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Fusion Protein:PTPRB-MYRFL

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: PTPRB-MYRFL
	FusionPDB ID: 70326
	FusionGDB2.0 ID: 70326
		Hgene	Tgene
	Gene symbol	PTPRB	MYRFL
	Gene ID	5787	196446
	Gene name	protein tyrosine phosphatase receptor type B	myelin regulatory factor like
	Synonyms	HPTP-BETA\|HPTPB\|PTPB\|R-PTP-BETA\|VEPTP	C12orf15\|C12orf28\|bcm1377
	Cytomap	12q15	12q15
	Type of gene	protein-coding	protein-coding
	Description	receptor-type tyrosine-protein phosphatase betaVE-PTPprotein tyrosine phosphatase, receptor type, beta polypeptidevascular endothelial protein tyrosine phosphatase	myelin regulatory factor-like protein
	Modification date	20200327	20200322
	UniProtAcc	.	Q96LU7 Main function of 5'-partner protein:
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000261266, ENST00000334414, ENST00000451516, ENST00000538708, ENST00000550358, ENST00000550857, ENST00000551525, ENST00000538174,	ENST00000299350, ENST00000535034, ENST00000547771, ENST00000552032,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	2 X 2 X 2=8	29 X 16 X 7=3248
	# samples	2	26
	** MAII score	log2(2/8*10)=1.32192809488736	log2(26/3248*10)=-3.64296810415672 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: PTPRB [Title/Abstract] AND MYRFL [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: PTPRB [Title/Abstract] AND MYRFL [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	PTPRB(70974816)-MYRFL(70345893), # samples:1
Anticipated loss of major functional domain due to fusion event.	PTPRB-MYRFL 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. PTPRB-MYRFL 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. PTPRB-MYRFL 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. PTPRB-MYRFL 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	PTPRB	GO:0016311	dephosphorylation	19116766\|19136612

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr12:70974816/chr12:70345893)
- 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 PTPRB (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 MYRFL (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)
ENST00000451516	PTPRB	chr12	70974816	-	ENST00000552032	MYRFL	chr12	70345893	+	2355	1654	0	2162	720
ENST00000451516	PTPRB	chr12	70974816	-	ENST00000547771	MYRFL	chr12	70345893	+	2726	1654	0	2159	719
ENST00000451516	PTPRB	chr12	70974816	-	ENST00000299350	MYRFL	chr12	70345893	+	2355	1654	0	2162	720
ENST00000451516	PTPRB	chr12	70974816	-	ENST00000535034	MYRFL	chr12	70345893	+	2164	1654	0	2087	695
ENST00000334414	PTPRB	chr12	70974816	-	ENST00000552032	MYRFL	chr12	70345893	+	3324	2623	45	3131	1028
ENST00000334414	PTPRB	chr12	70974816	-	ENST00000547771	MYRFL	chr12	70345893	+	3695	2623	45	3128	1027
ENST00000334414	PTPRB	chr12	70974816	-	ENST00000299350	MYRFL	chr12	70345893	+	3324	2623	45	3131	1028
ENST00000334414	PTPRB	chr12	70974816	-	ENST00000535034	MYRFL	chr12	70345893	+	3133	2623	45	3056	1003
ENST00000550358	PTPRB	chr12	70974816	-	ENST00000552032	MYRFL	chr12	70345893	+	3305	2604	26	3112	1028
ENST00000550358	PTPRB	chr12	70974816	-	ENST00000547771	MYRFL	chr12	70345893	+	3676	2604	26	3109	1027
ENST00000550358	PTPRB	chr12	70974816	-	ENST00000299350	MYRFL	chr12	70345893	+	3305	2604	26	3112	1028
ENST00000550358	PTPRB	chr12	70974816	-	ENST00000535034	MYRFL	chr12	70345893	+	3114	2604	26	3037	1003
ENST00000538708	PTPRB	chr12	70974816	-	ENST00000552032	MYRFL	chr12	70345893	+	2654	1953	20	2461	813
ENST00000538708	PTPRB	chr12	70974816	-	ENST00000547771	MYRFL	chr12	70345893	+	3025	1953	20	2458	812
ENST00000538708	PTPRB	chr12	70974816	-	ENST00000299350	MYRFL	chr12	70345893	+	2654	1953	20	2461	813
ENST00000538708	PTPRB	chr12	70974816	-	ENST00000535034	MYRFL	chr12	70345893	+	2463	1953	20	2386	788
ENST00000550857	PTPRB	chr12	70974816	-	ENST00000552032	MYRFL	chr12	70345893	+	2384	1683	20	2191	723
ENST00000550857	PTPRB	chr12	70974816	-	ENST00000547771	MYRFL	chr12	70345893	+	2755	1683	20	2188	722
ENST00000550857	PTPRB	chr12	70974816	-	ENST00000299350	MYRFL	chr12	70345893	+	2384	1683	20	2191	723
ENST00000550857	PTPRB	chr12	70974816	-	ENST00000535034	MYRFL	chr12	70345893	+	2193	1683	20	2116	698
ENST00000261266	PTPRB	chr12	70974816	-	ENST00000552032	MYRFL	chr12	70345893	+	2655	1954	21	2462	813
ENST00000261266	PTPRB	chr12	70974816	-	ENST00000547771	MYRFL	chr12	70345893	+	3026	1954	21	2459	812
ENST00000261266	PTPRB	chr12	70974816	-	ENST00000299350	MYRFL	chr12	70345893	+	2655	1954	21	2462	813
ENST00000261266	PTPRB	chr12	70974816	-	ENST00000535034	MYRFL	chr12	70345893	+	2464	1954	21	2387	788
ENST00000551525	PTPRB	chr12	70974816	-	ENST00000552032	MYRFL	chr12	70345893	+	3301	2600	25	3108	1027
ENST00000551525	PTPRB	chr12	70974816	-	ENST00000547771	MYRFL	chr12	70345893	+	3672	2600	25	3105	1026
ENST00000551525	PTPRB	chr12	70974816	-	ENST00000299350	MYRFL	chr12	70345893	+	3301	2600	25	3108	1027
ENST00000551525	PTPRB	chr12	70974816	-	ENST00000535034	MYRFL	chr12	70345893	+	3110	2600	25	3033	1002

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
ENST00000451516	ENST00000552032	PTPRB	chr12	70974816	-	MYRFL	chr12	70345893	+	0.000278178	0.9997218
ENST00000451516	ENST00000547771	PTPRB	chr12	70974816	-	MYRFL	chr12	70345893	+	0.000168317	0.9998317
ENST00000451516	ENST00000299350	PTPRB	chr12	70974816	-	MYRFL	chr12	70345893	+	0.000278178	0.9997218
ENST00000451516	ENST00000535034	PTPRB	chr12	70974816	-	MYRFL	chr12	70345893	+	0.0005862	0.99941385
ENST00000334414	ENST00000552032	PTPRB	chr12	70974816	-	MYRFL	chr12	70345893	+	0.000265546	0.99973446
ENST00000334414	ENST00000547771	PTPRB	chr12	70974816	-	MYRFL	chr12	70345893	+	0.000205223	0.9997948
ENST00000334414	ENST00000299350	PTPRB	chr12	70974816	-	MYRFL	chr12	70345893	+	0.000265546	0.99973446
ENST00000334414	ENST00000535034	PTPRB	chr12	70974816	-	MYRFL	chr12	70345893	+	0.000614103	0.99938583
ENST00000550358	ENST00000552032	PTPRB	chr12	70974816	-	MYRFL	chr12	70345893	+	0.000264882	0.99973506
ENST00000550358	ENST00000547771	PTPRB	chr12	70974816	-	MYRFL	chr12	70345893	+	0.00020337	0.9997967
ENST00000550358	ENST00000299350	PTPRB	chr12	70974816	-	MYRFL	chr12	70345893	+	0.000264882	0.99973506
ENST00000550358	ENST00000535034	PTPRB	chr12	70974816	-	MYRFL	chr12	70345893	+	0.000605611	0.9993944
ENST00000538708	ENST00000552032	PTPRB	chr12	70974816	-	MYRFL	chr12	70345893	+	0.0002138	0.9997862
ENST00000538708	ENST00000547771	PTPRB	chr12	70974816	-	MYRFL	chr12	70345893	+	0.000132209	0.9998678
ENST00000538708	ENST00000299350	PTPRB	chr12	70974816	-	MYRFL	chr12	70345893	+	0.0002138	0.9997862
ENST00000538708	ENST00000535034	PTPRB	chr12	70974816	-	MYRFL	chr12	70345893	+	0.000337474	0.9996625
ENST00000550857	ENST00000552032	PTPRB	chr12	70974816	-	MYRFL	chr12	70345893	+	0.000272641	0.9997273
ENST00000550857	ENST00000547771	PTPRB	chr12	70974816	-	MYRFL	chr12	70345893	+	0.000169695	0.99983025
ENST00000550857	ENST00000299350	PTPRB	chr12	70974816	-	MYRFL	chr12	70345893	+	0.000272641	0.9997273
ENST00000550857	ENST00000535034	PTPRB	chr12	70974816	-	MYRFL	chr12	70345893	+	0.000551739	0.99944824
ENST00000261266	ENST00000552032	PTPRB	chr12	70974816	-	MYRFL	chr12	70345893	+	0.000212192	0.99978787
ENST00000261266	ENST00000547771	PTPRB	chr12	70974816	-	MYRFL	chr12	70345893	+	0.000131265	0.99986875
ENST00000261266	ENST00000299350	PTPRB	chr12	70974816	-	MYRFL	chr12	70345893	+	0.000212192	0.99978787
ENST00000261266	ENST00000535034	PTPRB	chr12	70974816	-	MYRFL	chr12	70345893	+	0.00033388	0.9996661
ENST00000551525	ENST00000552032	PTPRB	chr12	70974816	-	MYRFL	chr12	70345893	+	0.000260704	0.9997392
ENST00000551525	ENST00000547771	PTPRB	chr12	70974816	-	MYRFL	chr12	70345893	+	0.000202658	0.9997974
ENST00000551525	ENST00000299350	PTPRB	chr12	70974816	-	MYRFL	chr12	70345893	+	0.000260704	0.9997392
ENST00000551525	ENST00000535034	PTPRB	chr12	70974816	-	MYRFL	chr12	70345893	+	0.000502639	0.9994973

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 PTPRB-MYRFL

+/-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
PTPRB	chr12	70974816	MYRFL	chr12	70345893	1654	551	GISSRQVVVEGRTDKSKSVLARNALS
PTPRB	chr12	70974816	MYRFL	chr12	70345893	1654	551	GISSRQVVVEGRTEDKSKSVLARNAL
PTPRB	chr12	70974816	MYRFL	chr12	70345893	1683	554	GISSRQVVVEGRTDKSKSVLARNALS
PTPRB	chr12	70974816	MYRFL	chr12	70345893	1683	554	GISSRQVVVEGRTEDKSKSVLARNAL
PTPRB	chr12	70974816	MYRFL	chr12	70345893	1953	644	GISSRQVVVEGRTDKSKSVLARNALS
PTPRB	chr12	70974816	MYRFL	chr12	70345893	1953	644	GISSRQVVVEGRTEDKSKSVLARNAL
PTPRB	chr12	70974816	MYRFL	chr12	70345893	1954	644	GISSRQVVVEGRTDKSKSVLARNALS
PTPRB	chr12	70974816	MYRFL	chr12	70345893	1954	644	GISSRQVVVEGRTEDKSKSVLARNAL
PTPRB	chr12	70974816	MYRFL	chr12	70345893	2600	858	GISSRQVVVEGRTDKSKSVLARNALS
PTPRB	chr12	70974816	MYRFL	chr12	70345893	2600	858	GISSRQVVVEGRTEDKSKSVLARNAL
PTPRB	chr12	70974816	MYRFL	chr12	70345893	2604	859	GISSRQVVVEGRTDKSKSVLARNALS
PTPRB	chr12	70974816	MYRFL	chr12	70345893	2604	859	GISSRQVVVEGRTEDKSKSVLARNAL
PTPRB	chr12	70974816	MYRFL	chr12	70345893	2623	859	GISSRQVVVEGRTDKSKSVLARNALS
PTPRB	chr12	70974816	MYRFL	chr12	70345893	2623	859	GISSRQVVVEGRTEDKSKSVLARNAL

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Potential FusionNeoAntigen Information of PTPRB-MYRFL 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.

PTPRB-MYRFL_70974816_70345893.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)
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-B41:01	TEDKSKSV	0.9924	0.6923	12	20
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-B44:03	TEDKSKSVL	0.948	0.9374	12	21
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-B45:01	TEDKSKSVL	0.8868	0.6409	12	21
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-B18:01	TEDKSKSVL	0.7907	0.7828	12	21
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-B39:13	TEDKSKSVL	0.7703	0.7907	12	21
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-B39:01	TEDKSKSVL	0.7367	0.7948	12	21
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-B38:02	TEDKSKSVL	0.7351	0.8638	12	21
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-B15:10	TEDKSKSVL	0.6949	0.5201	12	21
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-B41:01	TEDKSKSVL	0.6175	0.7061	12	21
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-B50:01	TEDKSKSVL	0.5482	0.6377	12	21
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-B45:01	TEDKSKSVLA	0.9746	0.6649	12	22
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-A30:08	RTDKSKSVLA	0.8566	0.5591	11	21
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-B41:01	TEDKSKSVLA	0.8327	0.7322	12	22
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-B50:01	TEDKSKSVLA	0.8165	0.6902	12	22
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-B39:13	RTEDKSKSVL	0.4951	0.7355	11	21
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-B39:13	GRTEDKSKSVL	0.9984	0.6512	10	21
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-A74:09	RTDKSKSVLAR	0.9869	0.6085	11	22
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-A74:11	RTDKSKSVLAR	0.9869	0.6085	11	22
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-A74:03	RTDKSKSVLAR	0.9869	0.6085	11	22
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-A30:08	RTEDKSKSVLA	0.8985	0.7017	11	22
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-C05:09	RTDKSKSV	0.9999	0.7332	11	19
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-C08:15	RTDKSKSV	0.9994	0.7962	11	19
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-B39:08	TEDKSKSV	0.9912	0.7559	12	20
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-C04:10	RTDKSKSVL	0.9999	0.7452	11	20
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-C05:09	RTDKSKSVL	0.9999	0.8552	11	20
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-C04:07	RTDKSKSVL	0.9999	0.785	11	20
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-C08:15	RTDKSKSVL	0.9998	0.9406	11	20
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-C01:17	RTDKSKSVL	0.9995	0.9056	11	20
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-C03:07	RTDKSKSVL	0.9928	0.9165	11	20
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-C15:06	RTDKSKSVL	0.9927	0.7964	11	20
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-C03:19	RTDKSKSVL	0.9897	0.9482	11	20
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-C15:06	RTEDKSKSV	0.9894	0.9063	11	20
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-C03:08	RTDKSKSVL	0.9886	0.781	11	20
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-C01:30	RTDKSKSVL	0.9737	0.8989	11	20
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-C04:06	RTDKSKSVL	0.9704	0.6361	11	20
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-C08:04	RTDKSKSVL	0.9478	0.8555	11	20
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-C08:13	RTDKSKSVL	0.9478	0.8555	11	20
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-C04:14	RTDKSKSVL	0.9389	0.7681	11	20
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-B14:03	TEDKSKSVL	0.8951	0.7026	12	21
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-B39:08	TEDKSKSVL	0.8842	0.7653	12	21
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-C02:06	RTDKSKSVL	0.8421	0.8536	11	20
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-B39:08	RTDKSKSVL	0.7949	0.6598	11	20
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-B39:05	TEDKSKSVL	0.7464	0.7783	12	21
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-C08:03	RTDKSKSVL	0.7405	0.9484	11	20
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-C12:16	GRTDKSKSV	0.0008	0.8704	10	19
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-B39:08	RTEDKSKSVL	0.9288	0.7296	11	21
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-B39:08	GRTEDKSKSVL	0.9951	0.7523	10	21
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-C05:01	RTDKSKSV	0.9999	0.7332	11	19
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-C08:02	RTDKSKSV	0.9994	0.7962	11	19
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-C05:01	RTDKSKSVL	0.9999	0.8552	11	20
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-C04:01	RTDKSKSVL	0.9999	0.785	11	20
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-C04:03	RTDKSKSVL	0.9999	0.8134	11	20
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-C18:01	RTDKSKSVL	0.9998	0.7968	11	20
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-C01:03	RTDKSKSVL	0.9998	0.8494	11	20
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-C08:02	RTDKSKSVL	0.9998	0.9406	11	20
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-C01:02	RTDKSKSVL	0.9996	0.9048	11	20
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-C18:01	TEDKSKSVL	0.9995	0.8078	12	21
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-B40:04	TEDKSKSVL	0.9992	0.557	12	21
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-B27:09	GRTDKSKSV	0.9981	0.6155	10	19
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-B27:06	GRTDKSKSV	0.9981	0.5615	10	19
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-C15:02	RTEDKSKSV	0.9915	0.8754	11	20
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-C15:05	RTEDKSKSV	0.9906	0.8786	11	20
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-C15:05	RTDKSKSVL	0.99	0.7838	11	20
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-C15:02	RTDKSKSVL	0.9875	0.747	11	20
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-C03:03	RTDKSKSVL	0.9867	0.9634	11	20
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-C03:04	RTDKSKSVL	0.9867	0.9634	11	20
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-C03:17	RTDKSKSVL	0.9818	0.9358	11	20
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-C03:05	RTDKSKSVL	0.9779	0.8701	11	20
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-C16:02	RTDKSKSVL	0.9693	0.9765	11	20
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-B44:13	TEDKSKSVL	0.948	0.9374	12	21
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-B44:26	TEDKSKSVL	0.948	0.9374	12	21
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-B44:07	TEDKSKSVL	0.948	0.9374	12	21
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-B39:11	TEDKSKSVL	0.8724	0.7269	12	21
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-C03:06	RTDKSKSVL	0.8262	0.9617	11	20
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-B18:05	TEDKSKSVL	0.7907	0.7828	12	21
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-B39:02	TEDKSKSVL	0.7575	0.7949	12	21
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-B18:08	TEDKSKSVL	0.7438	0.6525	12	21
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-B39:31	TEDKSKSVL	0.7433	0.7957	12	21
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-C08:01	RTDKSKSVL	0.7405	0.9484	11	20
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-B18:03	TEDKSKSVL	0.7092	0.7666	12	21
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-B07:13	RTDKSKSVL	0.7004	0.7392	11	20
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-C06:08	GRTDKSKSV	0.6956	0.9487	10	19
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-B18:11	TEDKSKSVL	0.6936	0.7869	12	21
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-B50:04	TEDKSKSVL	0.5482	0.6377	12	21
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-B50:05	TEDKSKSVL	0.5482	0.6377	12	21
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-B15:09	TEDKSKSVL	0.5443	0.5324	12	21
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-C07:04	GRTDKSKSV	0.5197	0.8604	10	19
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-B57:02	RTDKSKSVL	0.4643	0.7908	11	20
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-C17:01	RTDKSKSVL	0.4386	0.7591	11	20
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-C06:02	GRTDKSKSV	0.0072	0.9448	10	19
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-C06:17	GRTDKSKSV	0.0072	0.9448	10	19
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-B27:06	GRTDKSKSVL	0.998	0.5084	10	20
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-A30:01	RTDKSKSVLA	0.8743	0.6854	11	21
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-B50:04	TEDKSKSVLA	0.8165	0.6902	12	22
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-B50:05	TEDKSKSVLA	0.8165	0.6902	12	22
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-B39:02	RTEDKSKSVL	0.6554	0.7344	11	21
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-B40:04	RTEDKSKSVL	0.5094	0.692	11	21
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-A74:01	RTDKSKSVLAR	0.9869	0.6085	11	22
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	HLA-A30:01	RTEDKSKSVLA	0.9125	0.8135	11	22

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Potential FusionNeoAntigen Information of PTPRB-MYRFL in HLA II

PTPRB-MYRFL_70974816_70345893.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)
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-0315	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-0324	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-0801	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-0805	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-0805	SSRQVVVEGRTEDKS	2	17
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-0806	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-0806	SSRQVVVEGRTEDKS	2	17
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-0810	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-0810	SSRQVVVEGRTEDKS	2	17
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-0812	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-0816	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-0818	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-0818	SSRQVVVEGRTEDKS	2	17
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-0822	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-0822	SSRQVVVEGRTEDKS	2	17
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-0826	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-0829	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-0839	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-0840	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-0840	SSRQVVVEGRTEDKS	2	17
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-0840	ISSRQVVVEGRTEDK	1	16
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-0840	RQVVVEGRTEDKSKS	4	19
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1134	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1150	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1153	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1156	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1179	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1183	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1183	SSRQVVVEGRTEDKS	2	17
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1188	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1303	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1303	SSRQVVVEGRTEDKS	2	17
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1303	ISSRQVVVEGRTEDK	1	16
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1303	RQVVVEGRTEDKSKS	4	19
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1304	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-13101	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-13101	SSRQVVVEGRTEDKS	2	17
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-13101	ISSRQVVVEGRTEDK	1	16
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-13101	RQVVVEGRTEDKSKS	4	19
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1310	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1310	SSRQVVVEGRTEDKS	2	17
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1310	ISSRQVVVEGRTEDK	1	16
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1310	RQVVVEGRTEDKSKS	4	19
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1312	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1312	SSRQVVVEGRTEDKS	2	17
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1312	ISSRQVVVEGRTEDK	1	16
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1312	RQVVVEGRTEDKSKS	4	19
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1313	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1313	SSRQVVVEGRTEDKS	2	17
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1321	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1330	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1330	SSRQVVVEGRTEDKS	2	17
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1332	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1332	SSRQVVVEGRTEDKS	2	17
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1333	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1333	SSRQVVVEGRTEDKS	2	17
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1333	ISSRQVVVEGRTEDK	1	16
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1333	RQVVVEGRTEDKSKS	4	19
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1337	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1338	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1338	SSRQVVVEGRTEDKS	2	17
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1344	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1348	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1348	SSRQVVVEGRTEDKS	2	17
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1349	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1349	SSRQVVVEGRTEDKS	2	17
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1355	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1358	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1358	SSRQVVVEGRTEDKS	2	17
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1358	ISSRQVVVEGRTEDK	1	16
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1358	RQVVVEGRTEDKSKS	4	19
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1365	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1365	SSRQVVVEGRTEDKS	2	17
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1366	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1366	SSRQVVVEGRTEDKS	2	17
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1366	ISSRQVVVEGRTEDK	1	16
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1366	RQVVVEGRTEDKSKS	4	19
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1375	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1381	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1381	SSRQVVVEGRTEDKS	2	17
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1381	ISSRQVVVEGRTEDK	1	16
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1381	RQVVVEGRTEDKSKS	4	19
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1388	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1388	SSRQVVVEGRTEDKS	2	17
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1388	ISSRQVVVEGRTEDK	1	16
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1388	RQVVVEGRTEDKSKS	4	19
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1389	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1389	SSRQVVVEGRTEDKS	2	17
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1389	ISSRQVVVEGRTEDK	1	16
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1389	RQVVVEGRTEDKSKS	4	19
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1390	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1390	SSRQVVVEGRTEDKS	2	17
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1390	ISSRQVVVEGRTEDK	1	16
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1390	RQVVVEGRTEDKSKS	4	19
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1393	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1394	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1394	SSRQVVVEGRTEDKS	2	17
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1394	ISSRQVVVEGRTEDK	1	16
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1394	RQVVVEGRTEDKSKS	4	19
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1395	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1395	SSRQVVVEGRTEDKS	2	17
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1395	ISSRQVVVEGRTEDK	1	16
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1395	RQVVVEGRTEDKSKS	4	19
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1409	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1413	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1413	SSRQVVVEGRTEDKS	2	17
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1417	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1421	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1421	SSRQVVVEGRTEDKS	2	17
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1422	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1422	SSRQVVVEGRTEDKS	2	17
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1425	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1425	SSRQVVVEGRTEDKS	2	17
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1433	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1433	SSRQVVVEGRTEDKS	2	17
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1437	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1465	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1465	SSRQVVVEGRTEDKS	2	17
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1469	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1469	SSRQVVVEGRTEDKS	2	17
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1473	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1474	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1474	SSRQVVVEGRTEDKS	2	17
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1474	ISSRQVVVEGRTEDK	1	16
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1478	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1480	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1480	SSRQVVVEGRTEDKS	2	17
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB1-1485	SRQVVVEGRTEDKSK	3	18
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB4-0101	RQVVVEGRTDKSKSV	4	19
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB4-0103	RQVVVEGRTDKSKSV	4	19
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB4-0104	RQVVVEGRTDKSKSV	4	19
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB4-0106	RQVVVEGRTDKSKSV	4	19
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB4-0107	RQVVVEGRTDKSKSV	4	19
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1954	DRB4-0108	RQVVVEGRTDKSKSV	4	19

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Fusion breakpoint peptide structures of PTPRB-MYRFL

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
10381	VVVEGRTDKSKSVL	PTPRB	MYRFL	chr12	70974816	chr12	70345893	1954

File name	BPseq	Hgene	Tgene	Hchr	Hbp	Tchr	Tbp	AAlen
10382	VVVEGRTEDKSKSV	PTPRB	MYRFL	chr12	70974816	chr12	70345893	1954

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of PTPRB-MYRFL

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	10381	VVVEGRTDKSKSVL	-7.9962	-8.1096
HLA-B14:02	3BVN	10381	VVVEGRTDKSKSVL	-5.70842	-6.74372
HLA-B52:01	3W39	10381	VVVEGRTDKSKSVL	-6.83737	-6.95077
HLA-B52:01	3W39	10381	VVVEGRTDKSKSVL	-4.4836	-5.5189
HLA-A11:01	4UQ2	10381	VVVEGRTDKSKSVL	-10.0067	-10.1201
HLA-A11:01	4UQ2	10381	VVVEGRTDKSKSVL	-9.03915	-10.0745
HLA-A24:02	5HGA	10381	VVVEGRTDKSKSVL	-6.56204	-6.67544
HLA-A24:02	5HGA	10381	VVVEGRTDKSKSVL	-5.42271	-6.45801
HLA-B44:05	3DX8	10381	VVVEGRTDKSKSVL	-7.85648	-8.89178
HLA-B44:05	3DX8	10381	VVVEGRTDKSKSVL	-5.3978	-5.5112
HLA-B35:01	1A1N	10381	VVVEGRTDKSKSVL	-6.27422	-6.38762
HLA-B35:01	1A1N	10381	VVVEGRTDKSKSVL	-5.27424	-6.30954
HLA-A02:01	6TDR	10381	VVVEGRTDKSKSVL	-3.37154	-4.40684
HLA-B14:02	3BVN	10382	VVVEGRTEDKSKSV	-7.9962	-8.1096
HLA-B14:02	3BVN	10382	VVVEGRTEDKSKSV	-5.70842	-6.74372
HLA-B52:01	3W39	10382	VVVEGRTEDKSKSV	-6.83737	-6.95077
HLA-B52:01	3W39	10382	VVVEGRTEDKSKSV	-4.4836	-5.5189
HLA-A11:01	4UQ2	10382	VVVEGRTEDKSKSV	-10.0067	-10.1201
HLA-A11:01	4UQ2	10382	VVVEGRTEDKSKSV	-9.03915	-10.0745
HLA-A24:02	5HGA	10382	VVVEGRTEDKSKSV	-6.56204	-6.67544
HLA-A24:02	5HGA	10382	VVVEGRTEDKSKSV	-5.42271	-6.45801
HLA-B44:05	3DX8	10382	VVVEGRTEDKSKSV	-7.85648	-8.89178
HLA-B44:05	3DX8	10382	VVVEGRTEDKSKSV	-5.3978	-5.5112
HLA-B35:01	1A1N	10382	VVVEGRTEDKSKSV	-6.27422	-6.38762
HLA-B35:01	1A1N	10382	VVVEGRTEDKSKSV	-5.27424	-6.30954
HLA-A02:01	6TDR	10382	VVVEGRTEDKSKSV	-3.37154	-4.40684

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Vaccine Design for the FusionNeoAntigens of PTPRB-MYRFL

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
PTPRB-MYRFL	chr12	70974816	chr12	70345893	10	19	GRTDKSKSV	GAAGAACAGACAAAAGCAAATCAGTTT
PTPRB-MYRFL	chr12	70974816	chr12	70345893	10	20	GRTDKSKSVL	GAAGAACAGACAAAAGCAAATCAGTTTTGG
PTPRB-MYRFL	chr12	70974816	chr12	70345893	10	21	GRTEDKSKSVL	GAAGAACAGAAGACAAAAGCAAATCAGTTTTGG
PTPRB-MYRFL	chr12	70974816	chr12	70345893	11	19	RTDKSKSV	GAACAGACAAAAGCAAATCAGTTT
PTPRB-MYRFL	chr12	70974816	chr12	70345893	11	20	RTDKSKSVL	GAACAGACAAAAGCAAATCAGTTTTGG
PTPRB-MYRFL	chr12	70974816	chr12	70345893	11	20	RTEDKSKSV	GAACAGAAGACAAAAGCAAATCAGTTT
PTPRB-MYRFL	chr12	70974816	chr12	70345893	11	21	RTDKSKSVLA	GAACAGACAAAAGCAAATCAGTTTTGGCAA
PTPRB-MYRFL	chr12	70974816	chr12	70345893	11	21	RTEDKSKSVL	GAACAGAAGACAAAAGCAAATCAGTTTTGG
PTPRB-MYRFL	chr12	70974816	chr12	70345893	11	22	RTDKSKSVLAR	GAACAGACAAAAGCAAATCAGTTTTGGCAAGAA
PTPRB-MYRFL	chr12	70974816	chr12	70345893	11	22	RTEDKSKSVLA	GAACAGAAGACAAAAGCAAATCAGTTTTGGCAA
PTPRB-MYRFL	chr12	70974816	chr12	70345893	12	20	TEDKSKSV	CAGAAGACAAAAGCAAATCAGTTT
PTPRB-MYRFL	chr12	70974816	chr12	70345893	12	21	TEDKSKSVL	CAGAAGACAAAAGCAAATCAGTTTTGG
PTPRB-MYRFL	chr12	70974816	chr12	70345893	12	22	TEDKSKSVLA	CAGAAGACAAAAGCAAATCAGTTTTGGCAA

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
PTPRB-MYRFL	chr12	70974816	chr12	70345893	1	16	ISSRQVVVEGRTEDK	TCTCTTCCCGACAAGTGGTTGTGGAGGGAAGAACAGAAGACAAAA
PTPRB-MYRFL	chr12	70974816	chr12	70345893	2	17	SSRQVVVEGRTEDKS	CTTCCCGACAAGTGGTTGTGGAGGGAAGAACAGAAGACAAAAGCA
PTPRB-MYRFL	chr12	70974816	chr12	70345893	3	18	SRQVVVEGRTEDKSK	CCCGACAAGTGGTTGTGGAGGGAAGAACAGAAGACAAAAGCAAAT
PTPRB-MYRFL	chr12	70974816	chr12	70345893	4	19	RQVVVEGRTDKSKSV	GACAAGTGGTTGTGGAGGGAAGAACAGACAAAAGCAAATCAGTTT
PTPRB-MYRFL	chr12	70974816	chr12	70345893	4	19	RQVVVEGRTEDKSKS	GACAAGTGGTTGTGGAGGGAAGAACAGAAGACAAAAGCAAATCAG

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Information of the samples that have these potential fusion neoantigens of PTPRB-MYRFL

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	PTPRB-MYRFL	chr12	70974816	ENST00000261266	chr12	70345893	ENST00000299350	TCGA-BR-A44T-01A
STAD	PTPRB-MYRFL	chr12	70974816	ENST00000261266	chr12	70345893	ENST00000547771	TCGA-BR-A44T-01A

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Potential target of CAR-T therapy development for PTPRB-MYRFL

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 PTPRB-MYRFL

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 PTPRB-MYRFL

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)