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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:RPS6KA3-NUP50

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: RPS6KA3-NUP50
FusionPDB ID: 78009
FusionGDB2.0 ID: 78009
HgeneTgene
Gene symbol

RPS6KA3

NUP50

Gene ID

6197

10762

Gene nameribosomal protein S6 kinase A3nucleoporin 50
SynonymsCLS|HU-3|ISPK-1|MAPKAPK1B|MRX19|RSK|RSK2|S6K-alpha3|p90-RSK2|pp90RSK2NPAP60|NPAP60L
Cytomap

Xp22.12

22q13.31

Type of geneprotein-codingprotein-coding
Descriptionribosomal protein S6 kinase alpha-3MAP kinase-activated protein kinase 1bMAPK-activated protein kinase 1bMAPKAP kinase 1bMAPKAPK-1bRSK-2S6K-alpha-3epididymis secretory sperm binding proteininsulin-stimulated protein kinase 1p90-RSK 3ribosomal S6nuclear pore complex protein Nup5050 kDa nucleoporinnuclear pore-associated protein 60Lnucleoporin 50kDnucleoporin 50kDanucleoporin Nup50
Modification date2020032720200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST idsENST00000379548, ENST00000379565, 
ENST00000540702, ENST00000544447, 
ENST00000479809, 
ENST00000486184, 
ENST00000396096, ENST00000407019, 
ENST00000425733, ENST00000347635, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score15 X 11 X 7=11552 X 2 X 2=8
# samples 192
** MAII scorelog2(19/1155*10)=-2.60382152797247
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(2/8*10)=1.32192809488736
Fusion gene context

PubMed: RPS6KA3 [Title/Abstract] AND NUP50 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: RPS6KA3 [Title/Abstract] AND NUP50 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)RPS6KA3(20187519)-NUP50(45567480), # samples:1
Anticipated loss of major functional domain due to fusion event.RPS6KA3-NUP50 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.
RPS6KA3-NUP50 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.
RPS6KA3-NUP50 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.
RPS6KA3-NUP50 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.
RPS6KA3-NUP50 seems lost the major protein functional domain in Hgene partner, which is a epigenetic factor due to the frame-shifted ORF.
RPS6KA3-NUP50 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
RPS6KA3-NUP50 seems lost the major protein functional domain in Hgene partner, which is a kinase due to the frame-shifted ORF.
RPS6KA3-NUP50 seems lost the major protein functional domain in Tgene partner, which is a cell metabolism 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
HgeneRPS6KA3

GO:0043154

negative regulation of cysteine-type endopeptidase activity involved in apoptotic process

18402937



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/chrX:20187519/chr22:45567480)
- 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 RPS6KA3 (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 NUP50 (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)
ENST00000379565RPS6KA3chrX20187519-ENST00000347635NUP50chr2245567480+634916512082988926
ENST00000379548RPS6KA3chrX20187519-ENST00000347635NUP50chr2245567480+60741376232713896
ENST00000540702RPS6KA3chrX20187519-ENST00000347635NUP50chr2245567480+620215041092841910

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
ENST00000379565ENST00000347635RPS6KA3chrX20187519-NUP50chr2245567480+6.88E-050.9999312
ENST00000379548ENST00000347635RPS6KA3chrX20187519-NUP50chr2245567480+7.35E-050.99992645
ENST00000540702ENST00000347635RPS6KA3chrX20187519-NUP50chr2245567480+0.0001149160.9998851

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 RPS6KA3-NUP50

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
RPS6KA3chrX20187519NUP50chr22455674801376451RYGQHPNIITLKDVGTFSMASEEVLK
RPS6KA3chrX20187519NUP50chr22455674801504465RYGQHPNIITLKDVGTFSMASEEVLK
RPS6KA3chrX20187519NUP50chr22455674801651481RYGQHPNIITLKDVGTFSMASEEVLK

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Potential FusionNeoAntigen Information of RPS6KA3-NUP50 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.
RPS6KA3-NUP50_20187519_45567480.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)
RPS6KA3-NUP50chrX20187519chr22455674801376HLA-B57:01ITLKDVGTF0.99580.8505817
RPS6KA3-NUP50chrX20187519chr22455674801376HLA-B15:17ITLKDVGTF0.99320.6846817
RPS6KA3-NUP50chrX20187519chr22455674801376HLA-B58:02ITLKDVGTF0.99220.7289817
RPS6KA3-NUP50chrX20187519chr22455674801376HLA-B57:03ITLKDVGTF0.99090.8355817
RPS6KA3-NUP50chrX20187519chr22455674801376HLA-B58:01ITLKDVGTF0.990.7817
RPS6KA3-NUP50chrX20187519chr22455674801376HLA-B39:01LKDVGTFSM0.98510.92241019
RPS6KA3-NUP50chrX20187519chr22455674801376HLA-B39:13LKDVGTFSM0.93570.93571019
RPS6KA3-NUP50chrX20187519chr22455674801376HLA-B15:10LKDVGTFSM0.80950.65211019
RPS6KA3-NUP50chrX20187519chr22455674801376HLA-B15:37LKDVGTFSM0.70.6591019
RPS6KA3-NUP50chrX20187519chr22455674801376HLA-B15:18LKDVGTFSM0.66520.7991019
RPS6KA3-NUP50chrX20187519chr22455674801376HLA-A32:13ITLKDVGTF0.59460.7857817
RPS6KA3-NUP50chrX20187519chr22455674801376HLA-B15:01TLKDVGTFSM0.99940.9293919
RPS6KA3-NUP50chrX20187519chr22455674801376HLA-B57:03IITLKDVGTF0.96510.7946717
RPS6KA3-NUP50chrX20187519chr22455674801376HLA-B15:02TLKDVGTFSM0.96350.9761919
RPS6KA3-NUP50chrX20187519chr22455674801376HLA-B39:09LKDVGTFSM0.98770.6121019
RPS6KA3-NUP50chrX20187519chr22455674801376HLA-B39:05LKDVGTFSM0.93780.90851019
RPS6KA3-NUP50chrX20187519chr22455674801376HLA-B39:08LKDVGTFSM0.67420.90721019
RPS6KA3-NUP50chrX20187519chr22455674801376HLA-B15:04TLKDVGTFSM0.99850.9519919
RPS6KA3-NUP50chrX20187519chr22455674801376HLA-B57:04ITLKDVGTF0.99670.581817
RPS6KA3-NUP50chrX20187519chr22455674801376HLA-B57:10ITLKDVGTF0.99580.8505817
RPS6KA3-NUP50chrX20187519chr22455674801376HLA-B58:06ITLKDVGTF0.99320.5531817
RPS6KA3-NUP50chrX20187519chr22455674801376HLA-B39:02LKDVGTFSM0.98640.93731019
RPS6KA3-NUP50chrX20187519chr22455674801376HLA-B39:31LKDVGTFSM0.98460.92281019
RPS6KA3-NUP50chrX20187519chr22455674801376HLA-B57:02ITLKDVGTF0.98130.6804817
RPS6KA3-NUP50chrX20187519chr22455674801376HLA-B15:24ITLKDVGTF0.97940.7147817
RPS6KA3-NUP50chrX20187519chr22455674801376HLA-A32:01ITLKDVGTF0.84790.8099817
RPS6KA3-NUP50chrX20187519chr22455674801376HLA-B39:11LKDVGTFSM0.7910.85631019
RPS6KA3-NUP50chrX20187519chr22455674801376HLA-B15:09LKDVGTFSM0.70370.71251019
RPS6KA3-NUP50chrX20187519chr22455674801376HLA-B15:33TLKDVGTFSM0.99940.9293919
RPS6KA3-NUP50chrX20187519chr22455674801376HLA-B15:34TLKDVGTFSM0.99940.9293919
RPS6KA3-NUP50chrX20187519chr22455674801376HLA-B15:125TLKDVGTFSM0.99940.9293919
RPS6KA3-NUP50chrX20187519chr22455674801376HLA-B15:50TLKDVGTFSM0.99930.9122919
RPS6KA3-NUP50chrX20187519chr22455674801376HLA-B15:73TLKDVGTFSM0.99460.8968919
RPS6KA3-NUP50chrX20187519chr22455674801376HLA-B15:30TLKDVGTFSM0.99270.8944919
RPS6KA3-NUP50chrX20187519chr22455674801376HLA-B57:02IITLKDVGTF0.95750.7311717

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Potential FusionNeoAntigen Information of RPS6KA3-NUP50 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.
RPS6KA3-NUP50_20187519_45567480.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)
RPS6KA3-NUP50chrX20187519chr22455674801376DRB1-0901KDVGTFSMASEEVLK1126
RPS6KA3-NUP50chrX20187519chr22455674801376DRB1-0904KDVGTFSMASEEVLK1126
RPS6KA3-NUP50chrX20187519chr22455674801376DRB1-0905KDVGTFSMASEEVLK1126
RPS6KA3-NUP50chrX20187519chr22455674801376DRB1-0907KDVGTFSMASEEVLK1126
RPS6KA3-NUP50chrX20187519chr22455674801376DRB1-0909KDVGTFSMASEEVLK1126

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Fusion breakpoint peptide structures of RPS6KA3-NUP50

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
6205NIITLKDVGTFSMARPS6KA3NUP50chrX20187519chr22455674801376

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of RPS6KA3-NUP50

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-B14:023BVN6205NIITLKDVGTFSMA-7.15543-7.26883
HLA-B14:023BVN6205NIITLKDVGTFSMA-4.77435-5.80965
HLA-B52:013W396205NIITLKDVGTFSMA-6.80875-6.92215
HLA-B52:013W396205NIITLKDVGTFSMA-4.20386-5.23916
HLA-A11:014UQ26205NIITLKDVGTFSMA-7.5194-8.5547
HLA-A11:014UQ26205NIITLKDVGTFSMA-6.9601-7.0735
HLA-A24:025HGA6205NIITLKDVGTFSMA-7.52403-7.63743
HLA-A24:025HGA6205NIITLKDVGTFSMA-5.82433-6.85963
HLA-B27:056PYJ6205NIITLKDVGTFSMA-3.28285-4.31815
HLA-B44:053DX86205NIITLKDVGTFSMA-5.91172-6.94702
HLA-B44:053DX86205NIITLKDVGTFSMA-4.24346-4.35686

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Vaccine Design for the FusionNeoAntigens of RPS6KA3-NUP50

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
RPS6KA3-NUP50chrX20187519chr22455674801019LKDVGTFSMCTAAAGGATGTGGGAACATTCTCCATG
RPS6KA3-NUP50chrX20187519chr2245567480717IITLKDVGTFATTATCACTCTAAAGGATGTGGGAACATTC
RPS6KA3-NUP50chrX20187519chr2245567480817ITLKDVGTFATCACTCTAAAGGATGTGGGAACATTC
RPS6KA3-NUP50chrX20187519chr2245567480919TLKDVGTFSMACTCTAAAGGATGTGGGAACATTCTCCATG

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
RPS6KA3-NUP50chrX20187519chr22455674801126KDVGTFSMASEEVLKAAGGATGTGGGAACATTCTCCATGGCCAGTGAGGAAGTCTTGAAG

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Information of the samples that have these potential fusion neoantigens of RPS6KA3-NUP50

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
ESCARPS6KA3-NUP50chrX20187519ENST00000379548chr2245567480ENST00000347635TCGA-IG-A97I

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Potential target of CAR-T therapy development for RPS6KA3-NUP50

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 RPS6KA3-NUP50

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 RPS6KA3-NUP50

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