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Fusion Protein:PPP2R5C-TRAF3IP3

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: PPP2R5C-TRAF3IP3
	FusionPDB ID: 68086
	FusionGDB2.0 ID: 68086
		Hgene	Tgene
	Gene symbol	PPP2R5C	TRAF3IP3
	Gene ID	5527	80342
	Gene name	protein phosphatase 2 regulatory subunit B'gamma	TRAF3 interacting protein 3
	Synonyms	B56G\|B56gamma\|PR61G	T3JAM
	Cytomap	14q32.31	1q32.2
	Type of gene	protein-coding	protein-coding
	Description	serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoformB' alpha regulatory subunitPP2A B subunit isoform B'-gammaPP2A B subunit isoform B56-gammaPP2A B subunit isoform PR61-gammaPP2A B subunit isoform R5-gammaprotein phosphat	TRAF3-interacting JNK-activating modulatorTRAF3 interacting Jun N terminal kinase (JNK) activating modulator
	Modification date	20200313	20200313
	UniProtAcc	.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000328724, ENST00000334743, ENST00000350249, ENST00000422945, ENST00000445439, ENST00000557095, ENST00000554442, ENST00000556068, ENST00000556260, ENST00000556946, ENST00000557714,	ENST00000467830, ENST00000010338, ENST00000367023, ENST00000367024, ENST00000367025, ENST00000367026, ENST00000400959, ENST00000477431,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	18 X 11 X 8=1584	4 X 4 X 3=48
	# samples	19	4
	** MAII score	log2(19/1584*10)=-3.05950101174866 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(4/48*10)=-0.263034405833794 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: PPP2R5C [Title/Abstract] AND TRAF3IP3 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: PPP2R5C [Title/Abstract] AND TRAF3IP3 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	PPP2R5C(102323222)-TRAF3IP3(209950697), # samples:1
Anticipated loss of major functional domain due to fusion event.	PPP2R5C-TRAF3IP3 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. PPP2R5C-TRAF3IP3 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)

Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner	Gene	GO ID	GO term	PubMed ID
Hgene	PPP2R5C	GO:0008285	negative regulation of cell proliferation	17245430

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr14:102323222/chr1:209950697)
- 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.

Retention 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.

Fusion gene breakpoints across PPP2R5C (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Fusion gene breakpoints across TRAF3IP3 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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Fusion Amino Acid Sequences

Fusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.

Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	Seq length (transcript)	BP loci (transcript)	Predicted start (transcript)	Predicted stop (transcript)	Seq length (amino acids)
ENST00000422945	PPP2R5C	chr14	102323222	+	ENST00000400959	TRAF3IP3	chr1	209950697	+	907	483	96	704	202
ENST00000422945	PPP2R5C	chr14	102323222	+	ENST00000367025	TRAF3IP3	chr1	209950697	+	1253	483	96	1085	329
ENST00000422945	PPP2R5C	chr14	102323222	+	ENST00000367026	TRAF3IP3	chr1	209950697	+	1258	483	96	1085	329
ENST00000422945	PPP2R5C	chr14	102323222	+	ENST00000367024	TRAF3IP3	chr1	209950697	+	1245	483	96	1085	329
ENST00000422945	PPP2R5C	chr14	102323222	+	ENST00000010338	TRAF3IP3	chr1	209950697	+	1257	483	96	1085	329
ENST00000422945	PPP2R5C	chr14	102323222	+	ENST00000367023	TRAF3IP3	chr1	209950697	+	1024	483	96	770	224
ENST00000422945	PPP2R5C	chr14	102323222	+	ENST00000477431	TRAF3IP3	chr1	209950697	+	877	483	96	692	198
ENST00000328724	PPP2R5C	chr14	102323222	+	ENST00000400959	TRAF3IP3	chr1	209950697	+	892	468	9	689	226
ENST00000328724	PPP2R5C	chr14	102323222	+	ENST00000367025	TRAF3IP3	chr1	209950697	+	1238	468	9	1070	353
ENST00000328724	PPP2R5C	chr14	102323222	+	ENST00000367026	TRAF3IP3	chr1	209950697	+	1243	468	9	1070	353
ENST00000328724	PPP2R5C	chr14	102323222	+	ENST00000367024	TRAF3IP3	chr1	209950697	+	1230	468	9	1070	353
ENST00000328724	PPP2R5C	chr14	102323222	+	ENST00000010338	TRAF3IP3	chr1	209950697	+	1242	468	9	1070	353
ENST00000328724	PPP2R5C	chr14	102323222	+	ENST00000367023	TRAF3IP3	chr1	209950697	+	1009	468	9	755	248
ENST00000328724	PPP2R5C	chr14	102323222	+	ENST00000477431	TRAF3IP3	chr1	209950697	+	862	468	9	677	222
ENST00000350249	PPP2R5C	chr14	102323222	+	ENST00000400959	TRAF3IP3	chr1	209950697	+	858	434	140	655	171
ENST00000350249	PPP2R5C	chr14	102323222	+	ENST00000367025	TRAF3IP3	chr1	209950697	+	1204	434	140	1036	298
ENST00000350249	PPP2R5C	chr14	102323222	+	ENST00000367026	TRAF3IP3	chr1	209950697	+	1209	434	140	1036	298
ENST00000350249	PPP2R5C	chr14	102323222	+	ENST00000367024	TRAF3IP3	chr1	209950697	+	1196	434	140	1036	298
ENST00000350249	PPP2R5C	chr14	102323222	+	ENST00000010338	TRAF3IP3	chr1	209950697	+	1208	434	140	1036	298
ENST00000350249	PPP2R5C	chr14	102323222	+	ENST00000367023	TRAF3IP3	chr1	209950697	+	975	434	140	721	193
ENST00000350249	PPP2R5C	chr14	102323222	+	ENST00000477431	TRAF3IP3	chr1	209950697	+	828	434	140	643	167
ENST00000445439	PPP2R5C	chr14	102323222	+	ENST00000400959	TRAF3IP3	chr1	209950697	+	766	342	48	563	171
ENST00000445439	PPP2R5C	chr14	102323222	+	ENST00000367025	TRAF3IP3	chr1	209950697	+	1112	342	48	944	298
ENST00000445439	PPP2R5C	chr14	102323222	+	ENST00000367026	TRAF3IP3	chr1	209950697	+	1117	342	48	944	298
ENST00000445439	PPP2R5C	chr14	102323222	+	ENST00000367024	TRAF3IP3	chr1	209950697	+	1104	342	48	944	298
ENST00000445439	PPP2R5C	chr14	102323222	+	ENST00000010338	TRAF3IP3	chr1	209950697	+	1116	342	48	944	298
ENST00000445439	PPP2R5C	chr14	102323222	+	ENST00000367023	TRAF3IP3	chr1	209950697	+	883	342	48	629	193
ENST00000445439	PPP2R5C	chr14	102323222	+	ENST00000477431	TRAF3IP3	chr1	209950697	+	736	342	48	551	167
ENST00000334743	PPP2R5C	chr14	102323222	+	ENST00000400959	TRAF3IP3	chr1	209950697	+	766	342	48	563	171
ENST00000334743	PPP2R5C	chr14	102323222	+	ENST00000367025	TRAF3IP3	chr1	209950697	+	1112	342	48	944	298
ENST00000334743	PPP2R5C	chr14	102323222	+	ENST00000367026	TRAF3IP3	chr1	209950697	+	1117	342	48	944	298
ENST00000334743	PPP2R5C	chr14	102323222	+	ENST00000367024	TRAF3IP3	chr1	209950697	+	1104	342	48	944	298
ENST00000334743	PPP2R5C	chr14	102323222	+	ENST00000010338	TRAF3IP3	chr1	209950697	+	1116	342	48	944	298
ENST00000334743	PPP2R5C	chr14	102323222	+	ENST00000367023	TRAF3IP3	chr1	209950697	+	883	342	48	629	193
ENST00000334743	PPP2R5C	chr14	102323222	+	ENST00000477431	TRAF3IP3	chr1	209950697	+	736	342	48	551	167
ENST00000557095	PPP2R5C	chr14	102323222	+	ENST00000400959	TRAF3IP3	chr1	209950697	+	756	332	38	553	171
ENST00000557095	PPP2R5C	chr14	102323222	+	ENST00000367025	TRAF3IP3	chr1	209950697	+	1102	332	38	934	298
ENST00000557095	PPP2R5C	chr14	102323222	+	ENST00000367026	TRAF3IP3	chr1	209950697	+	1107	332	38	934	298
ENST00000557095	PPP2R5C	chr14	102323222	+	ENST00000367024	TRAF3IP3	chr1	209950697	+	1094	332	38	934	298
ENST00000557095	PPP2R5C	chr14	102323222	+	ENST00000010338	TRAF3IP3	chr1	209950697	+	1106	332	38	934	298
ENST00000557095	PPP2R5C	chr14	102323222	+	ENST00000367023	TRAF3IP3	chr1	209950697	+	873	332	38	619	193
ENST00000557095	PPP2R5C	chr14	102323222	+	ENST00000477431	TRAF3IP3	chr1	209950697	+	726	332	38	541	167

DeepORF 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.

Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	No-coding score	Coding score
ENST00000422945	ENST00000400959	PPP2R5C	chr14	102323222	+	TRAF3IP3	chr1	209950697	+	0.003671806	0.9963282
ENST00000422945	ENST00000367025	PPP2R5C	chr14	102323222	+	TRAF3IP3	chr1	209950697	+	0.005186203	0.9948138
ENST00000422945	ENST00000367026	PPP2R5C	chr14	102323222	+	TRAF3IP3	chr1	209950697	+	0.005092623	0.9949073
ENST00000422945	ENST00000367024	PPP2R5C	chr14	102323222	+	TRAF3IP3	chr1	209950697	+	0.005360847	0.9946392
ENST00000422945	ENST00000010338	PPP2R5C	chr14	102323222	+	TRAF3IP3	chr1	209950697	+	0.005089477	0.99491054
ENST00000422945	ENST00000367023	PPP2R5C	chr14	102323222	+	TRAF3IP3	chr1	209950697	+	0.002165427	0.9978346
ENST00000422945	ENST00000477431	PPP2R5C	chr14	102323222	+	TRAF3IP3	chr1	209950697	+	0.003533896	0.99646604
ENST00000328724	ENST00000400959	PPP2R5C	chr14	102323222	+	TRAF3IP3	chr1	209950697	+	0.004146612	0.9958534
ENST00000328724	ENST00000367025	PPP2R5C	chr14	102323222	+	TRAF3IP3	chr1	209950697	+	0.006482313	0.99351776
ENST00000328724	ENST00000367026	PPP2R5C	chr14	102323222	+	TRAF3IP3	chr1	209950697	+	0.006306262	0.99369377
ENST00000328724	ENST00000367024	PPP2R5C	chr14	102323222	+	TRAF3IP3	chr1	209950697	+	0.006745696	0.99325436
ENST00000328724	ENST00000010338	PPP2R5C	chr14	102323222	+	TRAF3IP3	chr1	209950697	+	0.00635629	0.99364364
ENST00000328724	ENST00000367023	PPP2R5C	chr14	102323222	+	TRAF3IP3	chr1	209950697	+	0.004786155	0.99521387
ENST00000328724	ENST00000477431	PPP2R5C	chr14	102323222	+	TRAF3IP3	chr1	209950697	+	0.00405501	0.99594504
ENST00000350249	ENST00000400959	PPP2R5C	chr14	102323222	+	TRAF3IP3	chr1	209950697	+	0.004331296	0.99566865
ENST00000350249	ENST00000367025	PPP2R5C	chr14	102323222	+	TRAF3IP3	chr1	209950697	+	0.00496451	0.9950355
ENST00000350249	ENST00000367026	PPP2R5C	chr14	102323222	+	TRAF3IP3	chr1	209950697	+	0.004759097	0.9952409
ENST00000350249	ENST00000367024	PPP2R5C	chr14	102323222	+	TRAF3IP3	chr1	209950697	+	0.005132489	0.99486744
ENST00000350249	ENST00000010338	PPP2R5C	chr14	102323222	+	TRAF3IP3	chr1	209950697	+	0.004760014	0.99524
ENST00000350249	ENST00000367023	PPP2R5C	chr14	102323222	+	TRAF3IP3	chr1	209950697	+	0.00264999	0.99735
ENST00000350249	ENST00000477431	PPP2R5C	chr14	102323222	+	TRAF3IP3	chr1	209950697	+	0.00579252	0.9942075
ENST00000445439	ENST00000400959	PPP2R5C	chr14	102323222	+	TRAF3IP3	chr1	209950697	+	0.004457357	0.9955427
ENST00000445439	ENST00000367025	PPP2R5C	chr14	102323222	+	TRAF3IP3	chr1	209950697	+	0.004553649	0.99544626
ENST00000445439	ENST00000367026	PPP2R5C	chr14	102323222	+	TRAF3IP3	chr1	209950697	+	0.004385338	0.99561465
ENST00000445439	ENST00000367024	PPP2R5C	chr14	102323222	+	TRAF3IP3	chr1	209950697	+	0.004650912	0.9953491
ENST00000445439	ENST00000010338	PPP2R5C	chr14	102323222	+	TRAF3IP3	chr1	209950697	+	0.004387881	0.99561214
ENST00000445439	ENST00000367023	PPP2R5C	chr14	102323222	+	TRAF3IP3	chr1	209950697	+	0.002154541	0.9978454
ENST00000445439	ENST00000477431	PPP2R5C	chr14	102323222	+	TRAF3IP3	chr1	209950697	+	0.004994019	0.995006
ENST00000334743	ENST00000400959	PPP2R5C	chr14	102323222	+	TRAF3IP3	chr1	209950697	+	0.004457357	0.9955427
ENST00000334743	ENST00000367025	PPP2R5C	chr14	102323222	+	TRAF3IP3	chr1	209950697	+	0.004553649	0.99544626
ENST00000334743	ENST00000367026	PPP2R5C	chr14	102323222	+	TRAF3IP3	chr1	209950697	+	0.004385338	0.99561465
ENST00000334743	ENST00000367024	PPP2R5C	chr14	102323222	+	TRAF3IP3	chr1	209950697	+	0.004650912	0.9953491
ENST00000334743	ENST00000010338	PPP2R5C	chr14	102323222	+	TRAF3IP3	chr1	209950697	+	0.004387881	0.99561214
ENST00000334743	ENST00000367023	PPP2R5C	chr14	102323222	+	TRAF3IP3	chr1	209950697	+	0.002154541	0.9978454
ENST00000334743	ENST00000477431	PPP2R5C	chr14	102323222	+	TRAF3IP3	chr1	209950697	+	0.004994019	0.995006
ENST00000557095	ENST00000400959	PPP2R5C	chr14	102323222	+	TRAF3IP3	chr1	209950697	+	0.00441649	0.9955835
ENST00000557095	ENST00000367025	PPP2R5C	chr14	102323222	+	TRAF3IP3	chr1	209950697	+	0.004812894	0.9951871
ENST00000557095	ENST00000367026	PPP2R5C	chr14	102323222	+	TRAF3IP3	chr1	209950697	+	0.004637886	0.9953621
ENST00000557095	ENST00000367024	PPP2R5C	chr14	102323222	+	TRAF3IP3	chr1	209950697	+	0.004936481	0.9950635
ENST00000557095	ENST00000010338	PPP2R5C	chr14	102323222	+	TRAF3IP3	chr1	209950697	+	0.004631316	0.9953687
ENST00000557095	ENST00000367023	PPP2R5C	chr14	102323222	+	TRAF3IP3	chr1	209950697	+	0.002344328	0.99765563
ENST00000557095	ENST00000477431	PPP2R5C	chr14	102323222	+	TRAF3IP3	chr1	209950697	+	0.005010168	0.9949898

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 PPP2R5C-TRAF3IP3

+/-13 AA sequence from the breakpoints of the fusion protein sequences.

Hgene	Hchr	Hbp	Tgene	Tchr	Tbp	Length(fusion protein)	BP in fusion protein	Peptide
PPP2R5C	chr14	102323222	TRAF3IP3	chr1	209950697	332	98	VITEPIYPEVVHMGADSRDLQMNQAL
PPP2R5C	chr14	102323222	TRAF3IP3	chr1	209950697	342	98	VITEPIYPEVVHMGADSRDLQMNQAL
PPP2R5C	chr14	102323222	TRAF3IP3	chr1	209950697	434	98	VITEPIYPEVVHMGADSRDLQMNQAL
PPP2R5C	chr14	102323222	TRAF3IP3	chr1	209950697	468	153	VITEPIYPEVVHMGADSRDLQMNQAL
PPP2R5C	chr14	102323222	TRAF3IP3	chr1	209950697	483	129	VITEPIYPEVVHMGADSRDLQMNQAL

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Potential FusionNeoAntigen Information of PPP2R5C-TRAF3IP3 in HLA I

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.

PPP2R5C-TRAF3IP3_102323222_209950697.msa

Potential FusionNeoAntigen Information
* We used NetMHCpan v4.1 (%rank<0.5) and deepHLApan v1.1 (immunogenic score>0.5)

Fusion gene	Hchr	Hbp	Tgene	Tchr	Tbp	HLA I	FusionNeoAntigen peptide	Binding score	Immunogenic score	Neoantigen start (at BP 13)	Neoantigen end (at BP 13)
PPP2R5C-TRAF3IP3	chr14	102323222	chr1	209950697	468	HLA-B08:09	YPEVVHMGA	0.6325	0.5553	6	15
PPP2R5C-TRAF3IP3	chr14	102323222	chr1	209950697	468	HLA-A68:24	EVVHMGADSR	0.9973	0.6919	8	18
PPP2R5C-TRAF3IP3	chr14	102323222	chr1	209950697	468	HLA-A66:01	EVVHMGADSR	0.9969	0.7812	8	18
PPP2R5C-TRAF3IP3	chr14	102323222	chr1	209950697	468	HLA-A68:03	EVVHMGADSR	0.9964	0.6849	8	18
PPP2R5C-TRAF3IP3	chr14	102323222	chr1	209950697	468	HLA-A26:03	EVVHMGADSR	0.9901	0.8047	8	18
PPP2R5C-TRAF3IP3	chr14	102323222	chr1	209950697	468	HLA-B38:02	VHMGADSRDL	0.9838	0.83	10	20
PPP2R5C-TRAF3IP3	chr14	102323222	chr1	209950697	468	HLA-B38:01	VHMGADSRDL	0.9834	0.842	10	20
PPP2R5C-TRAF3IP3	chr14	102323222	chr1	209950697	468	HLA-A68:05	EVVHMGADSR	0.9607	0.6856	8	18
PPP2R5C-TRAF3IP3	chr14	102323222	chr1	209950697	468	HLA-A34:05	EVVHMGADSR	0.8897	0.695	8	18
PPP2R5C-TRAF3IP3	chr14	102323222	chr1	209950697	468	HLA-A34:01	EVVHMGADSR	0.8897	0.695	8	18
PPP2R5C-TRAF3IP3	chr14	102323222	chr1	209950697	468	HLA-A68:08	EVVHMGADSR	0.8334	0.7292	8	18
PPP2R5C-TRAF3IP3	chr14	102323222	chr1	209950697	468	HLA-B78:01	YPEVVHMGA	0.8443	0.5757	6	15
PPP2R5C-TRAF3IP3	chr14	102323222	chr1	209950697	468	HLA-C05:09	MGADSRDLQM	0.9998	0.9665	12	22
PPP2R5C-TRAF3IP3	chr14	102323222	chr1	209950697	468	HLA-C08:15	MGADSRDLQM	0.9996	0.9834	12	22
PPP2R5C-TRAF3IP3	chr14	102323222	chr1	209950697	468	HLA-A68:01	EVVHMGADSR	0.9973	0.6919	8	18
PPP2R5C-TRAF3IP3	chr14	102323222	chr1	209950697	468	HLA-B39:05	VHMGADSRDL	0.9833	0.7324	10	20
PPP2R5C-TRAF3IP3	chr14	102323222	chr1	209950697	468	HLA-C05:09	HMGADSRDLQM	0.9999	0.9522	11	22
PPP2R5C-TRAF3IP3	chr14	102323222	chr1	209950697	468	HLA-B78:02	YPEVVHMGA	0.6987	0.5839	6	15
PPP2R5C-TRAF3IP3	chr14	102323222	chr1	209950697	468	HLA-C05:01	MGADSRDLQM	0.9998	0.9665	12	22
PPP2R5C-TRAF3IP3	chr14	102323222	chr1	209950697	468	HLA-C08:02	MGADSRDLQM	0.9996	0.9834	12	22
PPP2R5C-TRAF3IP3	chr14	102323222	chr1	209950697	468	HLA-B38:05	VHMGADSRDL	0.9834	0.842	10	20
PPP2R5C-TRAF3IP3	chr14	102323222	chr1	209950697	468	HLA-B15:09	VHMGADSRDL	0.935	0.539	10	20
PPP2R5C-TRAF3IP3	chr14	102323222	chr1	209950697	468	HLA-C05:01	HMGADSRDLQM	0.9999	0.9522	11	22

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Potential FusionNeoAntigen Information of PPP2R5C-TRAF3IP3 in HLA II

PPP2R5C-TRAF3IP3_102323222_209950697.msa

Potential FusionNeoAntigen Information
* We used NetMHCIIpan v4.1 (%rank<0.5).

Fusion gene	Hchr	Hbp	Tgene	Tchr	Tbp	HLA II	FusionNeoAntigen peptide	Neoantigen start (at BP 13)	Neoantigen end (at BP 13)
PPP2R5C-TRAF3IP3	chr14	102323222	chr1	209950697	468	DRB1-0413	TEPIYPEVVHMGADS	2	17
PPP2R5C-TRAF3IP3	chr14	102323222	chr1	209950697	468	DRB1-0415	TEPIYPEVVHMGADS	2	17
PPP2R5C-TRAF3IP3	chr14	102323222	chr1	209950697	468	DRB1-0436	TEPIYPEVVHMGADS	2	17
PPP2R5C-TRAF3IP3	chr14	102323222	chr1	209950697	468	DRB1-0437	TEPIYPEVVHMGADS	2	17
PPP2R5C-TRAF3IP3	chr14	102323222	chr1	209950697	468	DRB1-0437	ITEPIYPEVVHMGAD	1	16
PPP2R5C-TRAF3IP3	chr14	102323222	chr1	209950697	468	DRB1-0444	TEPIYPEVVHMGADS	2	17
PPP2R5C-TRAF3IP3	chr14	102323222	chr1	209950697	468	DRB1-0458	TEPIYPEVVHMGADS	2	17
PPP2R5C-TRAF3IP3	chr14	102323222	chr1	209950697	468	DRB1-0473	TEPIYPEVVHMGADS	2	17
PPP2R5C-TRAF3IP3	chr14	102323222	chr1	209950697	468	DRB5-0205	YPEVVHMGADSRDLQ	6	21

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Fusion breakpoint peptide structures of PPP2R5C-TRAF3IP3

3D 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 name	BPseq	Hgene	Tgene	Hchr	Hbp	Tchr	Tbp	AAlen
10757	YPEVVHMGADSRDL	PPP2R5C	TRAF3IP3	chr14	102323222	chr1	209950697	468

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of PPP2R5C-TRAF3IP3

Virtual screening between 25 HLAs (from PDB) and FusionNeoAntigens
* We used Glide to predict the interaction between HLAs and neoantigens.

HLA allele	PDB ID	File name	BPseq	Docking score	Glide score
HLA-B14:02	3BVN	10757	YPEVVHMGADSRDL	-7.15543	-7.26883
HLA-B14:02	3BVN	10757	YPEVVHMGADSRDL	-4.77435	-5.80965
HLA-B52:01	3W39	10757	YPEVVHMGADSRDL	-6.80875	-6.92215
HLA-B52:01	3W39	10757	YPEVVHMGADSRDL	-4.20386	-5.23916
HLA-A11:01	4UQ2	10757	YPEVVHMGADSRDL	-7.5194	-8.5547
HLA-A11:01	4UQ2	10757	YPEVVHMGADSRDL	-6.9601	-7.0735
HLA-A24:02	5HGA	10757	YPEVVHMGADSRDL	-7.52403	-7.63743
HLA-A24:02	5HGA	10757	YPEVVHMGADSRDL	-5.82433	-6.85963
HLA-B27:05	6PYJ	10757	YPEVVHMGADSRDL	-3.28285	-4.31815
HLA-B44:05	3DX8	10757	YPEVVHMGADSRDL	-5.91172	-6.94702
HLA-B44:05	3DX8	10757	YPEVVHMGADSRDL	-4.24346	-4.35686

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Vaccine Design for the FusionNeoAntigens of PPP2R5C-TRAF3IP3

mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-Is.

Fusion gene	Hchr	Hbp	Tchr	Tbp	Start in +/-13AA	End in +/-13AA	FusionNeoAntigen peptide sequence	FusionNeoAntigen RNA sequence
PPP2R5C-TRAF3IP3	chr14	102323222	chr1	209950697	10	20	VHMGADSRDL	GTCCATATGGGAGCAGATAGCAGGGACTTA
PPP2R5C-TRAF3IP3	chr14	102323222	chr1	209950697	11	22	HMGADSRDLQM	CATATGGGAGCAGATAGCAGGGACTTACAGATG
PPP2R5C-TRAF3IP3	chr14	102323222	chr1	209950697	12	22	MGADSRDLQM	ATGGGAGCAGATAGCAGGGACTTACAGATG
PPP2R5C-TRAF3IP3	chr14	102323222	chr1	209950697	6	15	YPEVVHMGA	TACCCAGAAGTAGTCCATATGGGAGCA
PPP2R5C-TRAF3IP3	chr14	102323222	chr1	209950697	8	18	EVVHMGADSR	GAAGTAGTCCATATGGGAGCAGATAGCAGG

mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.

Fusion gene	Hchr	Hbp	Tchr	Tbp	Start in +/-13AA	End in +/-13AA	FusionNeoAntigen peptide	FusionNEoAntigen RNA sequence
PPP2R5C-TRAF3IP3	chr14	102323222	chr1	209950697	1	16	ITEPIYPEVVHMGAD	ATCACAGAGCCTATTTACCCAGAAGTAGTCCATATGGGAGCAGAT
PPP2R5C-TRAF3IP3	chr14	102323222	chr1	209950697	2	17	TEPIYPEVVHMGADS	ACAGAGCCTATTTACCCAGAAGTAGTCCATATGGGAGCAGATAGC
PPP2R5C-TRAF3IP3	chr14	102323222	chr1	209950697	6	21	YPEVVHMGADSRDLQ	TACCCAGAAGTAGTCCATATGGGAGCAGATAGCAGGGACTTACAG

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Information of the samples that have these potential fusion neoantigens of PPP2R5C-TRAF3IP3

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 type	Fusion gene	Hchr	Hbp	Henst	Tchr	Tbp	Tenst	Sample
STAD	PPP2R5C-TRAF3IP3	chr14	102323222	ENST00000328724	chr1	209950697	ENST00000010338	TCGA-BR-8366-01A

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Potential target of CAR-T therapy development for PPP2R5C-TRAF3IP3

Predicted 3D structure. We used RoseTTAFold.

Retention 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'.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

Tgene

TRAF3IP3

chr14:102323222

chr1:209950697

ENST00000010338

527_544

532.0

Transmembrane

Helical%3B Anchor for type IV membrane protein

Tgene

TRAF3IP3

chr14:102323222

chr1:209950697

ENST00000367024

527_544

552.0

Transmembrane

Helical%3B Anchor for type IV membrane protein

Tgene

TRAF3IP3

chr14:102323222

chr1:209950697

ENST00000367025

527_544

552.0

Transmembrane

Helical%3B Anchor for type IV membrane protein

Tgene

TRAF3IP3

chr14:102323222

chr1:209950697

ENST00000367026

527_544

532.0

Transmembrane

Helical%3B Anchor for type IV membrane protein

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.

Hgene

Hchr

Hbp

Henst

Tgene

Tchr

Tbp

Tenst

DeepLoc result

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Related Drugs to PPP2R5C-TRAF3IP3

Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)

Hgene

Tgene

Drug

Source

PMID

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Related Diseases to PPP2R5C-TRAF3IP3

Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)

Hgene

Tgene

Disease

Source

PMID

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source

	Fusion Gene and Fusion Protein Summary
	Fusion Amino Acid Sequences (multiple BPs and multiple gene isoforms)
	Fusion Protein Breakpoint Sequences - (for the Screening of the FusionNeoAntigens)
	Potential FusionNeoAntigens in HLA I - (netMHCpan v4.1 + deepHLApan v1.1)
	Potential FusionNeoAntigens in HLA II - (netMHCIIpan v4.1)
	Fusion Breakpoint 14 AA Peptide Structure - (RoseTTAFold)
	Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D - (Glide)
	Vaccine Design for the FusionNeoAntigens (RNA/protein sequences)
	Potential target of CAR-T therapy development
	Information on the samples that have these potential fusion neoantigens
	Fusion Protein Targeting Drugs - (Manual Curation)
	Fusion Protein Related diseases - (Manual Curation)