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Fusion Protein:PTPRU-EPB41

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: PTPRU-EPB41
	FusionPDB ID: 70570
	FusionGDB2.0 ID: 70570
		Hgene	Tgene
	Gene symbol	PTPRU	EPB41
	Gene ID	10076	2035
	Gene name	protein tyrosine phosphatase receptor type U	erythrocyte membrane protein band 4.1
	Synonyms	FMI\|PCP-2\|PTP\|PTP-J\|PTP-PI\|PTP-RO\|PTPPSI\|PTPRO\|PTPU2\|R-PTP-PSI\|R-PTP-U\|hPTP-J	4.1R\|EL1\|HE
	Cytomap	1p35.3	1p35.3
	Type of gene	protein-coding	protein-coding
	Description	receptor-type tyrosine-protein phosphatase UPTP piReceptor protein tyrosine phosphatase hPTP-Jpancreatic carcinoma phosphatase 2pi R-PTP-Psiprotein-tyrosine phosphatase Jprotein-tyrosine phosphatase piprotein-tyrosine phosphatase receptor omicronr	protein 4.1EPB4.1P4.1band 4.1elliptocytosis 1, RH-linkederythrocyte surface protein band 4.1
	Modification date	20200313	20200320
	UniProtAcc	.	Q9HCM4 Main function of 5'-partner protein: FUNCTION: Plays a role in the formation and organization of tight junctions during the establishment of polarity in epithelial cells. {ECO:0000269\|PubMed:17920587}.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000323874, ENST00000345512, ENST00000356870, ENST00000373779, ENST00000428026, ENST00000460170, ENST00000415600,	ENST00000460378, ENST00000343067, ENST00000347529, ENST00000349460, ENST00000356093, ENST00000373797, ENST00000373798, ENST00000373800, ENST00000398863,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	8 X 6 X 7=336	13 X 13 X 6=1014
	# samples	10	15
	** MAII score	log2(10/336*10)=-1.74846123300404 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(15/1014*10)=-2.75702324650746 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: PTPRU [Title/Abstract] AND EPB41 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: PTPRU [Title/Abstract] AND EPB41 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	PTPRU(29563229)-EPB41(29356911), # samples:1 PTPRU(29563229)-EPB41(29356912), # samples:1 PTPRU(29602268)-EPB41(29379616), # samples:1
Anticipated loss of major functional domain due to fusion event.	PTPRU-EPB41 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. PTPRU-EPB41 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. PTPRU-EPB41 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. PTPRU-EPB41 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. PTPRU-EPB41 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF. PTPRU-EPB41 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF. PTPRU-EPB41 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF. PTPRU-EPB41 seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target due to the frame-shifted ORF. PTPRU-EPB41 seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor due to the frame-shifted ORF.

* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

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	PTPRU	GO:0006470	protein dephosphorylation	12501215
Hgene	PTPRU	GO:0008285	negative regulation of cell proliferation	16574648
Hgene	PTPRU	GO:0030336	negative regulation of cell migration	12501215\|16574648
Hgene	PTPRU	GO:0034394	protein localization to cell surface	16574648
Hgene	PTPRU	GO:0090090	negative regulation of canonical Wnt signaling pathway	16574648
Hgene	PTPRU	GO:2000049	positive regulation of cell-cell adhesion mediated by cadherin	16574648
Tgene	EPB41	GO:0032092	positive regulation of protein binding	3693401

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr1:29563229/chr1:29356911)
- 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 PTPRU (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 EPB41 (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)
ENST00000345512	PTPRU	chr1	29602268	+	ENST00000356093	EPB41	chr1	29379616	+	5650	1582	129	2441	770
ENST00000345512	PTPRU	chr1	29602268	+	ENST00000398863	EPB41	chr1	29379616	+	5458	1582	129	2249	706
ENST00000345512	PTPRU	chr1	29602268	+	ENST00000343067	EPB41	chr1	29379616	+	5749	1582	129	2540	803
ENST00000345512	PTPRU	chr1	29602268	+	ENST00000349460	EPB41	chr1	29379616	+	2801	1582	129	2498	789
ENST00000345512	PTPRU	chr1	29602268	+	ENST00000373800	EPB41	chr1	29379616	+	2642	1582	129	2339	736
ENST00000345512	PTPRU	chr1	29602268	+	ENST00000347529	EPB41	chr1	29379616	+	2681	1582	129	2378	749
ENST00000345512	PTPRU	chr1	29602268	+	ENST00000373798	EPB41	chr1	29379616	+	5770	1582	129	2540	803
ENST00000345512	PTPRU	chr1	29602268	+	ENST00000373797	EPB41	chr1	29379616	+	2151	1582	129	2108	659
ENST00000373779	PTPRU	chr1	29602268	+	ENST00000356093	EPB41	chr1	29379616	+	5650	1582	129	2441	770
ENST00000373779	PTPRU	chr1	29602268	+	ENST00000398863	EPB41	chr1	29379616	+	5458	1582	129	2249	706
ENST00000373779	PTPRU	chr1	29602268	+	ENST00000343067	EPB41	chr1	29379616	+	5749	1582	129	2540	803
ENST00000373779	PTPRU	chr1	29602268	+	ENST00000349460	EPB41	chr1	29379616	+	2801	1582	129	2498	789
ENST00000373779	PTPRU	chr1	29602268	+	ENST00000373800	EPB41	chr1	29379616	+	2642	1582	129	2339	736
ENST00000373779	PTPRU	chr1	29602268	+	ENST00000347529	EPB41	chr1	29379616	+	2681	1582	129	2378	749
ENST00000373779	PTPRU	chr1	29602268	+	ENST00000373798	EPB41	chr1	29379616	+	5770	1582	129	2540	803
ENST00000373779	PTPRU	chr1	29602268	+	ENST00000373797	EPB41	chr1	29379616	+	2151	1582	129	2108	659
ENST00000356870	PTPRU	chr1	29602268	+	ENST00000356093	EPB41	chr1	29379616	+	5631	1563	110	2422	770
ENST00000356870	PTPRU	chr1	29602268	+	ENST00000398863	EPB41	chr1	29379616	+	5439	1563	110	2230	706
ENST00000356870	PTPRU	chr1	29602268	+	ENST00000343067	EPB41	chr1	29379616	+	5730	1563	110	2521	803
ENST00000356870	PTPRU	chr1	29602268	+	ENST00000349460	EPB41	chr1	29379616	+	2782	1563	110	2479	789
ENST00000356870	PTPRU	chr1	29602268	+	ENST00000373800	EPB41	chr1	29379616	+	2623	1563	110	2320	736
ENST00000356870	PTPRU	chr1	29602268	+	ENST00000347529	EPB41	chr1	29379616	+	2662	1563	110	2359	749
ENST00000356870	PTPRU	chr1	29602268	+	ENST00000373798	EPB41	chr1	29379616	+	5751	1563	110	2521	803
ENST00000356870	PTPRU	chr1	29602268	+	ENST00000373797	EPB41	chr1	29379616	+	2132	1563	110	2089	659
ENST00000323874	PTPRU	chr1	29602268	+	ENST00000356093	EPB41	chr1	29379616	+	5631	1563	110	2422	770
ENST00000323874	PTPRU	chr1	29602268	+	ENST00000398863	EPB41	chr1	29379616	+	5439	1563	110	2230	706
ENST00000323874	PTPRU	chr1	29602268	+	ENST00000343067	EPB41	chr1	29379616	+	5730	1563	110	2521	803
ENST00000323874	PTPRU	chr1	29602268	+	ENST00000349460	EPB41	chr1	29379616	+	2782	1563	110	2479	789
ENST00000323874	PTPRU	chr1	29602268	+	ENST00000373800	EPB41	chr1	29379616	+	2623	1563	110	2320	736
ENST00000323874	PTPRU	chr1	29602268	+	ENST00000347529	EPB41	chr1	29379616	+	2662	1563	110	2359	749
ENST00000323874	PTPRU	chr1	29602268	+	ENST00000373798	EPB41	chr1	29379616	+	5751	1563	110	2521	803
ENST00000323874	PTPRU	chr1	29602268	+	ENST00000373797	EPB41	chr1	29379616	+	2132	1563	110	2089	659
ENST00000428026	PTPRU	chr1	29602268	+	ENST00000356093	EPB41	chr1	29379616	+	5617	1549	96	2408	770
ENST00000428026	PTPRU	chr1	29602268	+	ENST00000398863	EPB41	chr1	29379616	+	5425	1549	96	2216	706
ENST00000428026	PTPRU	chr1	29602268	+	ENST00000343067	EPB41	chr1	29379616	+	5716	1549	96	2507	803
ENST00000428026	PTPRU	chr1	29602268	+	ENST00000349460	EPB41	chr1	29379616	+	2768	1549	96	2465	789
ENST00000428026	PTPRU	chr1	29602268	+	ENST00000373800	EPB41	chr1	29379616	+	2609	1549	96	2306	736
ENST00000428026	PTPRU	chr1	29602268	+	ENST00000347529	EPB41	chr1	29379616	+	2648	1549	96	2345	749
ENST00000428026	PTPRU	chr1	29602268	+	ENST00000373798	EPB41	chr1	29379616	+	5737	1549	96	2507	803
ENST00000428026	PTPRU	chr1	29602268	+	ENST00000373797	EPB41	chr1	29379616	+	2118	1549	96	2075	659
ENST00000460170	PTPRU	chr1	29602268	+	ENST00000356093	EPB41	chr1	29379616	+	5527	1459	6	2318	770
ENST00000460170	PTPRU	chr1	29602268	+	ENST00000398863	EPB41	chr1	29379616	+	5335	1459	6	2126	706
ENST00000460170	PTPRU	chr1	29602268	+	ENST00000343067	EPB41	chr1	29379616	+	5626	1459	6	2417	803
ENST00000460170	PTPRU	chr1	29602268	+	ENST00000349460	EPB41	chr1	29379616	+	2678	1459	6	2375	789
ENST00000460170	PTPRU	chr1	29602268	+	ENST00000373800	EPB41	chr1	29379616	+	2519	1459	6	2216	736
ENST00000460170	PTPRU	chr1	29602268	+	ENST00000347529	EPB41	chr1	29379616	+	2558	1459	6	2255	749
ENST00000460170	PTPRU	chr1	29602268	+	ENST00000373798	EPB41	chr1	29379616	+	5647	1459	6	2417	803
ENST00000460170	PTPRU	chr1	29602268	+	ENST00000373797	EPB41	chr1	29379616	+	2028	1459	6	1985	659

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
ENST00000345512	ENST00000356093	PTPRU	chr1	29602268	+	EPB41	chr1	29379616	+	0.00229631	0.99770373
ENST00000345512	ENST00000398863	PTPRU	chr1	29602268	+	EPB41	chr1	29379616	+	0.003053673	0.9969463
ENST00000345512	ENST00000343067	PTPRU	chr1	29602268	+	EPB41	chr1	29379616	+	0.001719552	0.9982805
ENST00000345512	ENST00000349460	PTPRU	chr1	29602268	+	EPB41	chr1	29379616	+	0.005555364	0.99444467
ENST00000345512	ENST00000373800	PTPRU	chr1	29602268	+	EPB41	chr1	29379616	+	0.008213496	0.99178654
ENST00000345512	ENST00000347529	PTPRU	chr1	29602268	+	EPB41	chr1	29379616	+	0.009042279	0.99095774
ENST00000345512	ENST00000373798	PTPRU	chr1	29602268	+	EPB41	chr1	29379616	+	0.001730504	0.99826944
ENST00000345512	ENST00000373797	PTPRU	chr1	29602268	+	EPB41	chr1	29379616	+	0.012612348	0.9873877
ENST00000373779	ENST00000356093	PTPRU	chr1	29602268	+	EPB41	chr1	29379616	+	0.00229631	0.99770373
ENST00000373779	ENST00000398863	PTPRU	chr1	29602268	+	EPB41	chr1	29379616	+	0.003053673	0.9969463
ENST00000373779	ENST00000343067	PTPRU	chr1	29602268	+	EPB41	chr1	29379616	+	0.001719552	0.9982805
ENST00000373779	ENST00000349460	PTPRU	chr1	29602268	+	EPB41	chr1	29379616	+	0.005555364	0.99444467
ENST00000373779	ENST00000373800	PTPRU	chr1	29602268	+	EPB41	chr1	29379616	+	0.008213496	0.99178654
ENST00000373779	ENST00000347529	PTPRU	chr1	29602268	+	EPB41	chr1	29379616	+	0.009042279	0.99095774
ENST00000373779	ENST00000373798	PTPRU	chr1	29602268	+	EPB41	chr1	29379616	+	0.001730504	0.99826944
ENST00000373779	ENST00000373797	PTPRU	chr1	29602268	+	EPB41	chr1	29379616	+	0.012612348	0.9873877
ENST00000356870	ENST00000356093	PTPRU	chr1	29602268	+	EPB41	chr1	29379616	+	0.002308186	0.99769187
ENST00000356870	ENST00000398863	PTPRU	chr1	29602268	+	EPB41	chr1	29379616	+	0.00307932	0.9969207
ENST00000356870	ENST00000343067	PTPRU	chr1	29602268	+	EPB41	chr1	29379616	+	0.001731316	0.9982686
ENST00000356870	ENST00000349460	PTPRU	chr1	29602268	+	EPB41	chr1	29379616	+	0.005686344	0.9943137
ENST00000356870	ENST00000373800	PTPRU	chr1	29602268	+	EPB41	chr1	29379616	+	0.008433046	0.99156696
ENST00000356870	ENST00000347529	PTPRU	chr1	29602268	+	EPB41	chr1	29379616	+	0.009283424	0.9907165
ENST00000356870	ENST00000373798	PTPRU	chr1	29602268	+	EPB41	chr1	29379616	+	0.001740106	0.99825984
ENST00000356870	ENST00000373797	PTPRU	chr1	29602268	+	EPB41	chr1	29379616	+	0.013144706	0.9868553
ENST00000323874	ENST00000356093	PTPRU	chr1	29602268	+	EPB41	chr1	29379616	+	0.002308186	0.99769187
ENST00000323874	ENST00000398863	PTPRU	chr1	29602268	+	EPB41	chr1	29379616	+	0.00307932	0.9969207
ENST00000323874	ENST00000343067	PTPRU	chr1	29602268	+	EPB41	chr1	29379616	+	0.001731316	0.9982686
ENST00000323874	ENST00000349460	PTPRU	chr1	29602268	+	EPB41	chr1	29379616	+	0.005686344	0.9943137
ENST00000323874	ENST00000373800	PTPRU	chr1	29602268	+	EPB41	chr1	29379616	+	0.008433046	0.99156696
ENST00000323874	ENST00000347529	PTPRU	chr1	29602268	+	EPB41	chr1	29379616	+	0.009283424	0.9907165
ENST00000323874	ENST00000373798	PTPRU	chr1	29602268	+	EPB41	chr1	29379616	+	0.001740106	0.99825984
ENST00000323874	ENST00000373797	PTPRU	chr1	29602268	+	EPB41	chr1	29379616	+	0.013144706	0.9868553
ENST00000428026	ENST00000356093	PTPRU	chr1	29602268	+	EPB41	chr1	29379616	+	0.002276687	0.9977233
ENST00000428026	ENST00000398863	PTPRU	chr1	29602268	+	EPB41	chr1	29379616	+	0.003044509	0.9969555
ENST00000428026	ENST00000343067	PTPRU	chr1	29602268	+	EPB41	chr1	29379616	+	0.001703286	0.9982967
ENST00000428026	ENST00000349460	PTPRU	chr1	29602268	+	EPB41	chr1	29379616	+	0.00556135	0.99443865
ENST00000428026	ENST00000373800	PTPRU	chr1	29602268	+	EPB41	chr1	29379616	+	0.008274646	0.9917253
ENST00000428026	ENST00000347529	PTPRU	chr1	29602268	+	EPB41	chr1	29379616	+	0.00911185	0.9908881
ENST00000428026	ENST00000373798	PTPRU	chr1	29602268	+	EPB41	chr1	29379616	+	0.001713291	0.99828666
ENST00000428026	ENST00000373797	PTPRU	chr1	29602268	+	EPB41	chr1	29379616	+	0.012949795	0.9870502
ENST00000460170	ENST00000356093	PTPRU	chr1	29602268	+	EPB41	chr1	29379616	+	0.002137398	0.99786264
ENST00000460170	ENST00000398863	PTPRU	chr1	29602268	+	EPB41	chr1	29379616	+	0.002853105	0.9971469
ENST00000460170	ENST00000343067	PTPRU	chr1	29602268	+	EPB41	chr1	29379616	+	0.001588804	0.9984112
ENST00000460170	ENST00000349460	PTPRU	chr1	29602268	+	EPB41	chr1	29379616	+	0.005094958	0.9949051
ENST00000460170	ENST00000373800	PTPRU	chr1	29602268	+	EPB41	chr1	29379616	+	0.007596661	0.9924034
ENST00000460170	ENST00000347529	PTPRU	chr1	29602268	+	EPB41	chr1	29379616	+	0.008511278	0.9914887
ENST00000460170	ENST00000373798	PTPRU	chr1	29602268	+	EPB41	chr1	29379616	+	0.001587492	0.9984125
ENST00000460170	ENST00000373797	PTPRU	chr1	29602268	+	EPB41	chr1	29379616	+	0.011633498	0.9883664

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 PTPRU-EPB41

+/-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
PTPRU	chr1	29602268	EPB41	chr1	29379616	1459	484	KEGKEVTFQTDEDAAAVDSADRSPRP
PTPRU	chr1	29602268	EPB41	chr1	29379616	1549	484	KEGKEVTFQTDEDAAAVDSADRSPRP
PTPRU	chr1	29602268	EPB41	chr1	29379616	1563	484	KEGKEVTFQTDEDAAAVDSADRSPRP
PTPRU	chr1	29602268	EPB41	chr1	29379616	1582	484	KEGKEVTFQTDEDAAAVDSADRSPRP

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Potential FusionNeoAntigen Information of PTPRU-EPB41 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.

PTPRU-EPB41_29602268_29379616.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)
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	HLA-C05:09	QTDEDAAAV	0.9998	0.9724	8	17
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	HLA-C08:15	QTDEDAAAV	0.9992	0.9855	8	17
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	HLA-C05:01	QTDEDAAAV	0.9998	0.9724	8	17
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	HLA-C04:03	QTDEDAAAV	0.9998	0.9474	8	17
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	HLA-C08:02	QTDEDAAAV	0.9992	0.9855	8	17
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	HLA-A69:01	QTDEDAAAV	0.6715	0.848	8	17

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Potential FusionNeoAntigen Information of PTPRU-EPB41 in HLA II

PTPRU-EPB41_29602268_29379616.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)
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB1-0401	EVTFQTDEDAAAVDS	4	19
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB1-0401	KEVTFQTDEDAAAVD	3	18
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB1-0401	VTFQTDEDAAAVDSA	5	20
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB1-0401	GKEVTFQTDEDAAAV	2	17
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB1-0407	EVTFQTDEDAAAVDS	4	19
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB1-0409	EVTFQTDEDAAAVDS	4	19
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB1-0409	KEVTFQTDEDAAAVD	3	18
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB1-0413	GKEVTFQTDEDAAAV	2	17
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB1-0419	EVTFQTDEDAAAVDS	4	19
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB1-0422	EVTFQTDEDAAAVDS	4	19
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB1-0422	KEVTFQTDEDAAAVD	3	18
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB1-0422	GKEVTFQTDEDAAAV	2	17
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB1-0433	EVTFQTDEDAAAVDS	4	19
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB1-0433	KEVTFQTDEDAAAVD	3	18
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB1-0433	VTFQTDEDAAAVDSA	5	20
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB1-0433	GKEVTFQTDEDAAAV	2	17
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB1-0434	EVTFQTDEDAAAVDS	4	19
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB1-0434	KEVTFQTDEDAAAVD	3	18
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB1-0435	EVTFQTDEDAAAVDS	4	19
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB1-0435	KEVTFQTDEDAAAVD	3	18
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB1-0435	GKEVTFQTDEDAAAV	2	17
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB1-0435	VTFQTDEDAAAVDSA	5	20
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB1-0438	EVTFQTDEDAAAVDS	4	19
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB1-0438	KEVTFQTDEDAAAVD	3	18
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB1-0438	VTFQTDEDAAAVDSA	5	20
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB1-0438	GKEVTFQTDEDAAAV	2	17
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB1-0461	EVTFQTDEDAAAVDS	4	19
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB1-0462	EVTFQTDEDAAAVDS	4	19
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB1-0462	KEVTFQTDEDAAAVD	3	18
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB1-0462	GKEVTFQTDEDAAAV	2	17
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB1-0462	VTFQTDEDAAAVDSA	5	20
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB1-0463	EVTFQTDEDAAAVDS	4	19
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB1-0463	KEVTFQTDEDAAAVD	3	18
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB1-0463	VTFQTDEDAAAVDSA	5	20
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB1-0463	GKEVTFQTDEDAAAV	2	17
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB1-0464	EVTFQTDEDAAAVDS	4	19
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB1-0464	KEVTFQTDEDAAAVD	3	18
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB1-0464	VTFQTDEDAAAVDSA	5	20
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB1-0464	GKEVTFQTDEDAAAV	2	17
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB1-0466	EVTFQTDEDAAAVDS	4	19
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB1-0470	GKEVTFQTDEDAAAV	2	17
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB1-0472	EVTFQTDEDAAAVDS	4	19
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB1-0472	KEVTFQTDEDAAAVD	3	18
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB1-0472	VTFQTDEDAAAVDSA	5	20
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB1-0472	GKEVTFQTDEDAAAV	2	17
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB1-0474	EVTFQTDEDAAAVDS	4	19
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB1-0474	KEVTFQTDEDAAAVD	3	18
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB1-0474	GKEVTFQTDEDAAAV	2	17
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB1-0474	VTFQTDEDAAAVDSA	5	20
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB1-0475	EVTFQTDEDAAAVDS	4	19
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB1-0475	KEVTFQTDEDAAAVD	3	18
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB1-0476	EVTFQTDEDAAAVDS	4	19
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB1-0476	KEVTFQTDEDAAAVD	3	18
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB1-0476	VTFQTDEDAAAVDSA	5	20
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB1-0476	GKEVTFQTDEDAAAV	2	17
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB1-0487	EVTFQTDEDAAAVDS	4	19
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB3-0101	EVTFQTDEDAAAVDS	4	19
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB3-0101	KEVTFQTDEDAAAVD	3	18
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB3-0104	EVTFQTDEDAAAVDS	4	19
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB3-0104	KEVTFQTDEDAAAVD	3	18
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB3-0105	EVTFQTDEDAAAVDS	4	19
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB3-0108	EVTFQTDEDAAAVDS	4	19
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB3-0108	KEVTFQTDEDAAAVD	3	18
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB3-0111	EVTFQTDEDAAAVDS	4	19
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB3-0111	KEVTFQTDEDAAAVD	3	18
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB3-0112	EVTFQTDEDAAAVDS	4	19
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB3-0112	KEVTFQTDEDAAAVD	3	18
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB3-0113	EVTFQTDEDAAAVDS	4	19
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB3-0113	KEVTFQTDEDAAAVD	3	18
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB3-0114	EVTFQTDEDAAAVDS	4	19
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB4-0101	GKEVTFQTDEDAAAV	2	17
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB4-0101	EGKEVTFQTDEDAAA	1	16
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB4-0103	GKEVTFQTDEDAAAV	2	17
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB4-0103	EGKEVTFQTDEDAAA	1	16
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB4-0104	GKEVTFQTDEDAAAV	2	17
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB4-0106	GKEVTFQTDEDAAAV	2	17
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB4-0106	EGKEVTFQTDEDAAA	1	16
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB4-0107	GKEVTFQTDEDAAAV	2	17
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB4-0107	EGKEVTFQTDEDAAA	1	16
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB4-0108	GKEVTFQTDEDAAAV	2	17
PTPRU-EPB41	chr1	29602268	chr1	29379616	1563	DRB4-0108	EGKEVTFQTDEDAAA	1	16

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Fusion breakpoint peptide structures of PTPRU-EPB41

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
9335	TFQTDEDAAAVDSA	PTPRU	EPB41	chr1	29602268	chr1	29379616	1563

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of PTPRU-EPB41

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	9335	TFQTDEDAAAVDSA	-8.55667	-8.74867
HLA-B14:02	3BVN	9335	TFQTDEDAAAVDSA	-3.49457	-4.25557
HLA-B52:01	3W39	9335	TFQTDEDAAAVDSA	-7.26725	-7.45925
HLA-B52:01	3W39	9335	TFQTDEDAAAVDSA	-4.01461	-4.77561
HLA-A24:02	5HGA	9335	TFQTDEDAAAVDSA	-7.65911	-8.42011
HLA-A24:02	5HGA	9335	TFQTDEDAAAVDSA	-7.10204	-7.29404
HLA-B44:05	3DX8	9335	TFQTDEDAAAVDSA	-7.5556	-8.3166
HLA-B44:05	3DX8	9335	TFQTDEDAAAVDSA	-2.76159	-2.95359

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Vaccine Design for the FusionNeoAntigens of PTPRU-EPB41

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
PTPRU-EPB41	chr1	29602268	chr1	29379616	8	17	QTDEDAAAV	AGACGGATGAGGATGCAGCAGCTGTCG

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
PTPRU-EPB41	chr1	29602268	chr1	29379616	1	16	EGKEVTFQTDEDAAA	AGGGCAAGGAGGTCACTTTCCAGACGGATGAGGATGCAGCAGCTG
PTPRU-EPB41	chr1	29602268	chr1	29379616	2	17	GKEVTFQTDEDAAAV	GCAAGGAGGTCACTTTCCAGACGGATGAGGATGCAGCAGCTGTCG
PTPRU-EPB41	chr1	29602268	chr1	29379616	3	18	KEVTFQTDEDAAAVD	AGGAGGTCACTTTCCAGACGGATGAGGATGCAGCAGCTGTCGATT
PTPRU-EPB41	chr1	29602268	chr1	29379616	4	19	EVTFQTDEDAAAVDS	AGGTCACTTTCCAGACGGATGAGGATGCAGCAGCTGTCGATTCGG
PTPRU-EPB41	chr1	29602268	chr1	29379616	5	20	VTFQTDEDAAAVDSA	TCACTTTCCAGACGGATGAGGATGCAGCAGCTGTCGATTCGGCAG

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Information of the samples that have these potential fusion neoantigens of PTPRU-EPB41

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
BRCA	PTPRU-EPB41	chr1	29602268	ENST00000323874	chr1	29379616	ENST00000343067	TCGA-BH-A0B9-01A

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Potential target of CAR-T therapy development for PTPRU-EPB41

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

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 PTPRU-EPB41

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 PTPRU-EPB41

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)