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Fusion Protein:PTPRU-UBIAD1

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: PTPRU-UBIAD1
	FusionPDB ID: 70576
	FusionGDB2.0 ID: 70576
		Hgene	Tgene
	Gene symbol	PTPRU	UBIAD1
	Gene ID	10076	29914
	Gene name	protein tyrosine phosphatase receptor type U	UbiA prenyltransferase domain containing 1
	Synonyms	FMI\|PCP-2\|PTP\|PTP-J\|PTP-PI\|PTP-RO\|PTPPSI\|PTPRO\|PTPU2\|R-PTP-PSI\|R-PTP-U\|hPTP-J	SCCD\|TERE1
	Cytomap	1p35.3	1p36.22
	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	ubiA prenyltransferase domain-containing protein 1transitional epithelia response proteintransitional epithelial response protein 1
	Modification date	20200313	20200313
	UniProtAcc	.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000323874, ENST00000345512, ENST00000356870, ENST00000373779, ENST00000428026, ENST00000460170, ENST00000415600,	ENST00000376804, ENST00000376810,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	8 X 6 X 7=336	3 X 2 X 3=18
	# samples	10	3
	** MAII score	log2(10/336*10)=-1.74846123300404 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(3/18*10)=0.736965594166206 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0
Fusion gene context	PubMed: PTPRU [Title/Abstract] AND UBIAD1 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: PTPRU [Title/Abstract] AND UBIAD1 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	PTPRU(29563229)-UBIAD1(11345701), # samples:2
Anticipated loss of major functional domain due to fusion event.	PTPRU-UBIAD1 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-UBIAD1 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	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	UBIAD1	GO:0042371	vitamin K biosynthetic process	20953171

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/chr1:11345701)
- 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 UBIAD1 (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	29563229	+	ENST00000376810	UBIAD1	chr1	11345701	+	2993	202	129	689	186
ENST00000373779	PTPRU	chr1	29563229	+	ENST00000376810	UBIAD1	chr1	11345701	+	2993	202	129	689	186
ENST00000356870	PTPRU	chr1	29563229	+	ENST00000376810	UBIAD1	chr1	11345701	+	2974	183	110	670	186
ENST00000323874	PTPRU	chr1	29563229	+	ENST00000376810	UBIAD1	chr1	11345701	+	2974	183	110	670	186
ENST00000428026	PTPRU	chr1	29563229	+	ENST00000376810	UBIAD1	chr1	11345701	+	2960	169	96	656	186
ENST00000460170	PTPRU	chr1	29563229	+	ENST00000376810	UBIAD1	chr1	11345701	+	2870	79	6	566	186

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	ENST00000376810	PTPRU	chr1	29563229	+	UBIAD1	chr1	11345701	+	0.004290438	0.99570954
ENST00000373779	ENST00000376810	PTPRU	chr1	29563229	+	UBIAD1	chr1	11345701	+	0.004290438	0.99570954
ENST00000356870	ENST00000376810	PTPRU	chr1	29563229	+	UBIAD1	chr1	11345701	+	0.004548261	0.99545175
ENST00000323874	ENST00000376810	PTPRU	chr1	29563229	+	UBIAD1	chr1	11345701	+	0.004548261	0.99545175
ENST00000428026	ENST00000376810	PTPRU	chr1	29563229	+	UBIAD1	chr1	11345701	+	0.004189158	0.99581087
ENST00000460170	ENST00000376810	PTPRU	chr1	29563229	+	UBIAD1	chr1	11345701	+	0.005820274	0.9941797

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-UBIAD1

+/-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	29563229	UBIAD1	chr1	11345701	169	23	LTFQLCAPETETPAGIGFKYVALGDL
PTPRU	chr1	29563229	UBIAD1	chr1	11345701	183	23	LTFQLCAPETETPAGIGFKYVALGDL
PTPRU	chr1	29563229	UBIAD1	chr1	11345701	202	23	LTFQLCAPETETPAGIGFKYVALGDL
PTPRU	chr1	29563229	UBIAD1	chr1	11345701	79	23	LTFQLCAPETETPAGIGFKYVALGDL

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Potential FusionNeoAntigen Information of PTPRU-UBIAD1 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-UBIAD1_29563229_11345701.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-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B35:01	TPAGIGFKY	0.9978	0.7835	11	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B35:08	TPAGIGFKY	0.9957	0.7406	11	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B44:03	TETPAGIGF	0.9926	0.8268	9	18
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B18:01	TETPAGIGF	0.9746	0.8935	9	18
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B35:05	TPAGIGFKY	0.9597	0.6087	11	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B15:02	TPAGIGFKY	0.9407	0.8574	11	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B35:04	TPAGIGFKY	0.4429	0.9258	11	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B35:02	TPAGIGFKY	0.4429	0.9258	11	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B18:01	TPAGIGFKY	0.2668	0.7436	11	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B39:13	TETPAGIGF	0.0354	0.9069	9	18
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B35:08	ETPAGIGFKY	0.9513	0.6608	10	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B35:01	ETPAGIGFKY	0.9028	0.6675	10	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-A26:14	ETETPAGIGF	0.6466	0.5028	8	18
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-A26:15	ETETPAGIGF	0.6466	0.5028	8	18
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B44:03	ETETPAGIGF	0.6361	0.8103	8	18
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B18:01	ETETPAGIGF	0.2402	0.8159	8	18
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B44:03	TETPAGIGFKY	0.9994	0.7653	9	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B35:08	TETPAGIGFKY	0.9917	0.7063	9	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B35:01	TETPAGIGFKY	0.9826	0.7157	9	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B18:01	TETPAGIGFKY	0.9814	0.7104	9	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B56:01	TPAGIGFKYVA	0.9769	0.5023	11	22
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B35:05	TETPAGIGFKY	0.9736	0.5859	9	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B15:31	TPAGIGFKY	0.9977	0.7919	11	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B44:10	TETPAGIGF	0.9568	0.5506	9	18
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B15:21	TPAGIGFKY	0.9527	0.8122	11	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B35:12	TPAGIGFKY	0.4429	0.9258	11	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B39:08	TETPAGIGF	0.2704	0.9064	9	18
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-A26:01	ETETPAGIGF	0.6466	0.5028	8	18
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B54:01	TPAGIGFKYVA	0.9969	0.595	11	22
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B35:77	TPAGIGFKY	0.9978	0.7835	11	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B35:23	TPAGIGFKY	0.9978	0.8008	11	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B35:20	TPAGIGFKY	0.9976	0.8401	11	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B44:13	TETPAGIGF	0.9926	0.8268	9	18
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B44:07	TETPAGIGF	0.9926	0.8268	9	18
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B44:26	TETPAGIGF	0.9926	0.8268	9	18
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B35:24	TPAGIGFKY	0.9888	0.7425	11	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B35:30	TPAGIGFKY	0.9882	0.7083	11	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B35:17	TPAGIGFKY	0.9882	0.7083	11	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B18:04	TETPAGIGF	0.9804	0.8869	9	18
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B40:04	TETPAGIGF	0.9804	0.7136	9	18
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B18:07	TETPAGIGF	0.9796	0.8549	9	18
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B18:08	TETPAGIGF	0.9762	0.7886	9	18
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B18:05	TETPAGIGF	0.9746	0.8935	9	18
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B18:06	TETPAGIGF	0.9642	0.9	9	18
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B35:11	TPAGIGFKY	0.9242	0.8061	11	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B18:03	TETPAGIGF	0.9163	0.876	9	18
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B18:11	TETPAGIGF	0.7877	0.8422	9	18
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B18:11	TPAGIGFKY	0.7736	0.7861	11	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B15:13	TPAGIGFKY	0.7715	0.7625	11	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B18:04	TPAGIGFKY	0.6933	0.755	11	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B35:09	TPAGIGFKY	0.4429	0.9258	11	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B35:20	TETPAGIGF	0.3679	0.8749	9	18
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B41:03	TETPAGIGF	0.3245	0.7598	9	18
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B18:07	TPAGIGFKY	0.3167	0.6828	11	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B18:03	TPAGIGFKY	0.2948	0.7292	11	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B18:06	TPAGIGFKY	0.2836	0.7449	11	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B18:05	TPAGIGFKY	0.2668	0.7436	11	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B18:08	TPAGIGFKY	0.2393	0.5265	11	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-A25:01	TPAGIGFKY	0.2006	0.6703	11	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B15:08	TPAGIGFKY	0.1953	0.7352	11	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B15:11	TPAGIGFKY	0.1769	0.7404	11	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B48:02	TETPAGIGF	0.1418	0.8534	9	18
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B35:43	TPAGIGFKY	0.1354	0.7359	11	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B15:53	TETPAGIGF	0.125	0.8483	9	18
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-A25:01	ETPAGIGFKY	0.9922	0.5917	10	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B35:23	ETPAGIGFKY	0.907	0.6942	10	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B35:77	ETPAGIGFKY	0.9028	0.6675	10	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B15:08	ETPAGIGFKY	0.89	0.667	10	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B15:11	ETPAGIGFKY	0.8866	0.6693	10	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B35:43	ETPAGIGFKY	0.8838	0.6685	10	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B35:24	ETPAGIGFKY	0.8693	0.7095	10	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B35:17	ETPAGIGFKY	0.8397	0.5368	10	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B35:30	ETPAGIGFKY	0.8397	0.5368	10	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-A25:01	ETETPAGIGF	0.7549	0.7814	8	18
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B44:07	ETETPAGIGF	0.6361	0.8103	8	18
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B44:13	ETETPAGIGF	0.6361	0.8103	8	18
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B44:26	ETETPAGIGF	0.6361	0.8103	8	18
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B18:07	ETPAGIGFKY	0.4759	0.688	10	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B18:11	ETETPAGIGF	0.3989	0.7757	8	18
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B18:05	ETETPAGIGF	0.2402	0.8159	8	18
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B18:03	ETETPAGIGF	0.2331	0.8031	8	18
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B44:26	TETPAGIGFKY	0.9994	0.7653	9	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B44:07	TETPAGIGFKY	0.9994	0.7653	9	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B44:13	TETPAGIGFKY	0.9994	0.7653	9	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B15:11	TETPAGIGFKY	0.9956	0.7521	9	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B18:04	TETPAGIGFKY	0.9859	0.7193	9	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B18:08	TETPAGIGFKY	0.9855	0.5592	9	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B35:17	TETPAGIGFKY	0.9841	0.661	9	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B35:30	TETPAGIGFKY	0.9841	0.661	9	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B18:03	TETPAGIGFKY	0.9837	0.7025	9	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B35:77	TETPAGIGFKY	0.9826	0.7157	9	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B35:23	TETPAGIGFKY	0.9817	0.7366	9	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B18:05	TETPAGIGFKY	0.9814	0.7104	9	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B18:06	TETPAGIGFKY	0.978	0.7236	9	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B35:20	TETPAGIGFKY	0.9779	0.7527	9	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B18:11	TETPAGIGFKY	0.9686	0.7111	9	20
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	183	HLA-B35:24	TETPAGIGFKY	0.956	0.7279	9	20

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Potential FusionNeoAntigen Information of PTPRU-UBIAD1 in HLA II

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)

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Fusion breakpoint peptide structures of PTPRU-UBIAD1

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
477	APETETPAGIGFKY	PTPRU	UBIAD1	chr1	29563229	chr1	11345701	183

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of PTPRU-UBIAD1

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	477	APETETPAGIGFKY	-5.97758	-6.09098
HLA-B14:02	3BVN	477	APETETPAGIGFKY	-5.15013	-6.18543
HLA-B52:01	3W39	477	APETETPAGIGFKY	-6.29935	-6.41275
HLA-B52:01	3W39	477	APETETPAGIGFKY	-6.07479	-7.11009
HLA-A24:02	5HGA	477	APETETPAGIGFKY	-7.25246	-8.28776
HLA-A24:02	5HGA	477	APETETPAGIGFKY	-6.23064	-6.34404
HLA-B44:05	3DX8	477	APETETPAGIGFKY	-4.66421	-5.69951
HLA-B44:05	3DX8	477	APETETPAGIGFKY	-4.52141	-4.63481
HLA-A02:01	6TDR	477	APETETPAGIGFKY	-7.72945	-7.84285

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Vaccine Design for the FusionNeoAntigens of PTPRU-UBIAD1

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-UBIAD1	chr1	29563229	chr1	11345701	10	20	ETPAGIGFKY	CTCCGGCAGGAATTGGATTCAAGTACGTGG
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	11	20	TPAGIGFKY	CGGCAGGAATTGGATTCAAGTACGTGG
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	11	22	TPAGIGFKYVA	CGGCAGGAATTGGATTCAAGTACGTGGCTCTGG
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	8	18	ETETPAGIGF	CCGAGACTCCGGCAGGAATTGGATTCAAGT
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	9	18	TETPAGIGF	AGACTCCGGCAGGAATTGGATTCAAGT
PTPRU-UBIAD1	chr1	29563229	chr1	11345701	9	20	TETPAGIGFKY	AGACTCCGGCAGGAATTGGATTCAAGTACGTGG

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

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Information of the samples that have these potential fusion neoantigens of PTPRU-UBIAD1

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
GBM	PTPRU-UBIAD1	chr1	29563229	ENST00000323874	chr1	11345701	ENST00000376810	TCGA-32-5222-01A

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Potential target of CAR-T therapy development for PTPRU-UBIAD1

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

UBIAD1

chr1:29563229

chr1:11345701

ENST00000376804

134_154

180.0

Transmembrane

Helical

Tgene

UBIAD1

chr1:29563229

chr1:11345701

ENST00000376804

160_180

180.0

Transmembrane

Helical

Tgene

UBIAD1

chr1:29563229

chr1:11345701

ENST00000376804

188_208

180.0

Transmembrane

Helical

Tgene

UBIAD1

chr1:29563229

chr1:11345701

ENST00000376804

209_229

180.0

Transmembrane

Helical

Tgene

UBIAD1

chr1:29563229

chr1:11345701

ENST00000376804

245_267

180.0

Transmembrane

Helical

Tgene

UBIAD1

chr1:29563229

chr1:11345701

ENST00000376804

277_297

180.0

Transmembrane

Helical

Tgene

UBIAD1

chr1:29563229

chr1:11345701

ENST00000376804

315_335

180.0

Transmembrane

Helical

Tgene

UBIAD1

chr1:29563229

chr1:11345701

ENST00000376804

83_103

180.0

Transmembrane

Helical

Tgene

UBIAD1

chr1:29563229

chr1:11345701

ENST00000376810

188_208

339.0

Transmembrane

Helical

Tgene

UBIAD1

chr1:29563229

chr1:11345701

ENST00000376810

209_229

339.0

Transmembrane

Helical

Tgene

UBIAD1

chr1:29563229

chr1:11345701

ENST00000376810

245_267

339.0

Transmembrane

Helical

Tgene

UBIAD1

chr1:29563229

chr1:11345701

ENST00000376810

277_297

339.0

Transmembrane

Helical

Tgene

UBIAD1

chr1:29563229

chr1:11345701

ENST00000376810

315_335

339.0

Transmembrane

Helical

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-UBIAD1

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-UBIAD1

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)