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Fusion Protein:PTPRS-ZNF20

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: PTPRS-ZNF20
	FusionPDB ID: 70548
	FusionGDB2.0 ID: 70548
		Hgene	Tgene
	Gene symbol	PTPRS	ZNF20
	Gene ID	5802	10168
	Gene name	protein tyrosine phosphatase receptor type S	zinc finger protein 197
	Synonyms	PTPSIGMA\|R-PTP-S\|R-PTP-sigma	D3S1363E\|P18\|VHLaK\|ZKSCAN9\|ZNF166\|ZNF20\|ZSCAN41
	Cytomap	19p13.3	3p21.31
	Type of gene	protein-coding	protein-coding
	Description	receptor-type tyrosine-protein phosphatase Sprotein tyrosine phosphatase PTPsigmareceptor-type tyrosine-protein phosphatase sigma	zinc finger protein 197VHL-associated KRAB-A domain-containing proteinpVHL-associated KRAB domain-containing proteinzinc finger protein 166zinc finger protein 20zinc finger protein with KRAB and SCAN domains 9
	Modification date	20200322	20200313
	UniProtAcc	.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000262963, ENST00000348075, ENST00000353284, ENST00000357368, ENST00000372412, ENST00000587303, ENST00000588012, ENST00000590509, ENST00000592099, ENST00000588552,	ENST00000485451, ENST00000334213, ENST00000600335,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	20 X 19 X 8=3040	1 X 1 X 1=1
	# samples	23	1
	** MAII score	log2(23/3040*10)=-3.72436555738657 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(1/1*10)=3.32192809488736
Fusion gene context	PubMed: PTPRS [Title/Abstract] AND ZNF20 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: PTPRS [Title/Abstract] AND ZNF20 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	PTPRS(5274209)-ZNF20(12246710), # samples:1
Anticipated loss of major functional domain due to fusion event.	PTPRS-ZNF20 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. PTPRS-ZNF20 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. PTPRS-ZNF20 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. PTPRS-ZNF20 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	PTPRS	GO:0006470	protein dephosphorylation	8524829
Hgene	PTPRS	GO:0099560	synaptic membrane adhesion	23345436

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr19:5274209/chr19:12246710)
- 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 PTPRS (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 ZNF20 (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)
ENST00000262963	PTPRS	chr19	5274209	-	ENST00000600335	ZNF20	chr19	12246710	-	869	471	225	863	212
ENST00000262963	PTPRS	chr19	5274209	-	ENST00000334213	ZNF20	chr19	12246710	-	3295	471	466	1869	467
ENST00000372412	PTPRS	chr19	5274209	-	ENST00000600335	ZNF20	chr19	12246710	-	869	471	225	863	212
ENST00000372412	PTPRS	chr19	5274209	-	ENST00000334213	ZNF20	chr19	12246710	-	3295	471	466	1869	467
ENST00000348075	PTPRS	chr19	5274209	-	ENST00000600335	ZNF20	chr19	12246710	-	869	471	225	863	212
ENST00000348075	PTPRS	chr19	5274209	-	ENST00000334213	ZNF20	chr19	12246710	-	3295	471	466	1869	467
ENST00000357368	PTPRS	chr19	5274209	-	ENST00000600335	ZNF20	chr19	12246710	-	869	471	225	863	212
ENST00000357368	PTPRS	chr19	5274209	-	ENST00000334213	ZNF20	chr19	12246710	-	3295	471	466	1869	467
ENST00000353284	PTPRS	chr19	5274209	-	ENST00000600335	ZNF20	chr19	12246710	-	869	471	225	863	212
ENST00000353284	PTPRS	chr19	5274209	-	ENST00000334213	ZNF20	chr19	12246710	-	3295	471	466	1869	467
ENST00000587303	PTPRS	chr19	5274209	-	ENST00000600335	ZNF20	chr19	12246710	-	735	337	91	729	212
ENST00000587303	PTPRS	chr19	5274209	-	ENST00000334213	ZNF20	chr19	12246710	-	3161	337	332	1735	467
ENST00000588012	PTPRS	chr19	5274209	-	ENST00000600335	ZNF20	chr19	12246710	-	658	260	14	652	212
ENST00000588012	PTPRS	chr19	5274209	-	ENST00000334213	ZNF20	chr19	12246710	-	3084	260	255	1658	467
ENST00000592099	PTPRS	chr19	5274209	-	ENST00000600335	ZNF20	chr19	12246710	-	658	260	14	652	212
ENST00000592099	PTPRS	chr19	5274209	-	ENST00000334213	ZNF20	chr19	12246710	-	3084	260	255	1658	467
ENST00000590509	PTPRS	chr19	5274209	-	ENST00000600335	ZNF20	chr19	12246710	-	883	485	239	877	212
ENST00000590509	PTPRS	chr19	5274209	-	ENST00000334213	ZNF20	chr19	12246710	-	3309	485	480	1883	467

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
ENST00000262963	ENST00000600335	PTPRS	chr19	5274209	-	ZNF20	chr19	12246710	-	0.003745625	0.9962543
ENST00000262963	ENST00000334213	PTPRS	chr19	5274209	-	ZNF20	chr19	12246710	-	0.000148584	0.99985135
ENST00000372412	ENST00000600335	PTPRS	chr19	5274209	-	ZNF20	chr19	12246710	-	0.003745625	0.9962543
ENST00000372412	ENST00000334213	PTPRS	chr19	5274209	-	ZNF20	chr19	12246710	-	0.000148584	0.99985135
ENST00000348075	ENST00000600335	PTPRS	chr19	5274209	-	ZNF20	chr19	12246710	-	0.003745625	0.9962543
ENST00000348075	ENST00000334213	PTPRS	chr19	5274209	-	ZNF20	chr19	12246710	-	0.000148584	0.99985135
ENST00000357368	ENST00000600335	PTPRS	chr19	5274209	-	ZNF20	chr19	12246710	-	0.003745625	0.9962543
ENST00000357368	ENST00000334213	PTPRS	chr19	5274209	-	ZNF20	chr19	12246710	-	0.000148584	0.99985135
ENST00000353284	ENST00000600335	PTPRS	chr19	5274209	-	ZNF20	chr19	12246710	-	0.003745625	0.9962543
ENST00000353284	ENST00000334213	PTPRS	chr19	5274209	-	ZNF20	chr19	12246710	-	0.000148584	0.99985135
ENST00000587303	ENST00000600335	PTPRS	chr19	5274209	-	ZNF20	chr19	12246710	-	0.005145657	0.9948544
ENST00000587303	ENST00000334213	PTPRS	chr19	5274209	-	ZNF20	chr19	12246710	-	0.000121801	0.99987817
ENST00000588012	ENST00000600335	PTPRS	chr19	5274209	-	ZNF20	chr19	12246710	-	0.006317513	0.9936825
ENST00000588012	ENST00000334213	PTPRS	chr19	5274209	-	ZNF20	chr19	12246710	-	0.000119315	0.9998807
ENST00000592099	ENST00000600335	PTPRS	chr19	5274209	-	ZNF20	chr19	12246710	-	0.006317513	0.9936825
ENST00000592099	ENST00000334213	PTPRS	chr19	5274209	-	ZNF20	chr19	12246710	-	0.000119315	0.9998807
ENST00000590509	ENST00000600335	PTPRS	chr19	5274209	-	ZNF20	chr19	12246710	-	0.00545629	0.9945437
ENST00000590509	ENST00000334213	PTPRS	chr19	5274209	-	ZNF20	chr19	12246710	-	0.000128448	0.9998715

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 PTPRS-ZNF20

+/-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
PTPRS	chr19	5274209	ZNF20	chr19	12246710	260	103	DSFQSHDKACTKEKPYDGKECTETFI
PTPRS	chr19	5274209	ZNF20	chr19	12246710	260	122	ECTETFISHSCIQRHRVMHSGDGPYK
PTPRS	chr19	5274209	ZNF20	chr19	12246710	260	127	FISHSCIQRHRVMHSGDGPYKCKFCG
PTPRS	chr19	5274209	ZNF20	chr19	12246710	260	15	LMREKLCESKESHHCGESFNQIADDM
PTPRS	chr19	5274209	ZNF20	chr19	12246710	260	32	SFNQIADDMLNRKTLPGITPCESSVC
PTPRS	chr19	5274209	ZNF20	chr19	12246710	260	34	NQIADDMLNRKTLPGITPCESSVCGE
PTPRS	chr19	5274209	ZNF20	chr19	12246710	260	38	DDMLNRKTLPGITPCESSVCGEVGTG
PTPRS	chr19	5274209	ZNF20	chr19	12246710	260	46	LPGITPCESSVCGEVGTGHSSLNTHI
PTPRS	chr19	5274209	ZNF20	chr19	12246710	260	73	ADTGHKSSEYQEYGENPYRNKECKKA
PTPRS	chr19	5274209	ZNF20	chr19	12246710	260	76	GHKSSEYQEYGENPYRNKECKKAFSY
PTPRS	chr19	5274209	ZNF20	chr19	12246710	260	80	TWNKKGKKVNSQRFEDSVAFEDVAVS
PTPRS	chr19	5274209	ZNF20	chr19	12246710	337	103	DSFQSHDKACTKEKPYDGKECTETFI
PTPRS	chr19	5274209	ZNF20	chr19	12246710	337	122	ECTETFISHSCIQRHRVMHSGDGPYK
PTPRS	chr19	5274209	ZNF20	chr19	12246710	337	127	FISHSCIQRHRVMHSGDGPYKCKFCG
PTPRS	chr19	5274209	ZNF20	chr19	12246710	337	15	LMREKLCESKESHHCGESFNQIADDM
PTPRS	chr19	5274209	ZNF20	chr19	12246710	337	32	SFNQIADDMLNRKTLPGITPCESSVC
PTPRS	chr19	5274209	ZNF20	chr19	12246710	337	34	NQIADDMLNRKTLPGITPCESSVCGE
PTPRS	chr19	5274209	ZNF20	chr19	12246710	337	38	DDMLNRKTLPGITPCESSVCGEVGTG
PTPRS	chr19	5274209	ZNF20	chr19	12246710	337	46	LPGITPCESSVCGEVGTGHSSLNTHI
PTPRS	chr19	5274209	ZNF20	chr19	12246710	337	73	ADTGHKSSEYQEYGENPYRNKECKKA
PTPRS	chr19	5274209	ZNF20	chr19	12246710	337	76	GHKSSEYQEYGENPYRNKECKKAFSY
PTPRS	chr19	5274209	ZNF20	chr19	12246710	337	80	TWNKKGKKVNSQRFEDSVAFEDVAVS
PTPRS	chr19	5274209	ZNF20	chr19	12246710	471	103	DSFQSHDKACTKEKPYDGKECTETFI
PTPRS	chr19	5274209	ZNF20	chr19	12246710	471	122	ECTETFISHSCIQRHRVMHSGDGPYK
PTPRS	chr19	5274209	ZNF20	chr19	12246710	471	127	FISHSCIQRHRVMHSGDGPYKCKFCG
PTPRS	chr19	5274209	ZNF20	chr19	12246710	471	15	LMREKLCESKESHHCGESFNQIADDM
PTPRS	chr19	5274209	ZNF20	chr19	12246710	471	32	SFNQIADDMLNRKTLPGITPCESSVC
PTPRS	chr19	5274209	ZNF20	chr19	12246710	471	34	NQIADDMLNRKTLPGITPCESSVCGE
PTPRS	chr19	5274209	ZNF20	chr19	12246710	471	38	DDMLNRKTLPGITPCESSVCGEVGTG
PTPRS	chr19	5274209	ZNF20	chr19	12246710	471	46	LPGITPCESSVCGEVGTGHSSLNTHI
PTPRS	chr19	5274209	ZNF20	chr19	12246710	471	73	ADTGHKSSEYQEYGENPYRNKECKKA
PTPRS	chr19	5274209	ZNF20	chr19	12246710	471	76	GHKSSEYQEYGENPYRNKECKKAFSY
PTPRS	chr19	5274209	ZNF20	chr19	12246710	471	80	TWNKKGKKVNSQRFEDSVAFEDVAVS
PTPRS	chr19	5274209	ZNF20	chr19	12246710	485	103	DSFQSHDKACTKEKPYDGKECTETFI
PTPRS	chr19	5274209	ZNF20	chr19	12246710	485	122	ECTETFISHSCIQRHRVMHSGDGPYK
PTPRS	chr19	5274209	ZNF20	chr19	12246710	485	127	FISHSCIQRHRVMHSGDGPYKCKFCG
PTPRS	chr19	5274209	ZNF20	chr19	12246710	485	15	LMREKLCESKESHHCGESFNQIADDM
PTPRS	chr19	5274209	ZNF20	chr19	12246710	485	32	SFNQIADDMLNRKTLPGITPCESSVC
PTPRS	chr19	5274209	ZNF20	chr19	12246710	485	34	NQIADDMLNRKTLPGITPCESSVCGE
PTPRS	chr19	5274209	ZNF20	chr19	12246710	485	38	DDMLNRKTLPGITPCESSVCGEVGTG
PTPRS	chr19	5274209	ZNF20	chr19	12246710	485	46	LPGITPCESSVCGEVGTGHSSLNTHI
PTPRS	chr19	5274209	ZNF20	chr19	12246710	485	73	ADTGHKSSEYQEYGENPYRNKECKKA
PTPRS	chr19	5274209	ZNF20	chr19	12246710	485	76	GHKSSEYQEYGENPYRNKECKKAFSY
PTPRS	chr19	5274209	ZNF20	chr19	12246710	485	80	TWNKKGKKVNSQRFEDSVAFEDVAVS

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Potential FusionNeoAntigen Information of PTPRS-ZNF20 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.

PTPRS-ZNF20_5274209_12246710.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)
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B39:06	QRFEDSVA	0.9995	0.8006	11	19
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B18:01	QEYGENPY	0.9965	0.9316	10	18
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B27:04	QRFEDSVAF	0.9997	0.7551	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B27:05	QRFEDSVAF	0.9997	0.7408	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B27:07	QRFEDSVAF	0.9991	0.5366	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B14:01	QRFEDSVAF	0.9885	0.6877	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B14:02	QRFEDSVAF	0.9885	0.6877	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B39:01	QRFEDSVAF	0.9855	0.8679	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B39:06	QRFEDSVAF	0.9798	0.6024	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B38:01	QRFEDSVAF	0.9659	0.9468	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B38:02	QRFEDSVAF	0.9643	0.9413	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B39:13	QRFEDSVAF	0.9538	0.8696	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B15:25	YQEYGENPY	0.9142	0.9092	9	18
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B15:03	QRFEDSVAF	0.8835	0.8892	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B15:18	QRFEDSVAF	0.8687	0.821	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B15:10	QRFEDSVAF	0.8338	0.6453	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B15:02	YQEYGENPY	0.8317	0.9152	9	18
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B15:37	QRFEDSVAF	0.6607	0.6764	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B15:18	YQEYGENPY	0.427	0.7528	9	18
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B15:03	YQEYGENPY	0.3931	0.7822	9	18
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B15:03	GKKVNSQRF	0.153	0.7033	5	14
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B07:10	QRFEDSVAF	0.066	0.5219	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B15:01	SQRFEDSVAF	0.9999	0.8581	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B27:04	SQRFEDSVAF	0.9979	0.7002	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B27:05	SQRFEDSVAF	0.9979	0.6638	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B15:25	SQRFEDSVAF	0.988	0.8662	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B15:03	SQRFEDSVAF	0.9803	0.7444	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B45:01	SEYQEYGENP	0.9742	0.7892	7	17
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B15:02	SQRFEDSVAF	0.9671	0.8849	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B50:02	SEYQEYGENP	0.9554	0.6981	7	17
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B15:18	SQRFEDSVAF	0.9248	0.7018	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B13:01	SQRFEDSVAF	0.897	0.7948	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B50:01	SEYQEYGENP	0.8883	0.7694	7	17
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B39:01	SQRFEDSVAF	0.8761	0.7134	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B41:01	SEYQEYGENP	0.8229	0.846	7	17
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B39:13	SQRFEDSVAF	0.7935	0.7189	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B38:01	SQRFEDSVAF	0.7932	0.8733	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B38:02	SQRFEDSVAF	0.784	0.8798	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B15:10	SQRFEDSVAF	0.78	0.5339	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B15:37	SQRFEDSVAF	0.6692	0.6008	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B44:03	SEYQEYGENPY	0.9997	0.9129	7	18
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B27:04	NSQRFEDSVAF	0.9989	0.5266	9	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B27:05	NSQRFEDSVAF	0.9988	0.5235	9	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B18:01	SEYQEYGENPY	0.9916	0.9094	7	18
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B38:01	NSQRFEDSVAF	0.7255	0.7401	9	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B38:02	NSQRFEDSVAF	0.706	0.7727	9	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B73:01	QRFEDSVA	0.9975	0.644	11	19
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-C04:10	RFEDSVAF	0.9968	0.8248	12	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-C04:07	RFEDSVAF	0.9967	0.8156	12	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-C04:14	RFEDSVAF	0.98	0.815	12	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B27:14	QRFEDSVAF	0.9996	0.731	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-C07:05	QRFEDSVAF	0.9977	0.9496	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-C07:95	QRFEDSVAF	0.9967	0.7341	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-C07:29	QRFEDSVAF	0.9964	0.9345	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-C07:13	QRFEDSVAF	0.9961	0.948	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-C07:27	QRFEDSVAF	0.994	0.9501	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B39:09	QRFEDSVAF	0.9855	0.5522	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B27:03	QRFEDSVAF	0.9855	0.7601	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B39:12	QRFEDSVAF	0.9842	0.8723	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-C07:46	QRFEDSVAF	0.9784	0.9008	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B39:05	QRFEDSVAF	0.9597	0.8422	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-C07:19	QRFEDSVAF	0.9497	0.7607	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-C07:80	QRFEDSVAF	0.9372	0.9491	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-C07:67	QRFEDSVAF	0.9372	0.9491	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-C07:10	QRFEDSVAF	0.9092	0.9684	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B15:05	YQEYGENPY	0.9046	0.8577	9	18
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B15:31	YQEYGENPY	0.8504	0.8644	9	18
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B15:21	YQEYGENPY	0.8476	0.9043	9	18
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B15:04	SQRFEDSVA	0.84	0.9115	10	19
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B15:21	QRFEDSVAF	0.796	0.9297	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B73:01	QRFEDSVAF	0.7316	0.5454	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-C12:16	QRFEDSVAF	0.4567	0.9512	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B14:03	QRFEDSVAF	0.366	0.7998	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B15:04	SQRFEDSVAF	0.9997	0.8855	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B15:07	SQRFEDSVAF	0.9997	0.6988	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-C12:16	SQRFEDSVAF	0.999	0.9448	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B27:14	SQRFEDSVAF	0.9978	0.6286	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-C07:05	SQRFEDSVAF	0.9918	0.9183	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-C07:19	SQRFEDSVAF	0.9811	0.632	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-C07:46	SQRFEDSVAF	0.9798	0.8631	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-C07:80	SQRFEDSVAF	0.9796	0.9204	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-C07:67	SQRFEDSVAF	0.9796	0.9204	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-C07:10	SQRFEDSVAF	0.9745	0.9426	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B40:06	SEYQEYGENP	0.9723	0.5942	7	17
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B15:21	SQRFEDSVAF	0.9723	0.8498	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-C07:95	SQRFEDSVAF	0.9687	0.5981	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-C07:27	SQRFEDSVAF	0.9648	0.9272	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B27:03	SQRFEDSVAF	0.9059	0.6845	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B39:08	SQRFEDSVAF	0.9033	0.7931	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B15:05	SQRFEDSVAF	0.8875	0.7905	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B15:31	SQRFEDSVAF	0.884	0.7945	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B39:12	SQRFEDSVAF	0.8825	0.7346	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B27:03	NSQRFEDSVAF	0.9683	0.567	9	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B39:12	NSQRFEDSVAF	0.8731	0.6246	9	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B18:08	QEYGENPY	0.9968	0.9073	10	18
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B18:04	QEYGENPY	0.9967	0.9397	10	18
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-C04:01	RFEDSVAF	0.9967	0.8156	12	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B18:05	QEYGENPY	0.9965	0.9316	10	18
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-C18:01	RFEDSVAF	0.9965	0.8158	12	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B18:06	QEYGENPY	0.9962	0.9364	10	18
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B18:03	QEYGENPY	0.9929	0.9219	10	18
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B18:11	QEYGENPY	0.9874	0.9338	10	18
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-C14:02	RFEDSVAF	0.9853	0.9725	12	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-C14:03	RFEDSVAF	0.9853	0.9725	12	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B27:06	QRFEDSVAF	0.9997	0.7703	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B27:08	QRFEDSVAF	0.9997	0.6289	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B27:10	QRFEDSVAF	0.9997	0.8624	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B27:09	QRFEDSVAF	0.9985	0.7385	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-C07:01	QRFEDSVAF	0.9977	0.7132	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-C07:17	QRFEDSVAF	0.9932	0.9556	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B15:50	YQEYGENPY	0.9876	0.9081	9	18
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B39:02	QRFEDSVAF	0.9846	0.8674	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B39:31	QRFEDSVAF	0.9842	0.8721	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B15:12	YQEYGENPY	0.976	0.8126	9	18
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B38:05	QRFEDSVAF	0.9659	0.9468	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-C06:08	QRFEDSVAF	0.9454	0.9821	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-C07:22	QRFEDSVAF	0.9433	0.7597	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-C07:02	QRFEDSVAF	0.9372	0.9491	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-C07:04	QRFEDSVAF	0.927	0.9521	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B15:39	YQEYGENPY	0.9101	0.8437	9	18
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B15:20	YQEYGENPY	0.9058	0.9071	9	18
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B15:53	YQEYGENPY	0.8814	0.8355	9	18
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B35:28	YQEYGENPY	0.8616	0.9053	9	18
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B35:20	YQEYGENPY	0.8485	0.9106	9	18
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B18:04	YQEYGENPY	0.8297	0.9441	9	18
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B48:02	QRFEDSVAF	0.8089	0.9611	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B15:09	QRFEDSVAF	0.7398	0.7803	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B39:11	QRFEDSVAF	0.6861	0.8448	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-C03:67	QRFEDSVAF	0.6419	0.9777	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B15:54	YQEYGENPY	0.6332	0.8113	9	18
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B18:07	QRFEDSVAF	0.5901	0.7646	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B18:03	QRFEDSVAF	0.5801	0.8409	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B15:54	QRFEDSVAF	0.5498	0.8817	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B15:68	QRFEDSVAF	0.5151	0.7382	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B15:53	QRFEDSVAF	0.5068	0.8979	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-C06:06	QRFEDSVAF	0.4967	0.9888	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B48:02	YQEYGENPY	0.3782	0.8872	9	18
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-C06:17	QRFEDSVAF	0.172	0.985	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-C06:02	QRFEDSVAF	0.172	0.985	11	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B15:68	GKKVNSQRF	0.1598	0.511	5	14
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B15:54	GKKVNSQRF	0.0719	0.8115	5	14
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B15:53	GKKVNSQRF	0.0504	0.8302	5	14
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B15:27	SQRFEDSVAF	0.9999	0.8652	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B15:24	SQRFEDSVAF	0.9999	0.8636	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B15:50	SQRFEDSVAF	0.9999	0.8718	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B15:53	SQRFEDSVAF	0.9999	0.8236	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B15:125	SQRFEDSVAF	0.9999	0.8581	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B15:135	SQRFEDSVAF	0.9999	0.8753	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B15:33	SQRFEDSVAF	0.9999	0.8581	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B15:34	SQRFEDSVAF	0.9999	0.8581	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B15:35	SQRFEDSVAF	0.9997	0.8503	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B15:68	SQRFEDSVAF	0.9996	0.6365	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B15:54	SQRFEDSVAF	0.9994	0.8129	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B15:73	SQRFEDSVAF	0.9981	0.6932	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B27:10	SQRFEDSVAF	0.998	0.8046	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B27:08	SQRFEDSVAF	0.998	0.5494	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B15:30	SQRFEDSVAF	0.9972	0.6468	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B27:06	SQRFEDSVAF	0.997	0.6653	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B15:12	SQRFEDSVAF	0.9967	0.9038	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B27:09	SQRFEDSVAF	0.9965	0.6747	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B15:39	SQRFEDSVAF	0.9897	0.8003	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-C07:22	SQRFEDSVAF	0.9863	0.6673	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-C07:02	SQRFEDSVAF	0.9796	0.9204	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-C07:01	SQRFEDSVAF	0.9686	0.576	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B15:13	SQRFEDSVAF	0.9213	0.5589	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B48:02	SQRFEDSVAF	0.9141	0.8555	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B39:02	SQRFEDSVAF	0.8896	0.7301	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B50:04	SEYQEYGENP	0.8883	0.7694	7	17
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B50:05	SEYQEYGENP	0.8883	0.7694	7	17
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B15:20	SQRFEDSVAF	0.8843	0.8456	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B39:31	SQRFEDSVAF	0.8842	0.728	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B35:28	SQRFEDSVAF	0.8788	0.8807	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B35:20	SQRFEDSVAF	0.8609	0.8847	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B38:05	SQRFEDSVAF	0.7932	0.8733	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B18:04	SQRFEDSVAF	0.6653	0.888	10	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B44:13	SEYQEYGENPY	0.9997	0.9129	7	18
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B44:26	SEYQEYGENPY	0.9997	0.9129	7	18
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B44:07	SEYQEYGENPY	0.9997	0.9129	7	18
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B27:06	NSQRFEDSVAF	0.9989	0.5215	9	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B18:11	SEYQEYGENPY	0.9987	0.8427	7	18
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B27:09	NSQRFEDSVAF	0.9985	0.535	9	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B18:08	SEYQEYGENPY	0.9944	0.8587	7	18
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B18:04	SEYQEYGENPY	0.9926	0.9193	7	18
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B15:53	SEYQEYGENPY	0.9923	0.7232	7	18
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B18:06	SEYQEYGENPY	0.992	0.9077	7	18
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B18:05	SEYQEYGENPY	0.9916	0.9094	7	18
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B48:02	SEYQEYGENPY	0.9657	0.7927	7	18
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B39:31	NSQRFEDSVAF	0.8689	0.6219	9	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	HLA-B38:05	NSQRFEDSVAF	0.7255	0.7401	9	20

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Potential FusionNeoAntigen Information of PTPRS-ZNF20 in HLA II

PTPRS-ZNF20_5274209_12246710.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)
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	DRB1-0901	SQRFEDSVAFEDVAV	10	25
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	DRB1-0901	NSQRFEDSVAFEDVA	9	24
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	DRB1-0903	SQRFEDSVAFEDVAV	10	25
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	DRB1-0903	NSQRFEDSVAFEDVA	9	24
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	DRB1-0904	SQRFEDSVAFEDVAV	10	25
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	DRB1-0904	NSQRFEDSVAFEDVA	9	24
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	DRB1-0907	SQRFEDSVAFEDVAV	10	25
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	DRB1-0907	NSQRFEDSVAFEDVA	9	24
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	DRB1-0908	SQRFEDSVAFEDVAV	10	25
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	DRB1-0908	NSQRFEDSVAFEDVA	9	24
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	DRB1-0908	VNSQRFEDSVAFEDV	8	23
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	DRB1-0908	QRFEDSVAFEDVAVS	11	26
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	DRB1-0909	SQRFEDSVAFEDVAV	10	25
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	DRB1-0909	NSQRFEDSVAFEDVA	9	24
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	DRB1-1529	SSEYQEYGENPYRNK	6	21
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	DRB1-1529	KSSEYQEYGENPYRN	5	20
PTPRS-ZNF20	chr19	5274209	chr19	12246710	471	DRB1-1530	SSEYQEYGENPYRNK	6	21

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Fusion breakpoint peptide structures of PTPRS-ZNF20

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
4367	KKVNSQRFEDSVAF	PTPRS	ZNF20	chr19	5274209	chr19	12246710	471

File name	BPseq	Hgene	Tgene	Hchr	Hbp	Tchr	Tbp	AAlen
9003	SSEYQEYGENPYRN	PTPRS	ZNF20	chr19	5274209	chr19	12246710	471

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of PTPRS-ZNF20

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	4367	KKVNSQRFEDSVAF	-7.51877	-7.63217
HLA-B14:02	3BVN	4367	KKVNSQRFEDSVAF	-6.38909	-7.42439
HLA-B52:01	3W39	4367	KKVNSQRFEDSVAF	-7.0634	-7.1768
HLA-B52:01	3W39	4367	KKVNSQRFEDSVAF	-4.74892	-5.78422
HLA-A11:01	4UQ2	4367	KKVNSQRFEDSVAF	-8.33766	-8.45106
HLA-A24:02	5HGA	4367	KKVNSQRFEDSVAF	-6.72223	-6.83563
HLA-A24:02	5HGA	4367	KKVNSQRFEDSVAF	-6.06312	-7.09842
HLA-B44:05	3DX8	4367	KKVNSQRFEDSVAF	-8.7132	-8.8266
HLA-B44:05	3DX8	4367	KKVNSQRFEDSVAF	-3.64437	-4.67967
HLA-B14:02	3BVN	9003	SSEYQEYGENPYRN	-7.15543	-7.26883
HLA-B14:02	3BVN	9003	SSEYQEYGENPYRN	-4.77435	-5.80965
HLA-B52:01	3W39	9003	SSEYQEYGENPYRN	-6.80875	-6.92215
HLA-B52:01	3W39	9003	SSEYQEYGENPYRN	-4.20386	-5.23916
HLA-A11:01	4UQ2	9003	SSEYQEYGENPYRN	-7.5194	-8.5547
HLA-A11:01	4UQ2	9003	SSEYQEYGENPYRN	-6.9601	-7.0735
HLA-A24:02	5HGA	9003	SSEYQEYGENPYRN	-7.52403	-7.63743
HLA-A24:02	5HGA	9003	SSEYQEYGENPYRN	-5.82433	-6.85963
HLA-B27:05	6PYJ	9003	SSEYQEYGENPYRN	-3.28285	-4.31815
HLA-B44:05	3DX8	9003	SSEYQEYGENPYRN	-5.91172	-6.94702
HLA-B44:05	3DX8	9003	SSEYQEYGENPYRN	-4.24346	-4.35686

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Vaccine Design for the FusionNeoAntigens of PTPRS-ZNF20

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
PTPRS-ZNF20	chr19	5274209	chr19	12246710	10	18	QEYGENPY	CGCTTTGAGTCTTATGAGAGAGAA
PTPRS-ZNF20	chr19	5274209	chr19	12246710	10	19	SQRFEDSVA	CGCTTTGAGGATTCAGTGGCCTTTGAG
PTPRS-ZNF20	chr19	5274209	chr19	12246710	10	20	SQRFEDSVAF	CGCTTTGAGGATTCAGTGGCCTTTGAGGAT
PTPRS-ZNF20	chr19	5274209	chr19	12246710	11	19	QRFEDSVA	TTTGAGGATTCAGTGGCCTTTGAG
PTPRS-ZNF20	chr19	5274209	chr19	12246710	11	20	QRFEDSVAF	TTTGAGGATTCAGTGGCCTTTGAGGAT
PTPRS-ZNF20	chr19	5274209	chr19	12246710	12	20	RFEDSVAF	GAGGATTCAGTGGCCTTTGAGGAT
PTPRS-ZNF20	chr19	5274209	chr19	12246710	5	14	GKKVNSQRF	AAGGTCAACTCTCAGCGCTTTGAGGAT
PTPRS-ZNF20	chr19	5274209	chr19	12246710	7	17	SEYQEYGENP	AACTCTCAGCGCTTTGAGTCTTATGAGAGA
PTPRS-ZNF20	chr19	5274209	chr19	12246710	7	18	SEYQEYGENPY	AACTCTCAGCGCTTTGAGTCTTATGAGAGAGAA
PTPRS-ZNF20	chr19	5274209	chr19	12246710	9	18	YQEYGENPY	CAGCGCTTTGAGTCTTATGAGAGAGAA
PTPRS-ZNF20	chr19	5274209	chr19	12246710	9	20	NSQRFEDSVAF	CAGCGCTTTGAGGATTCAGTGGCCTTTGAGGAT

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
PTPRS-ZNF20	chr19	5274209	chr19	12246710	10	25	SQRFEDSVAFEDVAV	CGCTTTGAGGATTCAGTGGCCTTTGAGGATGTGGCTGTCAGCTTC
PTPRS-ZNF20	chr19	5274209	chr19	12246710	11	26	QRFEDSVAFEDVAVS	TTTGAGGATTCAGTGGCCTTTGAGGATGTGGCTGTCAGCTTCACC
PTPRS-ZNF20	chr19	5274209	chr19	12246710	5	20	KSSEYQEYGENPYRN	AAGGTCAACTCTCAGCGCTTTGAGTCTTATGAGAGAGAAACTCTG
PTPRS-ZNF20	chr19	5274209	chr19	12246710	6	21	SSEYQEYGENPYRNK	GTCAACTCTCAGCGCTTTGAGTCTTATGAGAGAGAAACTCTGTGA
PTPRS-ZNF20	chr19	5274209	chr19	12246710	8	23	VNSQRFEDSVAFEDV	TCTCAGCGCTTTGAGGATTCAGTGGCCTTTGAGGATGTGGCTGTC
PTPRS-ZNF20	chr19	5274209	chr19	12246710	9	24	NSQRFEDSVAFEDVA	CAGCGCTTTGAGGATTCAGTGGCCTTTGAGGATGTGGCTGTCAGC

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Information of the samples that have these potential fusion neoantigens of PTPRS-ZNF20

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
SARC	PTPRS-ZNF20	chr19	5274209	ENST00000262963	chr19	12246710	ENST00000334213	TCGA-DX-A6Z0
SARC	PTPRS-ZNF20	chr19	5274209	ENST00000262963	chr19	12246710	ENST00000600335	TCGA-DX-A6Z0

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Potential target of CAR-T therapy development for PTPRS-ZNF20

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 PTPRS-ZNF20

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 PTPRS-ZNF20

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)