPKKTGLYEYKVFGVL
MSI2chr1755339552PCTPchr1753844695521114DPKVAFPRRAQPKKTGLYEYKVFGVL
MSI2chr1755339553PCTPchr1753844695335100DPKVAFPRRAQPKKTGLYEYKVFGVL
MSI2chr1755339553PCTPchr175384469538196DPKVAFPRRAQPKKTGLYEYKVFGVL
MSI2chr1755339553PCTPchr1753844695521114DPKVAFPRRAQPKKTGLYEYKVFGVL
MSI2chr1755339553PCTPchr1753844696335100DPKVAFPRRAQPKKTGLYEYKVFGVL
MSI2chr1755339553PCTPchr175384469638196DPKVAFPRRAQPKKTGLYEYKVFGVL
MSI2chr1755339553PCTPchr1753844696521114DPKVAFPRRAQPKKTGLYEYKVFGVL

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Potential FusionNeoAntigen Information of MSI2-PCTP 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.
MSI2-PCTP_55339552_53844695.msa

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)
MSI2-PCTPchr1755339552chr1753844695521HLA-B15:01AQPKKTGLY0.99920.7202918
MSI2-PCTPchr1755339552chr1753844695521HLA-B08:01RAQPKKTGL0.94970.6067817
MSI2-PCTPchr1755339552chr1753844695521HLA-B15:25AQPKKTGLY0.94660.8142918
MSI2-PCTPchr1755339552chr1753844695521HLA-B14:02RAQPKKTGL0.79130.8305817
MSI2-PCTPchr1755339552chr1753844695521HLA-B14:01RAQPKKTGL0.79130.8305817
MSI2-PCTPchr1755339552chr1753844695521HLA-B15:03AQPKKTGLY0.30260.659918
MSI2-PCTPchr1755339552chr1753844695521HLA-B27:05RRAQPKKTGL0.99980.5251717
MSI2-PCTPchr1755339552chr1753844695521HLA-B27:04RRAQPKKTGL0.99970.6444717
MSI2-PCTPchr1755339552chr1753844695521HLA-B15:01RAQPKKTGLY0.99830.7574818
MSI2-PCTPchr1755339552chr1753844695521HLA-B35:01QPKKTGLYEY0.9440.83551020
MSI2-PCTPchr1755339552chr1753844695521HLA-B35:08QPKKTGLYEY0.93660.86281020
MSI2-PCTPchr1755339552chr1753844695521HLA-B15:02QPKKTGLYEY0.93430.78491020
MSI2-PCTPchr1755339552chr1753844695521HLA-B07:10RRAQPKKTGL0.89360.57717
MSI2-PCTPchr1755339552chr1753844695521HLA-B27:04RRAQPKKTGLY10.6172718
MSI2-PCTPchr1755339552chr1753844695521HLA-B27:05RRAQPKKTGLY10.6167718
MSI2-PCTPchr1755339552chr1753844695521HLA-B15:01AQPKKTGLYEY0.99990.6935920
MSI2-PCTPchr1755339552chr1753844695521HLA-B15:25AQPKKTGLYEY0.99420.787920
MSI2-PCTPchr1755339552chr1753844695521HLA-C15:06RAQPKKTGL0.99310.9138817
MSI2-PCTPchr1755339552chr1753844695521HLA-C03:07RAQPKKTGL0.99230.9693817
MSI2-PCTPchr1755339552chr1753844695521HLA-C03:19RAQPKKTGL0.9830.977817
MSI2-PCTPchr1755339552chr1753844695521HLA-C03:08RAQPKKTGL0.98290.8952817
MSI2-PCTPchr1755339552chr1753844695521HLA-B07:12RAQPKKTGL0.98110.6239817
MSI2-PCTPchr1755339552chr1753844695521HLA-B42:02RAQPKKTGL0.96690.607817
MSI2-PCTPchr1755339552chr1753844695521HLA-C02:06RAQPKKTGL0.96070.9399817
MSI2-PCTPchr1755339552chr1753844695521HLA-B42:01RAQPKKTGL0.95920.5983817
MSI2-PCTPchr1755339552chr1753844695521HLA-C04:06RAQPKKTGL0.93950.9294817
MSI2-PCTPchr1755339552chr1753844695521HLA-C01:17RAQPKKTGL0.93140.9557817
MSI2-PCTPchr1755339552chr1753844695521HLA-C12:12RAQPKKTGL0.90840.9325817
MSI2-PCTPchr1755339552chr1753844695521HLA-B15:04AQPKKTGLY0.89670.7582918
MSI2-PCTPchr1755339552chr1753844695521HLA-C06:03RAQPKKTGL0.89380.9896817
MSI2-PCTPchr1755339552chr1753844695521HLA-B14:03RAQPKKTGL0.89320.8302817
MSI2-PCTPchr1755339552chr1753844695521HLA-C12:04RAQPKKTGL0.8820.9888817
MSI2-PCTPchr1755339552chr1753844695521HLA-C08:13RAQPKKTGL0.66350.9618817
MSI2-PCTPchr1755339552chr1753844695521HLA-C08:04RAQPKKTGL0.66350.9618817
MSI2-PCTPchr1755339552chr1753844695521HLA-B15:05AQPKKTGLY0.56440.8263918
MSI2-PCTPchr1755339552chr1753844695521HLA-C01:30RAQPKKTGL0.53650.9526817
MSI2-PCTPchr1755339552chr1753844695521HLA-B27:14RRAQPKKTGL0.99980.5632717
MSI2-PCTPchr1755339552chr1753844695521HLA-B15:07RAQPKKTGLY0.99750.5231818
MSI2-PCTPchr1755339552chr1753844695521HLA-B27:03RRAQPKKTGL0.9890.5536717
MSI2-PCTPchr1755339552chr1753844695521HLA-C15:04RAQPKKTGLY0.98790.8549818
MSI2-PCTPchr1755339552chr1753844695521HLA-B15:31QPKKTGLYEY0.93850.80991020
MSI2-PCTPchr1755339552chr1753844695521HLA-B15:04AQPKKTGLYEY0.99880.7441920
MSI2-PCTPchr1755339552chr1753844695521HLA-B27:03RRAQPKKTGLY0.99880.6338718
MSI2-PCTPchr1755339552chr1753844695521HLA-C07:46RRAQPKKTGLY0.99590.8479718
MSI2-PCTPchr1755339552chr1753844695521HLA-B15:05AQPKKTGLYEY0.97350.7754920
MSI2-PCTPchr1755339552chr1753844695521HLA-B15:11QPKKTGLY0.98080.62621018
MSI2-PCTPchr1755339552chr1753844695521HLA-B15:125AQPKKTGLY0.99920.7202918
MSI2-PCTPchr1755339552chr1753844695521HLA-B15:27AQPKKTGLY0.99920.7331918
MSI2-PCTPchr1755339552chr1753844695521HLA-B15:33AQPKKTGLY0.99920.7202918
MSI2-PCTPchr1755339552chr1753844695521HLA-B15:34AQPKKTGLY0.99920.7202918
MSI2-PCTPchr1755339552chr1753844695521HLA-B15:135AQPKKTGLY0.99910.7283918
MSI2-PCTPchr1755339552chr1753844695521HLA-B15:50AQPKKTGLY0.99880.8017918
MSI2-PCTPchr1755339552chr1753844695521HLA-B15:24AQPKKTGLY0.99540.7272918
MSI2-PCTPchr1755339552chr1753844695521HLA-B15:12AQPKKTGLY0.99430.7756918
MSI2-PCTPchr1755339552chr1753844695521HLA-C15:05RAQPKKTGL0.9940.9089817
MSI2-PCTPchr1755339552chr1753844695521HLA-C15:02RAQPKKTGL0.99350.8778817
MSI2-PCTPchr1755339552chr1753844695521HLA-B15:35AQPKKTGLY0.99330.6961918
MSI2-PCTPchr1755339552chr1753844695521HLA-B07:13RAQPKKTGL0.98590.8691817
MSI2-PCTPchr1755339552chr1753844695521HLA-C03:05RAQPKKTGL0.98030.8948817
MSI2-PCTPchr1755339552chr1753844695521HLA-C06:06RAQPKKTGL0.98020.9907817
MSI2-PCTPchr1755339552chr1753844695521HLA-C03:17RAQPKKTGL0.97660.9543817
MSI2-PCTPchr1755339552chr1753844695521HLA-C03:67RAQPKKTGL0.97640.9659817
MSI2-PCTPchr1755339552chr1753844695521HLA-C03:04RAQPKKTGL0.9710.979817
MSI2-PCTPchr1755339552chr1753844695521HLA-C03:03RAQPKKTGL0.9710.979817
MSI2-PCTPchr1755339552chr1753844695521HLA-B15:53AQPKKTGLY0.96230.6894918
MSI2-PCTPchr1755339552chr1753844695521HLA-C01:03RAQPKKTGL0.95910.9463817
MSI2-PCTPchr1755339552chr1753844695521HLA-C07:04RAQPKKTGL0.95170.9523817
MSI2-PCTPchr1755339552chr1753844695521HLA-B08:18RAQPKKTGL0.94970.6067817
MSI2-PCTPchr1755339552chr1753844695521HLA-B15:39AQPKKTGLY0.94580.719918
MSI2-PCTPchr1755339552chr1753844695521HLA-C01:02RAQPKKTGL0.94080.9534817
MSI2-PCTPchr1755339552chr1753844695521HLA-B08:12RAQPKKTGL0.90850.749817
MSI2-PCTPchr1755339552chr1753844695521HLA-C16:02RAQPKKTGL0.88320.9911817
MSI2-PCTPchr1755339552chr1753844695521HLA-C16:04RAQPKKTGL0.8560.9724817
MSI2-PCTPchr1755339552chr1753844695521HLA-C12:03RAQPKKTGL0.82510.9762817
MSI2-PCTPchr1755339552chr1753844695521HLA-B15:54AQPKKTGLY0.79970.6586918
MSI2-PCTPchr1755339552chr1753844695521HLA-C16:01RAQPKKTGL0.79330.9779817
MSI2-PCTPchr1755339552chr1753844695521HLA-C17:01RAQPKKTGL0.61340.9411817
MSI2-PCTPchr1755339552chr1753844695521HLA-B15:20AQPKKTGLY0.57090.8899918
MSI2-PCTPchr1755339552chr1753844695521HLA-B35:28AQPKKTGLY0.4510.9002918
MSI2-PCTPchr1755339552chr1753844695521HLA-B48:02AQPKKTGLY0.09580.8806918
MSI2-PCTPchr1755339552chr1753844695521HLA-B27:10RRAQPKKTGL0.99970.741717
MSI2-PCTPchr1755339552chr1753844695521HLA-B27:06RRAQPKKTGL0.99950.6359717
MSI2-PCTPchr1755339552chr1753844695521HLA-B27:09RRAQPKKTGL0.99930.5145717
MSI2-PCTPchr1755339552chr1753844695521HLA-B15:34RAQPKKTGLY0.99830.7574818
MSI2-PCTPchr1755339552chr1753844695521HLA-B15:27RAQPKKTGLY0.99830.7824818
MSI2-PCTPchr1755339552chr1753844695521HLA-B15:125RAQPKKTGLY0.99830.7574818
MSI2-PCTPchr1755339552chr1753844695521HLA-B15:135RAQPKKTGLY0.99830.7721818
MSI2-PCTPchr1755339552chr1753844695521HLA-B15:33RAQPKKTGLY0.99830.7574818
MSI2-PCTPchr1755339552chr1753844695521HLA-B15:35RAQPKKTGLY0.99760.7574818
MSI2-PCTPchr1755339552chr1753844695521HLA-C07:01RRAQPKKTGL0.99470.5847717
MSI2-PCTPchr1755339552chr1753844695521HLA-B15:50RAQPKKTGLY0.99460.8371818
MSI2-PCTPchr1755339552chr1753844695521HLA-B15:54RAQPKKTGLY0.99020.7019818
MSI2-PCTPchr1755339552chr1753844695521HLA-C15:09RAQPKKTGLY0.98790.8549818
MSI2-PCTPchr1755339552chr1753844695521HLA-C07:22RRAQPKKTGL0.98730.6654717
MSI2-PCTPchr1755339552chr1753844695521HLA-B58:06RAQPKKTGLY0.98710.7057818
MSI2-PCTPchr1755339552chr1753844695521HLA-B35:77QPKKTGLYEY0.9440.83551020
MSI2-PCTPchr1755339552chr1753844695521HLA-B35:11QPKKTGLYEY0.94140.74131020
MSI2-PCTPchr1755339552chr1753844695521HLA-B35:23QPKKTGLYEY0.94030.83491020
MSI2-PCTPchr1755339552chr1753844695521HLA-B15:08QPKKTGLYEY0.9260.58461020
MSI2-PCTPchr1755339552chr1753844695521HLA-B15:11QPKKTGLYEY0.92580.6071020
MSI2-PCTPchr1755339552chr1753844695521HLA-B35:43QPKKTGLYEY0.91310.59141020
MSI2-PCTPchr1755339552chr1753844695521HLA-B35:17QPKKTGLYEY0.880.62651020
MSI2-PCTPchr1755339552chr1753844695521HLA-B35:30QPKKTGLYEY0.880.62651020
MSI2-PCTPchr1755339552chr1753844695521HLA-B35:24QPKKTGLYEY0.85930.72041020
MSI2-PCTPchr1755339552chr1753844695521HLA-B18:07QPKKTGLYEY0.38530.53421020
MSI2-PCTPchr1755339552chr1753844695521HLA-B27:08RRAQPKKTGLY10.5124718
MSI2-PCTPchr1755339552chr1753844695521HLA-B27:10RRAQPKKTGLY10.7366718
MSI2-PCTPchr1755339552chr1753844695521HLA-B15:34AQPKKTGLYEY0.99990.6935920
MSI2-PCTPchr1755339552chr1753844695521HLA-B15:50AQPKKTGLYEY0.99990.7816920
MSI2-PCTPchr1755339552chr1753844695521HLA-B15:27AQPKKTGLYEY0.99990.7208920
MSI2-PCTPchr1755339552chr1753844695521HLA-B15:33AQPKKTGLYEY0.99990.6935920
MSI2-PCTPchr1755339552chr1753844695521HLA-B15:135AQPKKTGLYEY0.99990.722920
MSI2-PCTPchr1755339552chr1753844695521HLA-B15:125AQPKKTGLYEY0.99990.6935920
MSI2-PCTPchr1755339552chr1753844695521HLA-B15:24AQPKKTGLYEY0.99980.735920
MSI2-PCTPchr1755339552chr1753844695521HLA-B15:35AQPKKTGLYEY0.99980.6723920
MSI2-PCTPchr1755339552chr1753844695521HLA-B15:53AQPKKTGLYEY0.99960.6538920
MSI2-PCTPchr1755339552chr1753844695521HLA-B15:12AQPKKTGLYEY0.99930.7849920
MSI2-PCTPchr1755339552chr1753844695521HLA-C07:01RRAQPKKTGLY0.99930.5414718
MSI2-PCTPchr1755339552chr1753844695521HLA-C07:22RRAQPKKTGLY0.9970.5837718
MSI2-PCTPchr1755339552chr1753844695521HLA-B15:54AQPKKTGLYEY0.99580.6189920
MSI2-PCTPchr1755339552chr1753844695521HLA-B15:39AQPKKTGLYEY0.99440.6864920
MSI2-PCTPchr1755339552chr1753844695521HLA-B15:20AQPKKTGLYEY0.97580.8561920
MSI2-PCTPchr1755339552chr1753844695521HLA-B35:28AQPKKTGLYEY0.96040.8741920
MSI2-PCTPchr1755339552chr1753844695521HLA-B15:54RRAQPKKTGLY0.95770.7822718
MSI2-PCTPchr1755339552chr1753844695521HLA-B15:68RRAQPKKTGLY0.90620.5298718

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Potential FusionNeoAntigen Information of MSI2-PCTP 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.

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)

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Fusion breakpoint peptide structures of MSI2-PCTP

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.
File nameBPseqHgeneTgeneHchrHbpTchrTbpAAlen
6959PRRAQPKKTGLYEYMSI2PCTPchr1755339552chr1753844695521

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of MSI2-PCTP

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
HLA-B14:023BVN6959PRRAQPKKTGLYEY-7.15543-7.26883
HLA-B14:023BVN6959PRRAQPKKTGLYEY-4.77435-5.80965
HLA-B52:013W396959PRRAQPKKTGLYEY-6.80875-6.92215
HLA-B52:013W396959PRRAQPKKTGLYEY-4.20386-5.23916
HLA-A11:014UQ26959PRRAQPKKTGLYEY-7.5194-8.5547
HLA-A11:014UQ26959PRRAQPKKTGLYEY-6.9601-7.0735
HLA-A24:025HGA6959PRRAQPKKTGLYEY-7.52403-7.63743
HLA-A24:025HGA6959PRRAQPKKTGLYEY-5.82433-6.85963
HLA-B27:056PYJ6959PRRAQPKKTGLYEY-3.28285-4.31815
HLA-B44:053DX86959PRRAQPKKTGLYEY-5.91172-6.94702
HLA-B44:053DX86959PRRAQPKKTGLYEY-4.24346-4.35686

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Vaccine Design for the FusionNeoAntigens of MSI2-PCTP

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
MSI2-PCTPchr1755339552chr17538446951018QPKKTGLYCAACCCAAGAAGACTGGACTTTAT
MSI2-PCTPchr1755339552chr17538446951020QPKKTGLYEYCAACCCAAGAAGACTGGACTTTATGAGTAT
MSI2-PCTPchr1755339552chr1753844695717RRAQPKKTGLCGTCGAGCGCAACCCAAGAAGACTGGACTT
MSI2-PCTPchr1755339552chr1753844695718RRAQPKKTGLYCGTCGAGCGCAACCCAAGAAGACTGGACTTTAT
MSI2-PCTPchr1755339552chr1753844695817RAQPKKTGLCGAGCGCAACCCAAGAAGACTGGACTT
MSI2-PCTPchr1755339552chr1753844695818RAQPKKTGLYCGAGCGCAACCCAAGAAGACTGGACTTTAT
MSI2-PCTPchr1755339552chr1753844695918AQPKKTGLYGCGCAACCCAAGAAGACTGGACTTTAT
MSI2-PCTPchr1755339552chr1753844695920AQPKKTGLYEYGCGCAACCCAAGAAGACTGGACTTTATGAGTAT

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

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Information of the samples that have these potential fusion neoantigens of MSI2-PCTP

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
BRCAMSI2-PCTPchr1755339552ENST00000284073chr1753844695ENST00000573500TCGA-D8-A27F-01A

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Potential target of CAR-T therapy development for MSI2-PCTP

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

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 MSI2-PCTP

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 MSI2-PCTP

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