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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:RAI14-MAPK9

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: RAI14-MAPK9
FusionPDB ID: 71853
FusionGDB2.0 ID: 71853
HgeneTgene
Gene symbol

RAI14

MAPK9

Gene ID

26064

5601

Gene nameretinoic acid induced 14mitogen-activated protein kinase 9
SynonymsNORPEG|RAI13JNK-55|JNK2|JNK2A|JNK2ALPHA|JNK2B|JNK2BETA|PRKM9|SAPK|SAPK1a|p54a|p54aSAPK
Cytomap

5p13.2

5q35.3

Type of geneprotein-codingprotein-coding
Descriptionankycorbinankyrin repeat and coiled-coil structure-containing proteinnovel retinal pigment epithelial cell proteinretinoic acid-induced protein 14mitogen-activated protein kinase 9Jun kinaseMAP kinase 9MAPK 9c-Jun N-terminal kinase 2c-Jun kinase 2stress-activated protein kinase 1astress-activated protein kinase JNK2
Modification date2020031320200327
UniProtAcc.

P45984

Main function of 5'-partner protein: FUNCTION: Serine/threonine-protein kinase involved in various processes such as cell proliferation, differentiation, migration, transformation and programmed cell death. Extracellular stimuli such as proinflammatory cytokines or physical stress stimulate the stress-activated protein kinase/c-Jun N-terminal kinase (SAP/JNK) signaling pathway. In this cascade, two dual specificity kinases MAP2K4/MKK4 and MAP2K7/MKK7 phosphorylate and activate MAPK9/JNK2. In turn, MAPK9/JNK2 phosphorylates a number of transcription factors, primarily components of AP-1 such as JUN and ATF2 and thus regulates AP-1 transcriptional activity. In response to oxidative or ribotoxic stresses, inhibits rRNA synthesis by phosphorylating and inactivating the RNA polymerase 1-specific transcription initiation factor RRN3. Promotes stressed cell apoptosis by phosphorylating key regulatory factors including TP53 and YAP1. In T-cells, MAPK8 and MAPK9 are required for polarized differentiation of T-helper cells into Th1 cells. Upon T-cell receptor (TCR) stimulation, is activated by CARMA1, BCL10, MAP2K7 and MAP3K7/TAK1 to regulate JUN protein levels. Plays an important role in the osmotic stress-induced epithelial tight-junctions disruption. When activated, promotes beta-catenin/CTNNB1 degradation and inhibits the canonical Wnt signaling pathway. Participates also in neurite growth in spiral ganglion neurons. Phosphorylates the CLOCK-ARNTL/BMAL1 heterodimer and plays a role in the regulation of the circadian clock (PubMed:22441692). Phosphorylates POU5F1, which results in the inhibition of POU5F1's transcriptional activity and enhances its proteosomal degradation (By similarity). {ECO:0000250|UniProtKB:Q9WTU6, ECO:0000269|PubMed:22441692}.; FUNCTION: MAPK9 isoforms display different binding patterns: alpha-1 and alpha-2 preferentially bind to JUN, whereas beta-1 and beta-2 bind to ATF2. However, there is no correlation between binding and phosphorylation, which is achieved at about the same efficiency by all isoforms. JUNB is not a substrate for JNK2 alpha-2, and JUND binds only weakly to it.
Ensembl transtripts involved in fusion geneENST idsENST00000507276, ENST00000265109, 
ENST00000397449, ENST00000428746, 
ENST00000503673, ENST00000506376, 
ENST00000512629, ENST00000515799, 
ENST00000343111, ENST00000347470, 
ENST00000393360, ENST00000397072, 
ENST00000425491, ENST00000452135, 
ENST00000455781, ENST00000539014, 
ENST00000524170, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score17 X 11 X 6=11225 X 6 X 3=90
# samples 176
** MAII scorelog2(17/1122*10)=-2.72246602447109
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(6/90*10)=-0.584962500721156
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: RAI14 [Title/Abstract] AND MAPK9 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: RAI14 [Title/Abstract] AND MAPK9 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)RAI14(34757703)-MAPK9(179696409), # samples:3
Anticipated loss of major functional domain due to fusion event.RAI14-MAPK9 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.
RAI14-MAPK9 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.
RAI14-MAPK9 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.
RAI14-MAPK9 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.
RAI14-MAPK9 seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
RAI14-MAPK9 seems lost the major protein functional domain in Tgene partner, which is a kinase due to the frame-shifted ORF.
RAI14-MAPK9 seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor 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
TgeneMAPK9

GO:0007254

JNK cascade

8654373

TgeneMAPK9

GO:0018105

peptidyl-serine phosphorylation

21856198



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/chr5:34757703/chr5:179696409)
- 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 RAI14 (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 MAPK9 (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)
ENST00000265109RAI14chr534757703+ENST00000452135MAPK9chr5179696409-48484542721606444
ENST00000265109RAI14chr534757703+ENST00000393360MAPK9chr5179696409-44024542721480402
ENST00000265109RAI14chr534757703+ENST00000455781MAPK9chr5179696409-43974542721606444
ENST00000265109RAI14chr534757703+ENST00000343111MAPK9chr5179696409-44024542721480402
ENST00000265109RAI14chr534757703+ENST00000347470MAPK9chr5179696409-15494542721351359
ENST00000265109RAI14chr534757703+ENST00000425491MAPK9chr5179696409-24314542721060262
ENST00000512629RAI14chr534757703+ENST00000452135MAPK9chr5179696409-4646252701404444
ENST00000512629RAI14chr534757703+ENST00000393360MAPK9chr5179696409-4200252701278402
ENST00000512629RAI14chr534757703+ENST00000455781MAPK9chr5179696409-4195252701404444
ENST00000512629RAI14chr534757703+ENST00000343111MAPK9chr5179696409-4200252701278402
ENST00000512629RAI14chr534757703+ENST00000347470MAPK9chr5179696409-1347252701149359
ENST00000512629RAI14chr534757703+ENST00000425491MAPK9chr5179696409-222925270858262
ENST00000428746RAI14chr534757703+ENST00000452135MAPK9chr5179696409-48364422601594444
ENST00000428746RAI14chr534757703+ENST00000393360MAPK9chr5179696409-43904422601468402
ENST00000428746RAI14chr534757703+ENST00000455781MAPK9chr5179696409-43854422601594444
ENST00000428746RAI14chr534757703+ENST00000343111MAPK9chr5179696409-43904422601468402
ENST00000428746RAI14chr534757703+ENST00000347470MAPK9chr5179696409-15374422601339359
ENST00000428746RAI14chr534757703+ENST00000425491MAPK9chr5179696409-24194422601048262
ENST00000503673RAI14chr534757703+ENST00000452135MAPK9chr5179696409-49175233411675444
ENST00000503673RAI14chr534757703+ENST00000393360MAPK9chr5179696409-44715233411549402
ENST00000503673RAI14chr534757703+ENST00000455781MAPK9chr5179696409-44665233411675444
ENST00000503673RAI14chr534757703+ENST00000343111MAPK9chr5179696409-44715233411549402
ENST00000503673RAI14chr534757703+ENST00000347470MAPK9chr5179696409-16185233411420359
ENST00000503673RAI14chr534757703+ENST00000425491MAPK9chr5179696409-25005233411129262
ENST00000515799RAI14chr534757703+ENST00000452135MAPK9chr5179696409-50626684831820445
ENST00000515799RAI14chr534757703+ENST00000393360MAPK9chr5179696409-46166684831694403
ENST00000515799RAI14chr534757703+ENST00000455781MAPK9chr5179696409-46116684831820445
ENST00000515799RAI14chr534757703+ENST00000343111MAPK9chr5179696409-46166684831694403
ENST00000515799RAI14chr534757703+ENST00000347470MAPK9chr5179696409-17636684831565360
ENST00000515799RAI14chr534757703+ENST00000425491MAPK9chr5179696409-26456684831274263
ENST00000506376RAI14chr534757703+ENST00000452135MAPK9chr5179696409-46892951521447431
ENST00000506376RAI14chr534757703+ENST00000393360MAPK9chr5179696409-42432951521321389
ENST00000506376RAI14chr534757703+ENST00000455781MAPK9chr5179696409-42382951521447431
ENST00000506376RAI14chr534757703+ENST00000343111MAPK9chr5179696409-42432951521321389
ENST00000506376RAI14chr534757703+ENST00000347470MAPK9chr5179696409-13902951521192346
ENST00000506376RAI14chr534757703+ENST00000425491MAPK9chr5179696409-2272295152901249
ENST00000397449RAI14chr534757703+ENST00000452135MAPK9chr5179696409-454014601298432
ENST00000397449RAI14chr534757703+ENST00000393360MAPK9chr5179696409-409414601172390
ENST00000397449RAI14chr534757703+ENST00000455781MAPK9chr5179696409-408914601298432
ENST00000397449RAI14chr534757703+ENST00000343111MAPK9chr5179696409-409414601172390
ENST00000397449RAI14chr534757703+ENST00000347470MAPK9chr5179696409-124114601043347
ENST00000397449RAI14chr534757703+ENST00000425491MAPK9chr5179696409-21231460752250

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
ENST00000265109ENST00000452135RAI14chr534757703+MAPK9chr5179696409-0.0005454390.99945456
ENST00000265109ENST00000393360RAI14chr534757703+MAPK9chr5179696409-0.0007105890.9992894
ENST00000265109ENST00000455781RAI14chr534757703+MAPK9chr5179696409-0.0005424840.99945754
ENST00000265109ENST00000343111RAI14chr534757703+MAPK9chr5179696409-0.0006217560.9993782
ENST00000265109ENST00000347470RAI14chr534757703+MAPK9chr5179696409-0.0033258680.99667406
ENST00000265109ENST00000425491RAI14chr534757703+MAPK9chr5179696409-0.0013715320.9986285
ENST00000512629ENST00000452135RAI14chr534757703+MAPK9chr5179696409-0.0004767890.9995233
ENST00000512629ENST00000393360RAI14chr534757703+MAPK9chr5179696409-0.0006204050.9993795
ENST00000512629ENST00000455781RAI14chr534757703+MAPK9chr5179696409-0.0004797020.9995203
ENST00000512629ENST00000343111RAI14chr534757703+MAPK9chr5179696409-0.0005632220.9994368
ENST00000512629ENST00000347470RAI14chr534757703+MAPK9chr5179696409-0.0028507840.9971493
ENST00000512629ENST00000425491RAI14chr534757703+MAPK9chr5179696409-0.001463880.9985361
ENST00000428746ENST00000452135RAI14chr534757703+MAPK9chr5179696409-0.0005050080.999495
ENST00000428746ENST00000393360RAI14chr534757703+MAPK9chr5179696409-0.0006648950.9993351
ENST00000428746ENST00000455781RAI14chr534757703+MAPK9chr5179696409-0.0005129850.99948704
ENST00000428746ENST00000343111RAI14chr534757703+MAPK9chr5179696409-0.0006069780.999393
ENST00000428746ENST00000347470RAI14chr534757703+MAPK9chr5179696409-0.0035120250.996488
ENST00000428746ENST00000425491RAI14chr534757703+MAPK9chr5179696409-0.0016249350.99837506
ENST00000503673ENST00000452135RAI14chr534757703+MAPK9chr5179696409-0.000565690.9994343
ENST00000503673ENST00000393360RAI14chr534757703+MAPK9chr5179696409-0.0007310460.99926895
ENST00000503673ENST00000455781RAI14chr534757703+MAPK9chr5179696409-0.0005608970.99943906
ENST00000503673ENST00000343111RAI14chr534757703+MAPK9chr5179696409-0.0006430990.9993569
ENST00000503673ENST00000347470RAI14chr534757703+MAPK9chr5179696409-0.0030862690.9969137
ENST00000503673ENST00000425491RAI14chr534757703+MAPK9chr5179696409-0.0016283710.99837166
ENST00000515799ENST00000452135RAI14chr534757703+MAPK9chr5179696409-0.0002014970.9997985
ENST00000515799ENST00000393360RAI14chr534757703+MAPK9chr5179696409-0.0001909260.9998091
ENST00000515799ENST00000455781RAI14chr534757703+MAPK9chr5179696409-0.0002657390.9997342
ENST00000515799ENST00000343111RAI14chr534757703+MAPK9chr5179696409-0.0002268110.9997732
ENST00000515799ENST00000347470RAI14chr534757703+MAPK9chr5179696409-0.0008170710.9991829
ENST00000515799ENST00000425491RAI14chr534757703+MAPK9chr5179696409-0.0003615250.99963844
ENST00000506376ENST00000452135RAI14chr534757703+MAPK9chr5179696409-0.0003387420.9996612
ENST00000506376ENST00000393360RAI14chr534757703+MAPK9chr5179696409-0.0003868320.9996132
ENST00000506376ENST00000455781RAI14chr534757703+MAPK9chr5179696409-0.0003418250.9996582
ENST00000506376ENST00000343111RAI14chr534757703+MAPK9chr5179696409-0.0003537750.9996462
ENST00000506376ENST00000347470RAI14chr534757703+MAPK9chr5179696409-0.0014019650.99859804
ENST00000506376ENST00000425491RAI14chr534757703+MAPK9chr5179696409-0.0006879040.99931204
ENST00000397449ENST00000452135RAI14chr534757703+MAPK9chr5179696409-0.0003268510.9996731
ENST00000397449ENST00000393360RAI14chr534757703+MAPK9chr5179696409-0.0003216250.9996784
ENST00000397449ENST00000455781RAI14chr534757703+MAPK9chr5179696409-0.0003645690.99963546
ENST00000397449ENST00000343111RAI14chr534757703+MAPK9chr5179696409-0.0003264350.9996736
ENST00000397449ENST00000347470RAI14chr534757703+MAPK9chr5179696409-0.000750940.99924904
ENST00000397449ENST00000425491RAI14chr534757703+MAPK9chr5179696409-0.0003163790.9996836

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 RAI14-MAPK9

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
RAI14chr534757703MAPK9chr517969640914649ASATKHDSEGKTAAAFDTVLGINVAV
RAI14chr534757703MAPK9chr517969640925261ASATKHDSEGKTAAAFDTVLGINVAV
RAI14chr534757703MAPK9chr517969640929548ASATKHDSEGKTAAAFDTVLGINVAV
RAI14chr534757703MAPK9chr517969640944261ASATKHDSEGKTAAAFDTVLGINVAV
RAI14chr534757703MAPK9chr517969640945461ASATKHDSEGKTAAAFDTVLGINVAV
RAI14chr534757703MAPK9chr517969640952361ASATKHDSEGKTAAAFDTVLGINVAV
RAI14chr534757703MAPK9chr517969640966862ASATKHDSEGKTAAAFDTVLGINVAV

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Potential FusionNeoAntigen Information of RAI14-MAPK9 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.
RAI14-MAPK9_34757703_179696409.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)
RAI14-MAPK9chr534757703chr5179696409454HLA-B50:02SEGKTAAA0.99950.7639715
RAI14-MAPK9chr534757703chr5179696409454HLA-B45:01SEGKTAAA0.99950.8727715
RAI14-MAPK9chr534757703chr5179696409454HLA-B41:01SEGKTAAA0.9820.7928715
RAI14-MAPK9chr534757703chr5179696409454HLA-B50:01SEGKTAAA0.88960.7863715
RAI14-MAPK9chr534757703chr5179696409454HLA-B44:03SEGKTAAAF0.9950.8377716
RAI14-MAPK9chr534757703chr5179696409454HLA-B35:03TAAAFDTVL0.97840.92241120
RAI14-MAPK9chr534757703chr5179696409454HLA-A02:21KTAAAFDTV0.94340.56961019
RAI14-MAPK9chr534757703chr5179696409454HLA-B35:04TAAAFDTVL0.93510.9771120
RAI14-MAPK9chr534757703chr5179696409454HLA-B35:02TAAAFDTVL0.93510.9771120
RAI14-MAPK9chr534757703chr5179696409454HLA-B18:01SEGKTAAAF0.90990.7701716
RAI14-MAPK9chr534757703chr5179696409454HLA-B39:13SEGKTAAAF0.13310.7627716
RAI14-MAPK9chr534757703chr5179696409454HLA-C03:07TAAAFDTVL0.99890.96451120
RAI14-MAPK9chr534757703chr5179696409454HLA-C03:08TAAAFDTVL0.99870.95561120
RAI14-MAPK9chr534757703chr5179696409454HLA-C03:19TAAAFDTVL0.99860.98691120
RAI14-MAPK9chr534757703chr5179696409454HLA-B44:10SEGKTAAAF0.96750.6092716
RAI14-MAPK9chr534757703chr5179696409454HLA-C08:13TAAAFDTVL0.960.88951120
RAI14-MAPK9chr534757703chr5179696409454HLA-C08:04TAAAFDTVL0.960.88951120
RAI14-MAPK9chr534757703chr5179696409454HLA-B35:12TAAAFDTVL0.93510.9771120
RAI14-MAPK9chr534757703chr5179696409454HLA-C08:03TAAAFDTVL0.91120.95081120
RAI14-MAPK9chr534757703chr5179696409454HLA-C01:17TAAAFDTVL0.8980.94281120
RAI14-MAPK9chr534757703chr5179696409454HLA-C12:12TAAAFDTVL0.8960.91581120
RAI14-MAPK9chr534757703chr5179696409454HLA-C02:06TAAAFDTVL0.80670.89121120
RAI14-MAPK9chr534757703chr5179696409454HLA-B39:08SEGKTAAAF0.33290.73716
RAI14-MAPK9chr534757703chr5179696409454HLA-B50:04SEGKTAAA0.88960.7863715
RAI14-MAPK9chr534757703chr5179696409454HLA-B50:05SEGKTAAA0.88960.7863715
RAI14-MAPK9chr534757703chr5179696409454HLA-C03:03TAAAFDTVL0.9990.98721120
RAI14-MAPK9chr534757703chr5179696409454HLA-C03:04TAAAFDTVL0.9990.98721120
RAI14-MAPK9chr534757703chr5179696409454HLA-C03:17TAAAFDTVL0.99780.96611120
RAI14-MAPK9chr534757703chr5179696409454HLA-C03:05TAAAFDTVL0.99780.92571120
RAI14-MAPK9chr534757703chr5179696409454HLA-C03:02TAAAFDTVL0.99640.96611120
RAI14-MAPK9chr534757703chr5179696409454HLA-B44:13SEGKTAAAF0.9950.8377716
RAI14-MAPK9chr534757703chr5179696409454HLA-B44:26SEGKTAAAF0.9950.8377716
RAI14-MAPK9chr534757703chr5179696409454HLA-B44:07SEGKTAAAF0.9950.8377716
RAI14-MAPK9chr534757703chr5179696409454HLA-B40:04SEGKTAAAF0.98920.7375716
RAI14-MAPK9chr534757703chr5179696409454HLA-C16:04TAAAFDTVL0.97950.94251120
RAI14-MAPK9chr534757703chr5179696409454HLA-B35:13TAAAFDTVL0.96910.92611120
RAI14-MAPK9chr534757703chr5179696409454HLA-C03:06TAAAFDTVL0.96350.98791120
RAI14-MAPK9chr534757703chr5179696409454HLA-A02:06KTAAAFDTV0.94340.56961019
RAI14-MAPK9chr534757703chr5179696409454HLA-B35:09TAAAFDTVL0.93510.9771120
RAI14-MAPK9chr534757703chr5179696409454HLA-B18:07SEGKTAAAF0.92040.694716
RAI14-MAPK9chr534757703chr5179696409454HLA-B18:04SEGKTAAAF0.91630.7769716
RAI14-MAPK9chr534757703chr5179696409454HLA-B18:06SEGKTAAAF0.91290.7771716
RAI14-MAPK9chr534757703chr5179696409454HLA-C08:01TAAAFDTVL0.91120.95081120
RAI14-MAPK9chr534757703chr5179696409454HLA-B18:05SEGKTAAAF0.90990.7701716
RAI14-MAPK9chr534757703chr5179696409454HLA-B35:22TAAAFDTVL0.90680.64841120
RAI14-MAPK9chr534757703chr5179696409454HLA-B18:08SEGKTAAAF0.90380.774716
RAI14-MAPK9chr534757703chr5179696409454HLA-C01:02TAAAFDTVL0.90160.94081120
RAI14-MAPK9chr534757703chr5179696409454HLA-B18:11SEGKTAAAF0.87280.6468716
RAI14-MAPK9chr534757703chr5179696409454HLA-B18:03SEGKTAAAF0.85810.7502716
RAI14-MAPK9chr534757703chr5179696409454HLA-B07:13TAAAFDTVL0.8290.81481120
RAI14-MAPK9chr534757703chr5179696409454HLA-C16:01TAAAFDTVL0.77620.95471120
RAI14-MAPK9chr534757703chr5179696409454HLA-C17:01TAAAFDTVL0.4990.89961120
RAI14-MAPK9chr534757703chr5179696409454HLA-B15:53SEGKTAAAF0.27560.666716
RAI14-MAPK9chr534757703chr5179696409454HLA-B48:02SEGKTAAAF0.19160.6961716
RAI14-MAPK9chr534757703chr5179696409454HLA-B15:54SEGKTAAAF0.08180.6409716
RAI14-MAPK9chr534757703chr5179696409454HLA-B18:03DSEGKTAAAF0.39980.7807616

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Potential FusionNeoAntigen Information of RAI14-MAPK9 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 RAI14-MAPK9

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
1398DSEGKTAAAFDTVLRAI14MAPK9chr534757703chr5179696409454

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of RAI14-MAPK9

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-B14:023BVN1398DSEGKTAAAFDTVL-7.81976-8.01426
HLA-B14:023BVN1398DSEGKTAAAFDTVL-3.37109-4.12559
HLA-B52:013W391398DSEGKTAAAFDTVL-5.5847-5.7792
HLA-B52:013W391398DSEGKTAAAFDTVL-4.33082-5.08532
HLA-A24:025HGA1398DSEGKTAAAFDTVL-8.85594-9.05044
HLA-A24:025HGA1398DSEGKTAAAFDTVL-5.79054-6.54504
HLA-B44:053DX81398DSEGKTAAAFDTVL-5.31446-5.50896
HLA-B44:053DX81398DSEGKTAAAFDTVL-4.00399-4.75849

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Vaccine Design for the FusionNeoAntigens of RAI14-MAPK9

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
RAI14-MAPK9chr534757703chr51796964091019KTAAAFDTVCAAGACCGCTGCTGCATTTGATACAGT
RAI14-MAPK9chr534757703chr51796964091120TAAAFDTVLGACCGCTGCTGCATTTGATACAGTTCT
RAI14-MAPK9chr534757703chr5179696409616DSEGKTAAAFCGACAGTGAGGGCAAGACCGCTGCTGCATT
RAI14-MAPK9chr534757703chr5179696409715SEGKTAAACAGTGAGGGCAAGACCGCTGCTGC
RAI14-MAPK9chr534757703chr5179696409716SEGKTAAAFCAGTGAGGGCAAGACCGCTGCTGCATT

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 RAI14-MAPK9

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
SKCMRAI14-MAPK9chr534757703ENST00000265109chr5179696409ENST00000343111TCGA-D3-A1Q3-06A

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Potential target of CAR-T therapy development for RAI14-MAPK9

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 RAI14-MAPK9

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 RAI14-MAPK9

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