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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:RPS29-MAP3K3

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: RPS29-MAP3K3
FusionPDB ID: 77810
FusionGDB2.0 ID: 77810
HgeneTgene
Gene symbol

RPS29

MAP3K3

Gene ID

6235

4215

Gene nameribosomal protein S29mitogen-activated protein kinase kinase kinase 3
SynonymsDBA13|S29|uS14MAPKKK3|MEKK3
Cytomap

14q21.3

17q23.3

Type of geneprotein-codingprotein-coding
Description40S ribosomal protein S29small ribosomal subunit protein uS14mitogen-activated protein kinase kinase kinase 3MAP/ERK kinase kinase 3MAPK/ERK kinase kinase 3MEK kinase 3MEKK 3
Modification date2020031320200313
UniProtAcc.

Q99759

Main function of 5'-partner protein: FUNCTION: Component of a protein kinase signal transduction cascade. Mediates activation of the NF-kappa-B, AP1 and DDIT3 transcriptional regulators. {ECO:0000269|PubMed:12912994, ECO:0000269|PubMed:14661019, ECO:0000269|PubMed:14743216, ECO:0000269|PubMed:9006902}.
Ensembl transtripts involved in fusion geneENST idsENST00000245458, ENST00000396020, 
ENST00000557111, 		ENST00000577784, 
ENST00000361357, ENST00000361733, 
ENST00000577395, ENST00000579585, 
ENST00000584573, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score28 X 15 X 5=21008 X 11 X 4=352
# samples 2911
** MAII scorelog2(29/2100*10)=-2.85626452253855
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(11/352*10)=-1.67807190511264
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: RPS29 [Title/Abstract] AND MAP3K3 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: RPS29 [Title/Abstract] AND MAP3K3 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)RPS29(50052668)-MAP3K3(61723394), # samples:1
Anticipated loss of major functional domain due to fusion event.RPS29-MAP3K3 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.
RPS29-MAP3K3 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.
RPS29-MAP3K3 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.
RPS29-MAP3K3 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
HgeneRPS29

GO:0002181

cytoplasmic translation

25957688

TgeneMAP3K3

GO:0035556

intracellular signal transduction

15001576

TgeneMAP3K3

GO:0046777

protein autophosphorylation

15001576



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/chr14:50052668/chr17:61723394)
- 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 RPS29 (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 MAP3K3 (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)
ENST00000396020RPS29chr1450052668-ENST00000579585MAP3K3chr1761723394+3259192301946638
ENST00000396020RPS29chr1450052668-ENST00000584573MAP3K3chr1761723394+2118192301934634
ENST00000396020RPS29chr1450052668-ENST00000361733MAP3K3chr1761723394+3275192301946638
ENST00000396020RPS29chr1450052668-ENST00000361357MAP3K3chr1761723394+4473192301946638
ENST00000396020RPS29chr1450052668-ENST00000577395MAP3K3chr1761723394+2032192301934634
ENST00000245458RPS29chr1450052668-ENST00000579585MAP3K3chr1761723394+3259192301946638
ENST00000245458RPS29chr1450052668-ENST00000584573MAP3K3chr1761723394+2118192301934634
ENST00000245458RPS29chr1450052668-ENST00000361733MAP3K3chr1761723394+3275192301946638
ENST00000245458RPS29chr1450052668-ENST00000361357MAP3K3chr1761723394+4473192301946638
ENST00000245458RPS29chr1450052668-ENST00000577395MAP3K3chr1761723394+2032192301934634

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
ENST00000396020ENST00000579585RPS29chr1450052668-MAP3K3chr1761723394+0.008450460.9915495
ENST00000396020ENST00000584573RPS29chr1450052668-MAP3K3chr1761723394+0.0135971080.9864029
ENST00000396020ENST00000361733RPS29chr1450052668-MAP3K3chr1761723394+0.0075006360.9924994
ENST00000396020ENST00000361357RPS29chr1450052668-MAP3K3chr1761723394+0.004005280.9959947
ENST00000396020ENST00000577395RPS29chr1450052668-MAP3K3chr1761723394+0.0134784240.9865216
ENST00000245458ENST00000579585RPS29chr1450052668-MAP3K3chr1761723394+0.008450460.9915495
ENST00000245458ENST00000584573RPS29chr1450052668-MAP3K3chr1761723394+0.0135971080.9864029
ENST00000245458ENST00000361733RPS29chr1450052668-MAP3K3chr1761723394+0.0075006360.9924994
ENST00000245458ENST00000361357RPS29chr1450052668-MAP3K3chr1761723394+0.004005280.9959947
ENST00000245458ENST00000577395RPS29chr1450052668-MAP3K3chr1761723394+0.0134784240.9865216

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 RPS29-MAP3K3

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
RPS29chr1450052668MAP3K3chr176172339419254CFRQYAKDIGFIKSDVRIKFEHNGER

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Potential FusionNeoAntigen Information of RPS29-MAP3K3 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.
RPS29-MAP3K3_50052668_61723394.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)
RPS29-MAP3K3chr1450052668chr1761723394192HLA-B15:03IKSDVRIKF0.60150.53921120
RPS29-MAP3K3chr1450052668chr1761723394192HLA-C05:09KSDVRIKF10.75941220
RPS29-MAP3K3chr1450052668chr1761723394192HLA-C08:15KSDVRIKF10.85691220
RPS29-MAP3K3chr1450052668chr1761723394192HLA-C07:95IKSDVRIKF0.99410.5281120
RPS29-MAP3K3chr1450052668chr1761723394192HLA-C07:05IKSDVRIKF0.99240.84411120
RPS29-MAP3K3chr1450052668chr1761723394192HLA-C07:27IKSDVRIKF0.98830.85091120
RPS29-MAP3K3chr1450052668chr1761723394192HLA-C07:80IKSDVRIKF0.8620.79341120
RPS29-MAP3K3chr1450052668chr1761723394192HLA-C07:67IKSDVRIKF0.8620.79341120
RPS29-MAP3K3chr1450052668chr1761723394192HLA-C07:46IKSDVRIKF0.85820.65411120
RPS29-MAP3K3chr1450052668chr1761723394192HLA-C07:10IKSDVRIKF0.84670.84951120
RPS29-MAP3K3chr1450052668chr1761723394192HLA-C12:16IKSDVRIKF0.06160.88381120
RPS29-MAP3K3chr1450052668chr1761723394192HLA-C04:03KSDVRIKF10.6511220
RPS29-MAP3K3chr1450052668chr1761723394192HLA-C08:02KSDVRIKF10.85691220
RPS29-MAP3K3chr1450052668chr1761723394192HLA-C05:01KSDVRIKF10.75941220
RPS29-MAP3K3chr1450052668chr1761723394192HLA-C16:02KSDVRIKF0.99920.97681220
RPS29-MAP3K3chr1450052668chr1761723394192HLA-B57:02KSDVRIKF0.99770.66321220
RPS29-MAP3K3chr1450052668chr1761723394192HLA-C07:17IKSDVRIKF0.89810.87211120
RPS29-MAP3K3chr1450052668chr1761723394192HLA-C07:22IKSDVRIKF0.86760.55881120
RPS29-MAP3K3chr1450052668chr1761723394192HLA-C07:02IKSDVRIKF0.8620.79341120
RPS29-MAP3K3chr1450052668chr1761723394192HLA-B48:02IKSDVRIKF0.53620.83771120
RPS29-MAP3K3chr1450052668chr1761723394192HLA-C06:06IKSDVRIKF0.39630.95211120
RPS29-MAP3K3chr1450052668chr1761723394192HLA-C06:08IKSDVRIKF0.37810.90321120
RPS29-MAP3K3chr1450052668chr1761723394192HLA-B15:54IKSDVRIKF0.08410.72671120
RPS29-MAP3K3chr1450052668chr1761723394192HLA-B15:53IKSDVRIKF0.07950.7551120
RPS29-MAP3K3chr1450052668chr1761723394192HLA-C06:17IKSDVRIKF0.05840.97841120
RPS29-MAP3K3chr1450052668chr1761723394192HLA-C06:02IKSDVRIKF0.05840.97841120

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Potential FusionNeoAntigen Information of RPS29-MAP3K3 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.
RPS29-MAP3K3_50052668_61723394.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)
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0301IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0301DIGFIKSDVRIKFEH722
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0301GFIKSDVRIKFEHNG924
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0301KDIGFIKSDVRIKFE621
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0303IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0303DIGFIKSDVRIKFEH722
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0303GFIKSDVRIKFEHNG924
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0303KDIGFIKSDVRIKFE621
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0305IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0305DIGFIKSDVRIKFEH722
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0305GFIKSDVRIKFEHNG924
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0305KDIGFIKSDVRIKFE621
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0307IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0307DIGFIKSDVRIKFEH722
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0307GFIKSDVRIKFEHNG924
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0307KDIGFIKSDVRIKFE621
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0310IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0310DIGFIKSDVRIKFEH722
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0310GFIKSDVRIKFEHNG924
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0310KDIGFIKSDVRIKFE621
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0310AKDIGFIKSDVRIKF520
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0313IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0313DIGFIKSDVRIKFEH722
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0313GFIKSDVRIKFEHNG924
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0313KDIGFIKSDVRIKFE621
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0315IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0315DIGFIKSDVRIKFEH722
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0315GFIKSDVRIKFEHNG924
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0315KDIGFIKSDVRIKFE621
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0318IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0318DIGFIKSDVRIKFEH722
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0318GFIKSDVRIKFEHNG924
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0318KDIGFIKSDVRIKFE621
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0320IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0320DIGFIKSDVRIKFEH722
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0320GFIKSDVRIKFEHNG924
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0320KDIGFIKSDVRIKFE621
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0322IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0322DIGFIKSDVRIKFEH722
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0322GFIKSDVRIKFEHNG924
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0322KDIGFIKSDVRIKFE621
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0324IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0324DIGFIKSDVRIKFEH722
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0324GFIKSDVRIKFEHNG924
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0324KDIGFIKSDVRIKFE621
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0326IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0326DIGFIKSDVRIKFEH722
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0326GFIKSDVRIKFEHNG924
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0326KDIGFIKSDVRIKFE621
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0328IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0328DIGFIKSDVRIKFEH722
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0328GFIKSDVRIKFEHNG924
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0328KDIGFIKSDVRIKFE621
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0330IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0330DIGFIKSDVRIKFEH722
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0330GFIKSDVRIKFEHNG924
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0330KDIGFIKSDVRIKFE621
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0332IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0332DIGFIKSDVRIKFEH722
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0332GFIKSDVRIKFEHNG924
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0332KDIGFIKSDVRIKFE621
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0334IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0334DIGFIKSDVRIKFEH722
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0334GFIKSDVRIKFEHNG924
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0334KDIGFIKSDVRIKFE621
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0336IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0336DIGFIKSDVRIKFEH722
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0336GFIKSDVRIKFEHNG924
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0336KDIGFIKSDVRIKFE621
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0338IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0338DIGFIKSDVRIKFEH722
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0340IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0340DIGFIKSDVRIKFEH722
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0340GFIKSDVRIKFEHNG924
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0340KDIGFIKSDVRIKFE621
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0342IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0342DIGFIKSDVRIKFEH722
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0342GFIKSDVRIKFEHNG924
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0342KDIGFIKSDVRIKFE621
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0344IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0344DIGFIKSDVRIKFEH722
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0344GFIKSDVRIKFEHNG924
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0344KDIGFIKSDVRIKFE621
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0346IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0346DIGFIKSDVRIKFEH722
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0346GFIKSDVRIKFEHNG924
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0346KDIGFIKSDVRIKFE621
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0348IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0348DIGFIKSDVRIKFEH722
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0348GFIKSDVRIKFEHNG924
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0348KDIGFIKSDVRIKFE621
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0350IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0350DIGFIKSDVRIKFEH722
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0350GFIKSDVRIKFEHNG924
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0350KDIGFIKSDVRIKFE621
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0352IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0352DIGFIKSDVRIKFEH722
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0352GFIKSDVRIKFEHNG924
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0352KDIGFIKSDVRIKFE621
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0354IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0354DIGFIKSDVRIKFEH722
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0354GFIKSDVRIKFEHNG924
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-0354KDIGFIKSDVRIKFE621
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1107IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1107DIGFIKSDVRIKFEH722
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1107GFIKSDVRIKFEHNG924
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1107KDIGFIKSDVRIKFE621
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1113IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1134IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1134DIGFIKSDVRIKFEH722
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1179IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1179DIGFIKSDVRIKFEH722
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1327IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1331IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1333IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1341IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1344IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1344DIGFIKSDVRIKFEH722
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1371IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1381IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1394IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1394DIGFIKSDVRIKFEH722
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1394GFIKSDVRIKFEHNG924
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1416IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1417IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1417DIGFIKSDVRIKFEH722
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1419IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1421IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1421DIGFIKSDVRIKFEH722
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1421GFIKSDVRIKFEHNG924
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1421KDIGFIKSDVRIKFE621
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1430IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1431IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1432IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1432DIGFIKSDVRIKFEH722
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1433IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1433DIGFIKSDVRIKFEH722
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1434IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1435IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1437IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1438IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1438DIGFIKSDVRIKFEH722
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1438KDIGFIKSDVRIKFE621
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1449IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1450IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1450DIGFIKSDVRIKFEH722
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1464IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1465IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1465DIGFIKSDVRIKFEH722
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1472IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1476IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1476DIGFIKSDVRIKFEH722
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1476GFIKSDVRIKFEHNG924
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1476KDIGFIKSDVRIKFE621
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1479IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1479DIGFIKSDVRIKFEH722
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1479GFIKSDVRIKFEHNG924
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1479KDIGFIKSDVRIKFE621
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1480IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1482IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1482DIGFIKSDVRIKFEH722
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1482KDIGFIKSDVRIKFE621
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1495IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1495DIGFIKSDVRIKFEH722
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1495KDIGFIKSDVRIKFE621
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1495GFIKSDVRIKFEHNG924
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1499IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB1-1499DIGFIKSDVRIKFEH722
RPS29-MAP3K3chr1450052668chr1761723394192DRB3-0114IGFIKSDVRIKFEHN823
RPS29-MAP3K3chr1450052668chr1761723394192DRB3-0114DIGFIKSDVRIKFEH722
RPS29-MAP3K3chr1450052668chr1761723394192DRB5-0106AKDIGFIKSDVRIKF520
RPS29-MAP3K3chr1450052668chr1761723394192DRB5-0106YAKDIGFIKSDVRIK419
RPS29-MAP3K3chr1450052668chr1761723394192DRB5-0112DIGFIKSDVRIKFEH722
RPS29-MAP3K3chr1450052668chr1761723394192DRB5-0202AKDIGFIKSDVRIKF520
RPS29-MAP3K3chr1450052668chr1761723394192DRB5-0205AKDIGFIKSDVRIKF520
RPS29-MAP3K3chr1450052668chr1761723394192DRB5-0205YAKDIGFIKSDVRIK419

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Fusion breakpoint peptide structures of RPS29-MAP3K3

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
4150KDIGFIKSDVRIKFRPS29MAP3K3chr1450052668chr1761723394192

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of RPS29-MAP3K3

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-B14:023BVN4150KDIGFIKSDVRIKF-7.15543-7.26883
HLA-B14:023BVN4150KDIGFIKSDVRIKF-4.77435-5.80965
HLA-B52:013W394150KDIGFIKSDVRIKF-6.80875-6.92215
HLA-B52:013W394150KDIGFIKSDVRIKF-4.20386-5.23916
HLA-A11:014UQ24150KDIGFIKSDVRIKF-7.5194-8.5547
HLA-A11:014UQ24150KDIGFIKSDVRIKF-6.9601-7.0735
HLA-A24:025HGA4150KDIGFIKSDVRIKF-7.52403-7.63743
HLA-A24:025HGA4150KDIGFIKSDVRIKF-5.82433-6.85963
HLA-B27:056PYJ4150KDIGFIKSDVRIKF-3.28285-4.31815
HLA-B44:053DX84150KDIGFIKSDVRIKF-5.91172-6.94702
HLA-B44:053DX84150KDIGFIKSDVRIKF-4.24346-4.35686

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Vaccine Design for the FusionNeoAntigens of RPS29-MAP3K3

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
RPS29-MAP3K3chr1450052668chr17617233941120IKSDVRIKFATTAAGAGTGACGTCAGAATCAAGTTC
RPS29-MAP3K3chr1450052668chr17617233941220KSDVRIKFAAGAGTGACGTCAGAATCAAGTTC

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
RPS29-MAP3K3chr1450052668chr1761723394419YAKDIGFIKSDVRIKTACGCGAAGGATATCGGTTTCATTAAGAGTGACGTCAGAATCAAG
RPS29-MAP3K3chr1450052668chr1761723394520AKDIGFIKSDVRIKFGCGAAGGATATCGGTTTCATTAAGAGTGACGTCAGAATCAAGTTC
RPS29-MAP3K3chr1450052668chr1761723394621KDIGFIKSDVRIKFEAAGGATATCGGTTTCATTAAGAGTGACGTCAGAATCAAGTTCGAG
RPS29-MAP3K3chr1450052668chr1761723394722DIGFIKSDVRIKFEHGATATCGGTTTCATTAAGAGTGACGTCAGAATCAAGTTCGAGCAC
RPS29-MAP3K3chr1450052668chr1761723394823IGFIKSDVRIKFEHNATCGGTTTCATTAAGAGTGACGTCAGAATCAAGTTCGAGCACAAC
RPS29-MAP3K3chr1450052668chr1761723394924GFIKSDVRIKFEHNGGGTTTCATTAAGAGTGACGTCAGAATCAAGTTCGAGCACAACGGG

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Information of the samples that have these potential fusion neoantigens of RPS29-MAP3K3

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
BRCARPS29-MAP3K3chr1450052668ENST00000245458chr1761723394ENST00000361357TCGA-A8-A06Q-01A

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Potential target of CAR-T therapy development for RPS29-MAP3K3

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 RPS29-MAP3K3

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 RPS29-MAP3K3

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