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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:RPS24-CTNND1

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: RPS24-CTNND1
FusionPDB ID: 77662
FusionGDB2.0 ID: 77662
HgeneTgene
Gene symbol

RPS24

CTNND1

Gene ID

6229

100528016

Gene nameribosomal protein S24TMX2-CTNND1 readthrough (NMD candidate)
SynonymsDBA3|S24|eS24CAS|CTNND1|p120(cas)|p120(ctn)
Cytomap

10q22.3

11q12.1

Type of geneprotein-codingncRNA
Description40S ribosomal protein S24small ribosomal subunit protein eS24Cadherin-associated Src substrateCatenin delta-1TMX2-CTNND1 readthrough (non-protein coding)p120 catenin
Modification date2020031320200313
UniProtAcc.

O60716

Main function of 5'-partner protein: FUNCTION: Key regulator of cell-cell adhesion that associates with and regulates the cell adhesion properties of both C-, E- and N-cadherins, being critical for their surface stability (PubMed:14610055, PubMed:20371349). Beside cell-cell adhesion, regulates gene transcription through several transcription factors including ZBTB33/Kaiso2 and GLIS2, and the activity of Rho family GTPases and downstream cytoskeletal dynamics (PubMed:10207085, PubMed:20371349). Implicated both in cell transformation by SRC and in ligand-induced receptor signaling through the EGF, PDGF, CSF-1 and ERBB2 receptors (PubMed:17344476). {ECO:0000269|PubMed:10207085, ECO:0000269|PubMed:14610055, ECO:0000269|PubMed:17344476, ECO:0000269|PubMed:20371349}.
Ensembl transtripts involved in fusion geneENST idsENST00000476545, ENST00000360830, 
ENST00000372360, ENST00000435275, 
ENST00000440692, 		ENST00000358694, 
ENST00000360682, ENST00000361332, 
ENST00000361391, ENST00000361796, 
ENST00000399039, ENST00000399050, 
ENST00000415361, ENST00000426142, 
ENST00000428599, ENST00000524630, 
ENST00000525902, ENST00000526357, 
ENST00000526772, ENST00000526938, 
ENST00000527467, ENST00000528232, 
ENST00000528621, ENST00000529526, 
ENST00000529873, ENST00000529919, 
ENST00000529986, ENST00000530094, 
ENST00000530748, ENST00000531014, 
ENST00000532245, ENST00000532463, 
ENST00000532649, ENST00000532787, 
ENST00000532844, ENST00000533667, 
ENST00000534579, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score25 X 17 X 3=127517 X 21 X 10=3570
# samples 2625
** MAII scorelog2(26/1275*10)=-2.29391371871777
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(25/3570*10)=-3.83592407425437
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: RPS24 [Title/Abstract] AND CTNND1 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: RPS24 [Title/Abstract] AND CTNND1 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)RPS24(79797005)-CTNND1(57575966), # samples:1
Anticipated loss of major functional domain due to fusion event.RPS24-CTNND1 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.
RPS24-CTNND1 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


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/chr10:79797005/chr11:57575966)
- 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 RPS24 (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 CTNND1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


Top

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)
ENST00000435275RPS24chr1079797005-ENST00000524630CTNND1chr1157575966-43404781421101319
ENST00000435275RPS24chr1079797005-ENST00000529919CTNND1chr1157575966-27314781421098318
ENST00000435275RPS24chr1079797005-ENST00000399039CTNND1chr1157575966-31394781421098318
ENST00000435275RPS24chr1079797005-ENST00000360682CTNND1chr1157575966-39974781421125327
ENST00000435275RPS24chr1079797005-ENST00000361796CTNND1chr1157575966-39734781421101319
ENST00000435275RPS24chr1079797005-ENST00000361391CTNND1chr1157575966-39964781421125327
ENST00000435275RPS24chr1079797005-ENST00000530094CTNND1chr1157575966-40594781421188348
ENST00000435275RPS24chr1079797005-ENST00000428599CTNND1chr1157575966-39724781421101319
ENST00000435275RPS24chr1079797005-ENST00000361332CTNND1chr1157575966-40594781421188348
ENST00000435275RPS24chr1079797005-ENST00000527467CTNND1chr1157575966-40594781421188348
ENST00000435275RPS24chr1079797005-ENST00000415361CTNND1chr1157575966-40594781421188348
ENST00000435275RPS24chr1079797005-ENST00000532245CTNND1chr1157575966-39724781421101319
ENST00000435275RPS24chr1079797005-ENST00000532463CTNND1chr1157575966-39724781421101319
ENST00000435275RPS24chr1079797005-ENST00000528232CTNND1chr1157575966-39724781421101319
ENST00000435275RPS24chr1079797005-ENST00000529986CTNND1chr1157575966-39724781421101319
ENST00000435275RPS24chr1079797005-ENST00000531014CTNND1chr1157575966-40594781421188348
ENST00000435275RPS24chr1079797005-ENST00000358694CTNND1chr1157575966-39724781421101319
ENST00000435275RPS24chr1079797005-ENST00000526772CTNND1chr1157575966-39724781421101319
ENST00000435275RPS24chr1079797005-ENST00000532787CTNND1chr1157575966-39964781421125327
ENST00000435275RPS24chr1079797005-ENST00000533667CTNND1chr1157575966-39964781421125327
ENST00000435275RPS24chr1079797005-ENST00000529873CTNND1chr1157575966-39964781421125327
ENST00000435275RPS24chr1079797005-ENST00000525902CTNND1chr1157575966-39724781421101319
ENST00000435275RPS24chr1079797005-ENST00000529526CTNND1chr1157575966-39724781421101319
ENST00000435275RPS24chr1079797005-ENST00000532649CTNND1chr1157575966-39724781421101319
ENST00000435275RPS24chr1079797005-ENST00000426142CTNND1chr1157575966-39724781421101319
ENST00000435275RPS24chr1079797005-ENST00000532844CTNND1chr1157575966-40594781421188348
ENST00000435275RPS24chr1079797005-ENST00000528621CTNND1chr1157575966-39724781421101319
ENST00000435275RPS24chr1079797005-ENST00000399050CTNND1chr1157575966-40594781421188348
ENST00000435275RPS24chr1079797005-ENST00000526357CTNND1chr1157575966-40594781421188348
ENST00000435275RPS24chr1079797005-ENST00000530748CTNND1chr1157575966-39724781421101319
ENST00000435275RPS24chr1079797005-ENST00000534579CTNND1chr1157575966-39724781421101319
ENST00000435275RPS24chr1079797005-ENST00000526938CTNND1chr1157575966-14484781421038298
ENST00000440692RPS24chr1079797005-ENST00000524630CTNND1chr1157575966-43404781421101319
ENST00000440692RPS24chr1079797005-ENST00000529919CTNND1chr1157575966-27314781421098318
ENST00000440692RPS24chr1079797005-ENST00000399039CTNND1chr1157575966-31394781421098318
ENST00000440692RPS24chr1079797005-ENST00000360682CTNND1chr1157575966-39974781421125327
ENST00000440692RPS24chr1079797005-ENST00000361796CTNND1chr1157575966-39734781421101319
ENST00000440692RPS24chr1079797005-ENST00000361391CTNND1chr1157575966-39964781421125327
ENST00000440692RPS24chr1079797005-ENST00000530094CTNND1chr1157575966-40594781421188348
ENST00000440692RPS24chr1079797005-ENST00000428599CTNND1chr1157575966-39724781421101319
ENST00000440692RPS24chr1079797005-ENST00000361332CTNND1chr1157575966-40594781421188348
ENST00000440692RPS24chr1079797005-ENST00000527467CTNND1chr1157575966-40594781421188348
ENST00000440692RPS24chr1079797005-ENST00000415361CTNND1chr1157575966-40594781421188348
ENST00000440692RPS24chr1079797005-ENST00000532245CTNND1chr1157575966-39724781421101319
ENST00000440692RPS24chr1079797005-ENST00000532463CTNND1chr1157575966-39724781421101319
ENST00000440692RPS24chr1079797005-ENST00000528232CTNND1chr1157575966-39724781421101319
ENST00000440692RPS24chr1079797005-ENST00000529986CTNND1chr1157575966-39724781421101319
ENST00000440692RPS24chr1079797005-ENST00000531014CTNND1chr1157575966-40594781421188348
ENST00000440692RPS24chr1079797005-ENST00000358694CTNND1chr1157575966-39724781421101319
ENST00000440692RPS24chr1079797005-ENST00000526772CTNND1chr1157575966-39724781421101319
ENST00000440692RPS24chr1079797005-ENST00000532787CTNND1chr1157575966-39964781421125327
ENST00000440692RPS24chr1079797005-ENST00000533667CTNND1chr1157575966-39964781421125327
ENST00000440692RPS24chr1079797005-ENST00000529873CTNND1chr1157575966-39964781421125327
ENST00000440692RPS24chr1079797005-ENST00000525902CTNND1chr1157575966-39724781421101319
ENST00000440692RPS24chr1079797005-ENST00000529526CTNND1chr1157575966-39724781421101319
ENST00000440692RPS24chr1079797005-ENST00000532649CTNND1chr1157575966-39724781421101319
ENST00000440692RPS24chr1079797005-ENST00000426142CTNND1chr1157575966-39724781421101319
ENST00000440692RPS24chr1079797005-ENST00000532844CTNND1chr1157575966-40594781421188348
ENST00000440692RPS24chr1079797005-ENST00000528621CTNND1chr1157575966-39724781421101319
ENST00000440692RPS24chr1079797005-ENST00000399050CTNND1chr1157575966-40594781421188348
ENST00000440692RPS24chr1079797005-ENST00000526357CTNND1chr1157575966-40594781421188348
ENST00000440692RPS24chr1079797005-ENST00000530748CTNND1chr1157575966-39724781421101319
ENST00000440692RPS24chr1079797005-ENST00000534579CTNND1chr1157575966-39724781421101319
ENST00000440692RPS24chr1079797005-ENST00000526938CTNND1chr1157575966-14484781421038298
ENST00000372360RPS24chr1079797005-ENST00000524630CTNND1chr1157575966-423537337996319
ENST00000372360RPS24chr1079797005-ENST00000529919CTNND1chr1157575966-262637337993318
ENST00000372360RPS24chr1079797005-ENST00000399039CTNND1chr1157575966-303437337993318
ENST00000372360RPS24chr1079797005-ENST00000360682CTNND1chr1157575966-3892373371020327
ENST00000372360RPS24chr1079797005-ENST00000361796CTNND1chr1157575966-386837337996319
ENST00000372360RPS24chr1079797005-ENST00000361391CTNND1chr1157575966-3891373371020327
ENST00000372360RPS24chr1079797005-ENST00000530094CTNND1chr1157575966-3954373371083348
ENST00000372360RPS24chr1079797005-ENST00000428599CTNND1chr1157575966-386737337996319
ENST00000372360RPS24chr1079797005-ENST00000361332CTNND1chr1157575966-3954373371083348
ENST00000372360RPS24chr1079797005-ENST00000527467CTNND1chr1157575966-3954373371083348
ENST00000372360RPS24chr1079797005-ENST00000415361CTNND1chr1157575966-3954373371083348
ENST00000372360RPS24chr1079797005-ENST00000532245CTNND1chr1157575966-386737337996319
ENST00000372360RPS24chr1079797005-ENST00000532463CTNND1chr1157575966-386737337996319
ENST00000372360RPS24chr1079797005-ENST00000528232CTNND1chr1157575966-386737337996319
ENST00000372360RPS24chr1079797005-ENST00000529986CTNND1chr1157575966-386737337996319
ENST00000372360RPS24chr1079797005-ENST00000531014CTNND1chr1157575966-3954373371083348
ENST00000372360RPS24chr1079797005-ENST00000358694CTNND1chr1157575966-386737337996319
ENST00000372360RPS24chr1079797005-ENST00000526772CTNND1chr1157575966-386737337996319
ENST00000372360RPS24chr1079797005-ENST00000532787CTNND1chr1157575966-3891373371020327
ENST00000372360RPS24chr1079797005-ENST00000533667CTNND1chr1157575966-3891373371020327
ENST00000372360RPS24chr1079797005-ENST00000529873CTNND1chr1157575966-3891373371020327
ENST00000372360RPS24chr1079797005-ENST00000525902CTNND1chr1157575966-386737337996319
ENST00000372360RPS24chr1079797005-ENST00000529526CTNND1chr1157575966-386737337996319
ENST00000372360RPS24chr1079797005-ENST00000532649CTNND1chr1157575966-386737337996319
ENST00000372360RPS24chr1079797005-ENST00000426142CTNND1chr1157575966-386737337996319
ENST00000372360RPS24chr1079797005-ENST00000532844CTNND1chr1157575966-3954373371083348
ENST00000372360RPS24chr1079797005-ENST00000528621CTNND1chr1157575966-386737337996319
ENST00000372360RPS24chr1079797005-ENST00000399050CTNND1chr1157575966-3954373371083348
ENST00000372360RPS24chr1079797005-ENST00000526357CTNND1chr1157575966-3954373371083348
ENST00000372360RPS24chr1079797005-ENST00000530748CTNND1chr1157575966-386737337996319
ENST00000372360RPS24chr1079797005-ENST00000534579CTNND1chr1157575966-386737337996319
ENST00000372360RPS24chr1079797005-ENST00000526938CTNND1chr1157575966-134337337933298
ENST00000360830RPS24chr1079797005-ENST00000524630CTNND1chr1157575966-421735519978319
ENST00000360830RPS24chr1079797005-ENST00000529919CTNND1chr1157575966-260835519975318
ENST00000360830RPS24chr1079797005-ENST00000399039CTNND1chr1157575966-301635519975318
ENST00000360830RPS24chr1079797005-ENST00000360682CTNND1chr1157575966-3874355191002327
ENST00000360830RPS24chr1079797005-ENST00000361796CTNND1chr1157575966-385035519978319
ENST00000360830RPS24chr1079797005-ENST00000361391CTNND1chr1157575966-3873355191002327
ENST00000360830RPS24chr1079797005-ENST00000530094CTNND1chr1157575966-3936355191065348
ENST00000360830RPS24chr1079797005-ENST00000428599CTNND1chr1157575966-384935519978319
ENST00000360830RPS24chr1079797005-ENST00000361332CTNND1chr1157575966-3936355191065348
ENST00000360830RPS24chr1079797005-ENST00000527467CTNND1chr1157575966-3936355191065348
ENST00000360830RPS24chr1079797005-ENST00000415361CTNND1chr1157575966-3936355191065348
ENST00000360830RPS24chr1079797005-ENST00000532245CTNND1chr1157575966-384935519978319
ENST00000360830RPS24chr1079797005-ENST00000532463CTNND1chr1157575966-384935519978319
ENST00000360830RPS24chr1079797005-ENST00000528232CTNND1chr1157575966-384935519978319
ENST00000360830RPS24chr1079797005-ENST00000529986CTNND1chr1157575966-384935519978319
ENST00000360830RPS24chr1079797005-ENST00000531014CTNND1chr1157575966-3936355191065348
ENST00000360830RPS24chr1079797005-ENST00000358694CTNND1chr1157575966-384935519978319
ENST00000360830RPS24chr1079797005-ENST00000526772CTNND1chr1157575966-384935519978319
ENST00000360830RPS24chr1079797005-ENST00000532787CTNND1chr1157575966-3873355191002327
ENST00000360830RPS24chr1079797005-ENST00000533667CTNND1chr1157575966-3873355191002327
ENST00000360830RPS24chr1079797005-ENST00000529873CTNND1chr1157575966-3873355191002327
ENST00000360830RPS24chr1079797005-ENST00000525902CTNND1chr1157575966-384935519978319
ENST00000360830RPS24chr1079797005-ENST00000529526CTNND1chr1157575966-384935519978319
ENST00000360830RPS24chr1079797005-ENST00000532649CTNND1chr1157575966-384935519978319
ENST00000360830RPS24chr1079797005-ENST00000426142CTNND1chr1157575966-384935519978319
ENST00000360830RPS24chr1079797005-ENST00000532844CTNND1chr1157575966-3936355191065348
ENST00000360830RPS24chr1079797005-ENST00000528621CTNND1chr1157575966-384935519978319
ENST00000360830RPS24chr1079797005-ENST00000399050CTNND1chr1157575966-3936355191065348
ENST00000360830RPS24chr1079797005-ENST00000526357CTNND1chr1157575966-3936355191065348
ENST00000360830RPS24chr1079797005-ENST00000530748CTNND1chr1157575966-384935519978319
ENST00000360830RPS24chr1079797005-ENST00000534579CTNND1chr1157575966-384935519978319
ENST00000360830RPS24chr1079797005-ENST00000526938CTNND1chr1157575966-132535519915298

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
ENST00000435275ENST00000524630RPS24chr1079797005-CTNND1chr1157575966-0.0005430560.99945694
ENST00000435275ENST00000529919RPS24chr1079797005-CTNND1chr1157575966-0.0011658860.9988341
ENST00000435275ENST00000399039RPS24chr1079797005-CTNND1chr1157575966-0.00096890.99903107
ENST00000435275ENST00000360682RPS24chr1079797005-CTNND1chr1157575966-0.0005596170.9994404
ENST00000435275ENST00000361796RPS24chr1079797005-CTNND1chr1157575966-0.0006103050.99938965
ENST00000435275ENST00000361391RPS24chr1079797005-CTNND1chr1157575966-0.0005714850.99942845
ENST00000435275ENST00000530094RPS24chr1079797005-CTNND1chr1157575966-0.0004691240.9995309
ENST00000435275ENST00000428599RPS24chr1079797005-CTNND1chr1157575966-0.0006220450.99937797
ENST00000435275ENST00000361332RPS24chr1079797005-CTNND1chr1157575966-0.0004691240.9995309
ENST00000435275ENST00000527467RPS24chr1079797005-CTNND1chr1157575966-0.0004691240.9995309
ENST00000435275ENST00000415361RPS24chr1079797005-CTNND1chr1157575966-0.0004691240.9995309
ENST00000435275ENST00000532245RPS24chr1079797005-CTNND1chr1157575966-0.0006220450.99937797
ENST00000435275ENST00000532463RPS24chr1079797005-CTNND1chr1157575966-0.0006220450.99937797
ENST00000435275ENST00000528232RPS24chr1079797005-CTNND1chr1157575966-0.0006220450.99937797
ENST00000435275ENST00000529986RPS24chr1079797005-CTNND1chr1157575966-0.0006220450.99937797
ENST00000435275ENST00000531014RPS24chr1079797005-CTNND1chr1157575966-0.0004691240.9995309
ENST00000435275ENST00000358694RPS24chr1079797005-CTNND1chr1157575966-0.0006220450.99937797
ENST00000435275ENST00000526772RPS24chr1079797005-CTNND1chr1157575966-0.0006220450.99937797
ENST00000435275ENST00000532787RPS24chr1079797005-CTNND1chr1157575966-0.0005714850.99942845
ENST00000435275ENST00000533667RPS24chr1079797005-CTNND1chr1157575966-0.0005714850.99942845
ENST00000435275ENST00000529873RPS24chr1079797005-CTNND1chr1157575966-0.0005714850.99942845
ENST00000435275ENST00000525902RPS24chr1079797005-CTNND1chr1157575966-0.0006220450.99937797
ENST00000435275ENST00000529526RPS24chr1079797005-CTNND1chr1157575966-0.0006220450.99937797
ENST00000435275ENST00000532649RPS24chr1079797005-CTNND1chr1157575966-0.0006220450.99937797
ENST00000435275ENST00000426142RPS24chr1079797005-CTNND1chr1157575966-0.0006220450.99937797
ENST00000435275ENST00000532844RPS24chr1079797005-CTNND1chr1157575966-0.0004691240.9995309
ENST00000435275ENST00000528621RPS24chr1079797005-CTNND1chr1157575966-0.0006220450.99937797
ENST00000435275ENST00000399050RPS24chr1079797005-CTNND1chr1157575966-0.0004691240.9995309
ENST00000435275ENST00000526357RPS24chr1079797005-CTNND1chr1157575966-0.0004691240.9995309
ENST00000435275ENST00000530748RPS24chr1079797005-CTNND1chr1157575966-0.0006220450.99937797
ENST00000435275ENST00000534579RPS24chr1079797005-CTNND1chr1157575966-0.0006220450.99937797
ENST00000435275ENST00000526938RPS24chr1079797005-CTNND1chr1157575966-0.0007941590.9992059
ENST00000440692ENST00000524630RPS24chr1079797005-CTNND1chr1157575966-0.0005430560.99945694
ENST00000440692ENST00000529919RPS24chr1079797005-CTNND1chr1157575966-0.0011658860.9988341
ENST00000440692ENST00000399039RPS24chr1079797005-CTNND1chr1157575966-0.00096890.99903107
ENST00000440692ENST00000360682RPS24chr1079797005-CTNND1chr1157575966-0.0005596170.9994404
ENST00000440692ENST00000361796RPS24chr1079797005-CTNND1chr1157575966-0.0006103050.99938965
ENST00000440692ENST00000361391RPS24chr1079797005-CTNND1chr1157575966-0.0005714850.99942845
ENST00000440692ENST00000530094RPS24chr1079797005-CTNND1chr1157575966-0.0004691240.9995309
ENST00000440692ENST00000428599RPS24chr1079797005-CTNND1chr1157575966-0.0006220450.99937797
ENST00000440692ENST00000361332RPS24chr1079797005-CTNND1chr1157575966-0.0004691240.9995309
ENST00000440692ENST00000527467RPS24chr1079797005-CTNND1chr1157575966-0.0004691240.9995309
ENST00000440692ENST00000415361RPS24chr1079797005-CTNND1chr1157575966-0.0004691240.9995309
ENST00000440692ENST00000532245RPS24chr1079797005-CTNND1chr1157575966-0.0006220450.99937797
ENST00000440692ENST00000532463RPS24chr1079797005-CTNND1chr1157575966-0.0006220450.99937797
ENST00000440692ENST00000528232RPS24chr1079797005-CTNND1chr1157575966-0.0006220450.99937797
ENST00000440692ENST00000529986RPS24chr1079797005-CTNND1chr1157575966-0.0006220450.99937797
ENST00000440692ENST00000531014RPS24chr1079797005-CTNND1chr1157575966-0.0004691240.9995309
ENST00000440692ENST00000358694RPS24chr1079797005-CTNND1chr1157575966-0.0006220450.99937797
ENST00000440692ENST00000526772RPS24chr1079797005-CTNND1chr1157575966-0.0006220450.99937797
ENST00000440692ENST00000532787RPS24chr1079797005-CTNND1chr1157575966-0.0005714850.99942845
ENST00000440692ENST00000533667RPS24chr1079797005-CTNND1chr1157575966-0.0005714850.99942845
ENST00000440692ENST00000529873RPS24chr1079797005-CTNND1chr1157575966-0.0005714850.99942845
ENST00000440692ENST00000525902RPS24chr1079797005-CTNND1chr1157575966-0.0006220450.99937797
ENST00000440692ENST00000529526RPS24chr1079797005-CTNND1chr1157575966-0.0006220450.99937797
ENST00000440692ENST00000532649RPS24chr1079797005-CTNND1chr1157575966-0.0006220450.99937797
ENST00000440692ENST00000426142RPS24chr1079797005-CTNND1chr1157575966-0.0006220450.99937797
ENST00000440692ENST00000532844RPS24chr1079797005-CTNND1chr1157575966-0.0004691240.9995309
ENST00000440692ENST00000528621RPS24chr1079797005-CTNND1chr1157575966-0.0006220450.99937797
ENST00000440692ENST00000399050RPS24chr1079797005-CTNND1chr1157575966-0.0004691240.9995309
ENST00000440692ENST00000526357RPS24chr1079797005-CTNND1chr1157575966-0.0004691240.9995309
ENST00000440692ENST00000530748RPS24chr1079797005-CTNND1chr1157575966-0.0006220450.99937797
ENST00000440692ENST00000534579RPS24chr1079797005-CTNND1chr1157575966-0.0006220450.99937797
ENST00000440692ENST00000526938RPS24chr1079797005-CTNND1chr1157575966-0.0007941590.9992059
ENST00000372360ENST00000524630RPS24chr1079797005-CTNND1chr1157575966-0.0005489550.9994511
ENST00000372360ENST00000529919RPS24chr1079797005-CTNND1chr1157575966-0.0013372690.9986627
ENST00000372360ENST00000399039RPS24chr1079797005-CTNND1chr1157575966-0.0009654880.9990345
ENST00000372360ENST00000360682RPS24chr1079797005-CTNND1chr1157575966-0.0005688950.9994311
ENST00000372360ENST00000361796RPS24chr1079797005-CTNND1chr1157575966-0.0006166260.99938333
ENST00000372360ENST00000361391RPS24chr1079797005-CTNND1chr1157575966-0.0005810780.999419
ENST00000372360ENST00000530094RPS24chr1079797005-CTNND1chr1157575966-0.000473750.99952626
ENST00000372360ENST00000428599RPS24chr1079797005-CTNND1chr1157575966-0.000629490.9993705
ENST00000372360ENST00000361332RPS24chr1079797005-CTNND1chr1157575966-0.000473750.99952626
ENST00000372360ENST00000527467RPS24chr1079797005-CTNND1chr1157575966-0.000473750.99952626
ENST00000372360ENST00000415361RPS24chr1079797005-CTNND1chr1157575966-0.000473750.99952626
ENST00000372360ENST00000532245RPS24chr1079797005-CTNND1chr1157575966-0.000629490.9993705
ENST00000372360ENST00000532463RPS24chr1079797005-CTNND1chr1157575966-0.000629490.9993705
ENST00000372360ENST00000528232RPS24chr1079797005-CTNND1chr1157575966-0.000629490.9993705
ENST00000372360ENST00000529986RPS24chr1079797005-CTNND1chr1157575966-0.000629490.9993705
ENST00000372360ENST00000531014RPS24chr1079797005-CTNND1chr1157575966-0.000473750.99952626
ENST00000372360ENST00000358694RPS24chr1079797005-CTNND1chr1157575966-0.000629490.9993705
ENST00000372360ENST00000526772RPS24chr1079797005-CTNND1chr1157575966-0.000629490.9993705
ENST00000372360ENST00000532787RPS24chr1079797005-CTNND1chr1157575966-0.0005810780.999419
ENST00000372360ENST00000533667RPS24chr1079797005-CTNND1chr1157575966-0.0005810780.999419
ENST00000372360ENST00000529873RPS24chr1079797005-CTNND1chr1157575966-0.0005810780.999419
ENST00000372360ENST00000525902RPS24chr1079797005-CTNND1chr1157575966-0.000629490.9993705
ENST00000372360ENST00000529526RPS24chr1079797005-CTNND1chr1157575966-0.000629490.9993705
ENST00000372360ENST00000532649RPS24chr1079797005-CTNND1chr1157575966-0.000629490.9993705
ENST00000372360ENST00000426142RPS24chr1079797005-CTNND1chr1157575966-0.000629490.9993705
ENST00000372360ENST00000532844RPS24chr1079797005-CTNND1chr1157575966-0.000473750.99952626
ENST00000372360ENST00000528621RPS24chr1079797005-CTNND1chr1157575966-0.000629490.9993705
ENST00000372360ENST00000399050RPS24chr1079797005-CTNND1chr1157575966-0.000473750.99952626
ENST00000372360ENST00000526357RPS24chr1079797005-CTNND1chr1157575966-0.000473750.99952626
ENST00000372360ENST00000530748RPS24chr1079797005-CTNND1chr1157575966-0.000629490.9993705
ENST00000372360ENST00000534579RPS24chr1079797005-CTNND1chr1157575966-0.000629490.9993705
ENST00000372360ENST00000526938RPS24chr1079797005-CTNND1chr1157575966-0.0008893370.99911064
ENST00000360830ENST00000524630RPS24chr1079797005-CTNND1chr1157575966-0.0005445970.9994554
ENST00000360830ENST00000529919RPS24chr1079797005-CTNND1chr1157575966-0.0012870370.998713
ENST00000360830ENST00000399039RPS24chr1079797005-CTNND1chr1157575966-0.0009618990.9990381
ENST00000360830ENST00000360682RPS24chr1079797005-CTNND1chr1157575966-0.0005643580.9994356
ENST00000360830ENST00000361796RPS24chr1079797005-CTNND1chr1157575966-0.0006120990.99938786
ENST00000360830ENST00000361391RPS24chr1079797005-CTNND1chr1157575966-0.0005764270.9994236
ENST00000360830ENST00000530094RPS24chr1079797005-CTNND1chr1157575966-0.0004705420.9995295
ENST00000360830ENST00000428599RPS24chr1079797005-CTNND1chr1157575966-0.0006248550.99937516
ENST00000360830ENST00000361332RPS24chr1079797005-CTNND1chr1157575966-0.0004705420.9995295
ENST00000360830ENST00000527467RPS24chr1079797005-CTNND1chr1157575966-0.0004705420.9995295
ENST00000360830ENST00000415361RPS24chr1079797005-CTNND1chr1157575966-0.0004705420.9995295
ENST00000360830ENST00000532245RPS24chr1079797005-CTNND1chr1157575966-0.0006248550.99937516
ENST00000360830ENST00000532463RPS24chr1079797005-CTNND1chr1157575966-0.0006248550.99937516
ENST00000360830ENST00000528232RPS24chr1079797005-CTNND1chr1157575966-0.0006248550.99937516
ENST00000360830ENST00000529986RPS24chr1079797005-CTNND1chr1157575966-0.0006248550.99937516
ENST00000360830ENST00000531014RPS24chr1079797005-CTNND1chr1157575966-0.0004705420.9995295
ENST00000360830ENST00000358694RPS24chr1079797005-CTNND1chr1157575966-0.0006248550.99937516
ENST00000360830ENST00000526772RPS24chr1079797005-CTNND1chr1157575966-0.0006248550.99937516
ENST00000360830ENST00000532787RPS24chr1079797005-CTNND1chr1157575966-0.0005764270.9994236
ENST00000360830ENST00000533667RPS24chr1079797005-CTNND1chr1157575966-0.0005764270.9994236
ENST00000360830ENST00000529873RPS24chr1079797005-CTNND1chr1157575966-0.0005764270.9994236
ENST00000360830ENST00000525902RPS24chr1079797005-CTNND1chr1157575966-0.0006248550.99937516
ENST00000360830ENST00000529526RPS24chr1079797005-CTNND1chr1157575966-0.0006248550.99937516
ENST00000360830ENST00000532649RPS24chr1079797005-CTNND1chr1157575966-0.0006248550.99937516
ENST00000360830ENST00000426142RPS24chr1079797005-CTNND1chr1157575966-0.0006248550.99937516
ENST00000360830ENST00000532844RPS24chr1079797005-CTNND1chr1157575966-0.0004705420.9995295
ENST00000360830ENST00000528621RPS24chr1079797005-CTNND1chr1157575966-0.0006248550.99937516
ENST00000360830ENST00000399050RPS24chr1079797005-CTNND1chr1157575966-0.0004705420.9995295
ENST00000360830ENST00000526357RPS24chr1079797005-CTNND1chr1157575966-0.0004705420.9995295
ENST00000360830ENST00000530748RPS24chr1079797005-CTNND1chr1157575966-0.0006248550.99937516
ENST00000360830ENST00000534579RPS24chr1079797005-CTNND1chr1157575966-0.0006248550.99937516
ENST00000360830ENST00000526938RPS24chr1079797005-CTNND1chr1157575966-0.0009245420.9990754

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 RPS24-CTNND1

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
RPS24chr1079797005CTNND1chr1157575966355112RGTAKANVGAGKKALRNLAVDARNKE
RPS24chr1079797005CTNND1chr1157575966373112RGTAKANVGAGKKALRNLAVDARNKE
RPS24chr1079797005CTNND1chr1157575966478112RGTAKANVGAGKKALRNLAVDARNKE

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Potential FusionNeoAntigen Information of RPS24-CTNND1 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.

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)

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Potential FusionNeoAntigen Information of RPS24-CTNND1 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.
RPS24-CTNND1_79797005_57575966.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)
RPS24-CTNND1chr1079797005chr1157575966355DRB1-1452KKALRNLAVDARNKE1126
RPS24-CTNND1chr1079797005chr1157575966355DRB4-0101KKALRNLAVDARNKE1126
RPS24-CTNND1chr1079797005chr1157575966355DRB4-0101GKKALRNLAVDARNK1025
RPS24-CTNND1chr1079797005chr1157575966355DRB4-0103KKALRNLAVDARNKE1126
RPS24-CTNND1chr1079797005chr1157575966355DRB4-0103GKKALRNLAVDARNK1025
RPS24-CTNND1chr1079797005chr1157575966355DRB4-0104KKALRNLAVDARNKE1126
RPS24-CTNND1chr1079797005chr1157575966355DRB4-0104GKKALRNLAVDARNK1025
RPS24-CTNND1chr1079797005chr1157575966355DRB4-0104AGKKALRNLAVDARN924
RPS24-CTNND1chr1079797005chr1157575966355DRB4-0106KKALRNLAVDARNKE1126
RPS24-CTNND1chr1079797005chr1157575966355DRB4-0106GKKALRNLAVDARNK1025
RPS24-CTNND1chr1079797005chr1157575966355DRB4-0107KKALRNLAVDARNKE1126
RPS24-CTNND1chr1079797005chr1157575966355DRB4-0107GKKALRNLAVDARNK1025
RPS24-CTNND1chr1079797005chr1157575966355DRB4-0108KKALRNLAVDARNKE1126
RPS24-CTNND1chr1079797005chr1157575966355DRB4-0108GKKALRNLAVDARNK1025

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Fusion breakpoint peptide structures of RPS24-CTNND1

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.

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of RPS24-CTNND1

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

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Vaccine Design for the FusionNeoAntigens of RPS24-CTNND1

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

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
RPS24-CTNND1chr1079797005chr11575759661025GKKALRNLAVDARNKGGCAAAAAGGCACTGAGAAACCTGGCTGTGGATGCTCGCAACAAA
RPS24-CTNND1chr1079797005chr11575759661126KKALRNLAVDARNKEAAAAAGGCACTGAGAAACCTGGCTGTGGATGCTCGCAACAAAGAA
RPS24-CTNND1chr1079797005chr1157575966924AGKKALRNLAVDARNGCTGGCAAAAAGGCACTGAGAAACCTGGCTGTGGATGCTCGCAAC

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Information of the samples that have these potential fusion neoantigens of RPS24-CTNND1

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

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Potential target of CAR-T therapy development for RPS24-CTNND1

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 RPS24-CTNND1

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 RPS24-CTNND1

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