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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-DHX40

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: MSI2-DHX40
FusionPDB ID: 55309
FusionGDB2.0 ID: 55309
HgeneTgene
Gene symbol

MSI2

DHX40

Gene ID

124540

79665

Gene namemusashi RNA binding protein 2DEAH-box helicase 40
SynonymsMSI2HARG147|DDX40|PAD
Cytomap

17q22

17q23.1

Type of geneprotein-codingprotein-coding
DescriptionRNA-binding protein Musashi homolog 2musashi homolog 2musashi-2probable ATP-dependent RNA helicase DHX40DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 40 (RNA helicase)DEAH (Asp-Glu-Ala-His) box polypeptide 40DEAH box protein 40
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}.

Q8IX18

Main function of 5'-partner protein: FUNCTION: Probable ATP-dependent RNA helicase. {ECO:0000250}.
Ensembl transtripts involved in fusion geneENST idsENST00000284073, ENST00000322684, 
ENST00000416426, ENST00000442934, 
ENST00000579180, ENST00000579505, 
ENST00000425628, ENST00000451169, 
ENST00000251241, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score40 X 16 X 16=102407 X 6 X 2=84
# samples 458
** MAII scorelog2(45/10240*10)=-4.50814690367033
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(8/84*10)=-0.070389327891398
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: MSI2 [Title/Abstract] AND DHX40 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: MSI2 [Title/Abstract] AND DHX40 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)MSI2(55478832)-DHX40(57643988), # samples:3
Anticipated loss of major functional domain due to fusion event.MSI2-DHX40 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-DHX40 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-DHX40 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-DHX40 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-DHX40 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
MSI2-DHX40 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
MSI2-DHX40 seems lost the major protein functional domain in Tgene partner, which is a essential gene 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


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/chr17:55478832/chr17:57643988)
- 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 DHX40 (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)
ENST00000416426MSI2chr1755478832+ENST00000251241DHX40chr1757650477+3561474932387764
ENST00000416426MSI2chr1755478832+ENST00000451169DHX40chr1757650477+3710474932540815
ENST00000416426MSI2chr1755478832+ENST00000425628DHX40chr1757650477+2474474932387764
ENST00000284073MSI2chr1755478832+ENST00000251241DHX40chr1757650477+37016141792527782
ENST00000284073MSI2chr1755478832+ENST00000451169DHX40chr1757650477+38506141792680833
ENST00000284073MSI2chr1755478832+ENST00000425628DHX40chr1757650477+26146141792527782
ENST00000322684MSI2chr1755478832+ENST00000251241DHX40chr1757650477+3515428352341768
ENST00000322684MSI2chr1755478832+ENST00000451169DHX40chr1757650477+3664428352494819
ENST00000322684MSI2chr1755478832+ENST00000425628DHX40chr1757650477+2428428352341768
ENST00000442934MSI2chr1755478832+ENST00000251241DHX40chr1757650477+3349262402175711
ENST00000442934MSI2chr1755478832+ENST00000451169DHX40chr1757650477+3498262402328762
ENST00000442934MSI2chr1755478832+ENST00000425628DHX40chr1757650477+2262262402175711
ENST00000579180MSI2chr1755478832+ENST00000251241DHX40chr1757650477+32851981052111668
ENST00000579180MSI2chr1755478832+ENST00000451169DHX40chr1757650477+34341981052264719
ENST00000579180MSI2chr1755478832+ENST00000425628DHX40chr1757650477+21981981052111668

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
ENST00000416426ENST00000251241MSI2chr1755478832+DHX40chr1757650477+0.0011221740.9988778
ENST00000416426ENST00000451169MSI2chr1755478832+DHX40chr1757650477+0.0010885350.9989115
ENST00000416426ENST00000425628MSI2chr1755478832+DHX40chr1757650477+0.0015896590.99841034
ENST00000284073ENST00000251241MSI2chr1755478832+DHX40chr1757650477+0.0007853590.99921465
ENST00000284073ENST00000451169MSI2chr1755478832+DHX40chr1757650477+0.0006689220.9993311
ENST00000284073ENST00000425628MSI2chr1755478832+DHX40chr1757650477+0.0012844230.99871564
ENST00000322684ENST00000251241MSI2chr1755478832+DHX40chr1757650477+0.000513920.9994861
ENST00000322684ENST00000451169MSI2chr1755478832+DHX40chr1757650477+0.0004655520.9995345
ENST00000322684ENST00000425628MSI2chr1755478832+DHX40chr1757650477+0.0007591810.9992409
ENST00000442934ENST00000251241MSI2chr1755478832+DHX40chr1757650477+0.0006344810.9993655
ENST00000442934ENST00000451169MSI2chr1755478832+DHX40chr1757650477+0.0007713630.9992286
ENST00000442934ENST00000425628MSI2chr1755478832+DHX40chr1757650477+0.0008703720.9991296
ENST00000579180ENST00000251241MSI2chr1755478832+DHX40chr1757650477+0.0012437230.9987563
ENST00000579180ENST00000451169MSI2chr1755478832+DHX40chr1757650477+0.0011541230.9988458
ENST00000579180ENST00000425628MSI2chr1755478832+DHX40chr1757650477+0.0019958170.99800414

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-DHX40

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
MSI2chr1755478832DHX40chr175765047719831VEDVKQYFEQFGKETAIKYMTDGCLL
MSI2chr1755478832DHX40chr175765047726274VEDVKQYFEQFGKETAIKYMTDGCLL
MSI2chr1755478832DHX40chr1757650477428131VEDVKQYFEQFGKETAIKYMTDGCLL
MSI2chr1755478832DHX40chr1757650477474127VEDVKQYFEQFGKETAIKYMTDGCLL
MSI2chr1755478832DHX40chr1757650477614145VEDVKQYFEQFGKETAIKYMTDGCLL

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Potential FusionNeoAntigen Information of MSI2-DHX40 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-DHX40_55478832_57650477.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-DHX40chr1755478832chr1757650477614HLA-B45:01FEQFGKETA0.99480.9458716
MSI2-DHX40chr1755478832chr1757650477614HLA-B14:01EQFGKETAI0.99280.949817
MSI2-DHX40chr1755478832chr1757650477614HLA-B14:02EQFGKETAI0.99280.949817
MSI2-DHX40chr1755478832chr1757650477614HLA-B15:25FGKETAIKY0.99240.83641019
MSI2-DHX40chr1755478832chr1757650477614HLA-B15:01FGKETAIKY0.98940.8581019
MSI2-DHX40chr1755478832chr1757650477614HLA-B39:06EQFGKETAI0.98540.8872817
MSI2-DHX40chr1755478832chr1757650477614HLA-B39:24EQFGKETAI0.98470.7226817
MSI2-DHX40chr1755478832chr1757650477614HLA-B15:02FGKETAIKY0.98440.8481019
MSI2-DHX40chr1755478832chr1757650477614HLA-B50:02FEQFGKETA0.98250.7928716
MSI2-DHX40chr1755478832chr1757650477614HLA-B48:01EQFGKETAI0.98080.6152817
MSI2-DHX40chr1755478832chr1757650477614HLA-B39:01EQFGKETAI0.97320.9634817
MSI2-DHX40chr1755478832chr1757650477614HLA-B39:13EQFGKETAI0.94930.9841817
MSI2-DHX40chr1755478832chr1757650477614HLA-B35:01FGKETAIKY0.94650.79941019
MSI2-DHX40chr1755478832chr1757650477614HLA-B13:02EQFGKETAI0.92280.7578817
MSI2-DHX40chr1755478832chr1757650477614HLA-B38:02EQFGKETAI0.88440.9864817
MSI2-DHX40chr1755478832chr1757650477614HLA-B15:10EQFGKETAI0.85170.5609817
MSI2-DHX40chr1755478832chr1757650477614HLA-B38:01EQFGKETAI0.84810.9853817
MSI2-DHX40chr1755478832chr1757650477614HLA-B13:01EQFGKETAI0.8070.9498817
MSI2-DHX40chr1755478832chr1757650477614HLA-B41:01FEQFGKETA0.79150.9787716
MSI2-DHX40chr1755478832chr1757650477614HLA-B15:37EQFGKETAI0.75660.611817
MSI2-DHX40chr1755478832chr1757650477614HLA-B50:01FEQFGKETA0.72030.866716
MSI2-DHX40chr1755478832chr1757650477614HLA-B15:03FGKETAIKY0.7110.60971019
MSI2-DHX40chr1755478832chr1757650477614HLA-B08:09EQFGKETAI0.65630.7995817
MSI2-DHX40chr1755478832chr1757650477614HLA-B52:01EQFGKETAI0.41790.9763817
MSI2-DHX40chr1755478832chr1757650477614HLA-B13:02FEQFGKETAI0.99510.8234717
MSI2-DHX40chr1755478832chr1757650477614HLA-B41:01YFEQFGKETA0.91470.979616
MSI2-DHX40chr1755478832chr1757650477614HLA-B45:01YFEQFGKETA0.8950.9145616
MSI2-DHX40chr1755478832chr1757650477614HLA-B50:01YFEQFGKETA0.88110.8187616
MSI2-DHX40chr1755478832chr1757650477614HLA-B15:01EQFGKETAIKY0.99990.8154819
MSI2-DHX40chr1755478832chr1757650477614HLA-B13:02YFEQFGKETAI0.99520.7583617
MSI2-DHX40chr1755478832chr1757650477614HLA-B15:02EQFGKETAIKY0.99040.8911819
MSI2-DHX40chr1755478832chr1757650477614HLA-B45:01QYFEQFGKETA0.9850.9963516
MSI2-DHX40chr1755478832chr1757650477614HLA-B40:06FEQFGKETA0.99940.6899716
MSI2-DHX40chr1755478832chr1757650477614HLA-B15:21FGKETAIKY0.98420.82981019
MSI2-DHX40chr1755478832chr1757650477614HLA-B39:09EQFGKETAI0.98170.8839817
MSI2-DHX40chr1755478832chr1757650477614HLA-B15:05FGKETAIKY0.97690.76381019
MSI2-DHX40chr1755478832chr1757650477614HLA-B39:12EQFGKETAI0.9740.9648817
MSI2-DHX40chr1755478832chr1757650477614HLA-B15:07FGKETAIKY0.97380.57581019
MSI2-DHX40chr1755478832chr1757650477614HLA-B15:31FGKETAIKY0.95430.77691019
MSI2-DHX40chr1755478832chr1757650477614HLA-B39:05EQFGKETAI0.89550.9589817
MSI2-DHX40chr1755478832chr1757650477614HLA-B39:08EQFGKETAI0.87370.9553817
MSI2-DHX40chr1755478832chr1757650477614HLA-C12:16FGKETAIKY0.79690.95541019
MSI2-DHX40chr1755478832chr1757650477614HLA-B15:04FGKETAIKY0.78410.83641019
MSI2-DHX40chr1755478832chr1757650477614HLA-B14:03EQFGKETAI0.73020.9116817
MSI2-DHX40chr1755478832chr1757650477614HLA-C07:19FGKETAIKY0.62880.59551019
MSI2-DHX40chr1755478832chr1757650477614HLA-C15:04FGKETAIKY0.55540.87741019
MSI2-DHX40chr1755478832chr1757650477614HLA-C07:95FGKETAIKY0.51910.58021019
MSI2-DHX40chr1755478832chr1757650477614HLA-C12:12FGKETAIKY0.4560.90011019
MSI2-DHX40chr1755478832chr1757650477614HLA-C12:04FGKETAIKY0.39430.99091019
MSI2-DHX40chr1755478832chr1757650477614HLA-C06:03FGKETAIKY0.3890.99121019
MSI2-DHX40chr1755478832chr1757650477614HLA-B51:07EQFGKETAI0.3320.933817
MSI2-DHX40chr1755478832chr1757650477614HLA-C03:14FGKETAIKY0.28630.97281019
MSI2-DHX40chr1755478832chr1757650477614HLA-B40:06YFEQFGKETA0.96670.6758616
MSI2-DHX40chr1755478832chr1757650477614HLA-B15:07EQFGKETAIKY0.99920.5171819
MSI2-DHX40chr1755478832chr1757650477614HLA-B15:21EQFGKETAIKY0.99120.8696819
MSI2-DHX40chr1755478832chr1757650477614HLA-B15:05EQFGKETAIKY0.98750.7851819
MSI2-DHX40chr1755478832chr1757650477614HLA-B15:31EQFGKETAIKY0.98150.7941819
MSI2-DHX40chr1755478832chr1757650477614HLA-B15:39FGKETAIKY0.99020.711019
MSI2-DHX40chr1755478832chr1757650477614HLA-B15:27FGKETAIKY0.98990.87051019
MSI2-DHX40chr1755478832chr1757650477614HLA-B15:34FGKETAIKY0.98940.8581019
MSI2-DHX40chr1755478832chr1757650477614HLA-B15:125FGKETAIKY0.98940.8581019
MSI2-DHX40chr1755478832chr1757650477614HLA-B15:33FGKETAIKY0.98940.8581019
MSI2-DHX40chr1755478832chr1757650477614HLA-B15:135FGKETAIKY0.98840.85451019
MSI2-DHX40chr1755478832chr1757650477614HLA-B15:08FGKETAIKY0.98420.81771019
MSI2-DHX40chr1755478832chr1757650477614HLA-B15:11FGKETAIKY0.98420.80651019
MSI2-DHX40chr1755478832chr1757650477614HLA-B15:50FGKETAIKY0.98390.91121019
MSI2-DHX40chr1755478832chr1757650477614HLA-B40:04FEQFGKETA0.98320.8288716
MSI2-DHX40chr1755478832chr1757650477614HLA-B39:31EQFGKETAI0.98230.9627817
MSI2-DHX40chr1755478832chr1757650477614HLA-B35:11FGKETAIKY0.98060.81831019
MSI2-DHX40chr1755478832chr1757650477614HLA-B35:43FGKETAIKY0.98030.80991019
MSI2-DHX40chr1755478832chr1757650477614HLA-B39:02EQFGKETAI0.98020.9846817
MSI2-DHX40chr1755478832chr1757650477614HLA-B15:20FGKETAIKY0.97440.83711019
MSI2-DHX40chr1755478832chr1757650477614HLA-B35:28FGKETAIKY0.96150.83291019
MSI2-DHX40chr1755478832chr1757650477614HLA-B35:23FGKETAIKY0.95030.81251019
MSI2-DHX40chr1755478832chr1757650477614HLA-B15:35FGKETAIKY0.94960.8261019
MSI2-DHX40chr1755478832chr1757650477614HLA-B35:77FGKETAIKY0.94650.79941019
MSI2-DHX40chr1755478832chr1757650477614HLA-B15:12FGKETAIKY0.94440.83821019
MSI2-DHX40chr1755478832chr1757650477614HLA-B35:20FGKETAIKY0.94280.84381019
MSI2-DHX40chr1755478832chr1757650477614HLA-B35:30FGKETAIKY0.91380.57981019
MSI2-DHX40chr1755478832chr1757650477614HLA-B35:17FGKETAIKY0.91380.57981019
MSI2-DHX40chr1755478832chr1757650477614HLA-B15:73EQFGKETAI0.9130.9703817
MSI2-DHX40chr1755478832chr1757650477614HLA-B41:03FEQFGKETA0.88780.8176716
MSI2-DHX40chr1755478832chr1757650477614HLA-B39:11EQFGKETAI0.85090.9192817
MSI2-DHX40chr1755478832chr1757650477614HLA-B15:30EQFGKETAI0.84830.9021817
MSI2-DHX40chr1755478832chr1757650477614HLA-B38:05EQFGKETAI0.84810.9853817
MSI2-DHX40chr1755478832chr1757650477614HLA-B08:12EQFGKETAI0.840.8059817
MSI2-DHX40chr1755478832chr1757650477614HLA-C03:02FGKETAIKY0.83960.94931019
MSI2-DHX40chr1755478832chr1757650477614HLA-C12:02FGKETAIKY0.76260.96291019
MSI2-DHX40chr1755478832chr1757650477614HLA-B35:24FGKETAIKY0.74510.8881019
MSI2-DHX40chr1755478832chr1757650477614HLA-B50:04FEQFGKETA0.72030.866716
MSI2-DHX40chr1755478832chr1757650477614HLA-B50:05FEQFGKETA0.72030.866716
MSI2-DHX40chr1755478832chr1757650477614HLA-C07:22FGKETAIKY0.61460.59481019
MSI2-DHX40chr1755478832chr1757650477614HLA-C15:09FGKETAIKY0.55540.87741019
MSI2-DHX40chr1755478832chr1757650477614HLA-C12:03FGKETAIKY0.51560.97261019
MSI2-DHX40chr1755478832chr1757650477614HLA-B15:09EQFGKETAI0.51380.9166817
MSI2-DHX40chr1755478832chr1757650477614HLA-C07:01FGKETAIKY0.51070.54141019
MSI2-DHX40chr1755478832chr1757650477614HLA-C07:17FGKETAIKY0.48730.9621019
MSI2-DHX40chr1755478832chr1757650477614HLA-C16:04FGKETAIKY0.4430.9741019
MSI2-DHX40chr1755478832chr1757650477614HLA-B18:04FGKETAIKY0.32120.93561019
MSI2-DHX40chr1755478832chr1757650477614HLA-C16:01FGKETAIKY0.17350.961019
MSI2-DHX40chr1755478832chr1757650477614HLA-B18:07FGKETAIKY0.12790.9031019
MSI2-DHX40chr1755478832chr1757650477614HLA-C16:02FGKETAIKY0.08140.9871019
MSI2-DHX40chr1755478832chr1757650477614HLA-C02:02FGKETAIKY0.07590.97311019
MSI2-DHX40chr1755478832chr1757650477614HLA-C02:10FGKETAIKY0.07590.97311019
MSI2-DHX40chr1755478832chr1757650477614HLA-B50:04YFEQFGKETA0.88110.8187616
MSI2-DHX40chr1755478832chr1757650477614HLA-B50:05YFEQFGKETA0.88110.8187616
MSI2-DHX40chr1755478832chr1757650477614HLA-B15:27EQFGKETAIKY0.99990.831819
MSI2-DHX40chr1755478832chr1757650477614HLA-B15:125EQFGKETAIKY0.99990.8154819
MSI2-DHX40chr1755478832chr1757650477614HLA-B15:135EQFGKETAIKY0.99990.7966819
MSI2-DHX40chr1755478832chr1757650477614HLA-B15:34EQFGKETAIKY0.99990.8154819
MSI2-DHX40chr1755478832chr1757650477614HLA-B15:33EQFGKETAIKY0.99990.8154819
MSI2-DHX40chr1755478832chr1757650477614HLA-B15:53EQFGKETAIKY0.99980.7696819
MSI2-DHX40chr1755478832chr1757650477614HLA-B15:50EQFGKETAIKY0.99980.8569819
MSI2-DHX40chr1755478832chr1757650477614HLA-B15:12EQFGKETAIKY0.99940.8238819
MSI2-DHX40chr1755478832chr1757650477614HLA-B15:35EQFGKETAIKY0.99880.8025819
MSI2-DHX40chr1755478832chr1757650477614HLA-B15:54EQFGKETAIKY0.99660.7238819
MSI2-DHX40chr1755478832chr1757650477614HLA-B15:20EQFGKETAIKY0.98790.8435819
MSI2-DHX40chr1755478832chr1757650477614HLA-B35:28EQFGKETAIKY0.9810.8492819
MSI2-DHX40chr1755478832chr1757650477614HLA-B35:20EQFGKETAIKY0.97660.8638819
MSI2-DHX40chr1755478832chr1757650477614HLA-B18:04EQFGKETAIKY0.95820.8543819
MSI2-DHX40chr1755478832chr1757650477614HLA-B18:06EQFGKETAIKY0.95460.8546819
MSI2-DHX40chr1755478832chr1757650477614HLA-B15:13EQFGKETAIKY0.92780.6265819
MSI2-DHX40chr1755478832chr1757650477614HLA-B48:02EQFGKETAIKY0.92650.8285819

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Potential FusionNeoAntigen Information of MSI2-DHX40 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.
MSI2-DHX40_55478832_57650477.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)
MSI2-DHX40chr1755478832chr1757650477614DRB1-1105KQYFEQFGKETAIKY419
MSI2-DHX40chr1755478832chr1757650477614DRB1-1111KQYFEQFGKETAIKY419
MSI2-DHX40chr1755478832chr1757650477614DRB1-1145KQYFEQFGKETAIKY419
MSI2-DHX40chr1755478832chr1757650477614DRB1-1169KQYFEQFGKETAIKY419
MSI2-DHX40chr1755478832chr1757650477614DRB1-1169VKQYFEQFGKETAIK318
MSI2-DHX40chr1755478832chr1757650477614DRB1-1182KQYFEQFGKETAIKY419
MSI2-DHX40chr1755478832chr1757650477614DRB1-1182VKQYFEQFGKETAIK318
MSI2-DHX40chr1755478832chr1757650477614DRB1-1222FEQFGKETAIKYMTD722
MSI2-DHX40chr1755478832chr1757650477614DRB1-1363KQYFEQFGKETAIKY419
MSI2-DHX40chr1755478832chr1757650477614DRB1-1424KQYFEQFGKETAIKY419
MSI2-DHX40chr1755478832chr1757650477614DRB1-1424VKQYFEQFGKETAIK318
MSI2-DHX40chr1755478832chr1757650477614DRB1-1503VEDVKQYFEQFGKET015
MSI2-DHX40chr1755478832chr1757650477614DRB1-1523VEDVKQYFEQFGKET015

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Fusion breakpoint peptide structures of MSI2-DHX40

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
10620YFEQFGKETAIKYMMSI2DHX40chr1755478832chr1757650477614

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of MSI2-DHX40

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-B53:011A1O10620YFEQFGKETAIKYM-4.17128-4.28468
HLA-B53:011A1O10620YFEQFGKETAIKYM-3.4824-4.5177
HLA-B51:011E2810620YFEQFGKETAIKYM-3.8039-3.9173
HLA-B51:011E2810620YFEQFGKETAIKYM-3.0982-4.1335
HLA-B57:032BVO10620YFEQFGKETAIKYM-2.25252-3.28782
HLA-B57:032BVO10620YFEQFGKETAIKYM-1.1301-1.2435
HLA-A03:012XPG10620YFEQFGKETAIKYM-4.44786-4.56126
HLA-A03:012XPG10620YFEQFGKETAIKYM-4.14835-5.18365
HLA-B14:023BVN10620YFEQFGKETAIKYM-5.80238-5.91578
HLA-B14:023BVN10620YFEQFGKETAIKYM-3.55223-4.58753
HLA-B52:013W3910620YFEQFGKETAIKYM-5.11856-5.23196
HLA-B52:013W3910620YFEQFGKETAIKYM-3.25922-4.29452
HLA-B18:014JQV10620YFEQFGKETAIKYM-4.41315-4.52655
HLA-B18:014JQV10620YFEQFGKETAIKYM-3.36095-4.39625
HLA-A11:014UQ210620YFEQFGKETAIKYM-8.56989-8.68329
HLA-A11:014UQ210620YFEQFGKETAIKYM-6.72556-7.76086
HLA-A24:025HGA10620YFEQFGKETAIKYM-6.2734-6.3868
HLA-A24:025HGA10620YFEQFGKETAIKYM-4.24193-5.27723
HLA-B57:015VUD10620YFEQFGKETAIKYM-3.95679-4.99209
HLA-B57:015VUD10620YFEQFGKETAIKYM-2.97944-3.09284
HLA-C08:026JTP10620YFEQFGKETAIKYM-4.74128-4.85468
HLA-C08:026JTP10620YFEQFGKETAIKYM-2.44773-3.48303
HLA-B37:016MT410620YFEQFGKETAIKYM-3.77829-4.81359
HLA-B27:056PYJ10620YFEQFGKETAIKYM-3.40019-3.51359
HLA-B27:056PYJ10620YFEQFGKETAIKYM-1.99024-3.02554
HLA-B27:036PZ510620YFEQFGKETAIKYM-3.1249-3.2383
HLA-B27:036PZ510620YFEQFGKETAIKYM-0.148491-1.18379
HLA-B44:053DX810620YFEQFGKETAIKYM-5.76333-5.87673
HLA-B44:053DX810620YFEQFGKETAIKYM-3.98513-5.02043
HLA-B44:021M6O10620YFEQFGKETAIKYM-1.76802-2.80332
HLA-B07:025EO010620YFEQFGKETAIKYM-3.47003-3.58343
HLA-B07:025EO010620YFEQFGKETAIKYM0.983323-0.0519774
HLA-A02:016TDR10620YFEQFGKETAIKYM-2.71064-3.74594
HLA-A02:016TDR10620YFEQFGKETAIKYM-2.80613-2.91953

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Vaccine Design for the FusionNeoAntigens of MSI2-DHX40

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-DHX40chr1755478832chr17576504771019FGKETAIKYTTTGGCAAGGAGACAGCAATCAAATAT
MSI2-DHX40chr1755478832chr1757650477516QYFEQFGKETACAATATTTCGAGCAGTTTGGCAAGGAGACAGCA
MSI2-DHX40chr1755478832chr1757650477616YFEQFGKETATATTTCGAGCAGTTTGGCAAGGAGACAGCA
MSI2-DHX40chr1755478832chr1757650477617YFEQFGKETAITATTTCGAGCAGTTTGGCAAGGAGACAGCAATC
MSI2-DHX40chr1755478832chr1757650477716FEQFGKETATTCGAGCAGTTTGGCAAGGAGACAGCA
MSI2-DHX40chr1755478832chr1757650477717FEQFGKETAITTCGAGCAGTTTGGCAAGGAGACAGCAATC
MSI2-DHX40chr1755478832chr1757650477817EQFGKETAIGAGCAGTTTGGCAAGGAGACAGCAATC
MSI2-DHX40chr1755478832chr1757650477819EQFGKETAIKYGAGCAGTTTGGCAAGGAGACAGCAATCAAATAT

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
MSI2-DHX40chr1755478832chr1757650477015VEDVKQYFEQFGKETGTGGAAGATGTAAAGCAATATTTCGAGCAGTTTGGCAAGGAGACA
MSI2-DHX40chr1755478832chr1757650477318VKQYFEQFGKETAIKGTAAAGCAATATTTCGAGCAGTTTGGCAAGGAGACAGCAATCAAA
MSI2-DHX40chr1755478832chr1757650477419KQYFEQFGKETAIKYAAGCAATATTTCGAGCAGTTTGGCAAGGAGACAGCAATCAAATAT
MSI2-DHX40chr1755478832chr1757650477722FEQFGKETAIKYMTDTTCGAGCAGTTTGGCAAGGAGACAGCAATCAAATATATGACTGAT

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Information of the samples that have these potential fusion neoantigens of MSI2-DHX40

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-DHX40chr1755478832ENST00000284073chr1757650477ENST00000251241TCGA-EW-A6SD-01A

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Potential target of CAR-T therapy development for MSI2-DHX40

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-DHX40

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-DHX40

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