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Fusion Protein:YWHAE-TXLNB

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: YWHAE-TXLNB
	FusionPDB ID: 100162
	FusionGDB2.0 ID: 100162
		Hgene	Tgene
	Gene symbol	YWHAE	TXLNB
	Gene ID	7531	167838
	Gene name	tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein epsilon	taxilin beta
	Synonyms	14-3-3E\|HEL2\|KCIP-1\|MDCR\|MDS	C6orf198\|LST001\|MDP77\|dJ522B19.2
	Cytomap	17p13.3	6q24.1
	Type of gene	protein-coding	protein-coding
	Description	14-3-3 protein epsilon14-3-3 epsilonepididymis luminal protein 2mitochondrial import stimulation factor L subunitprotein kinase C inhibitor protein-1tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptidetyrosine	beta-taxilinmuscle-derived protein 77
	Modification date	20200327	20200327
	UniProtAcc	P62258 Main function of 5'-partner protein: FUNCTION: Adapter protein implicated in the regulation of a large spectrum of both general and specialized signaling pathways. Binds to a large number of partners, usually by recognition of a phosphoserine or phosphothreonine motif. Binding generally results in the modulation of the activity of the binding partner (By similarity). Positively regulates phosphorylated protein HSF1 nuclear export to the cytoplasm (PubMed:12917326). {ECO:0000250\|UniProtKB:P62261, ECO:0000269\|PubMed:12917326}.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000498643, ENST00000571732, ENST00000264335, ENST00000573026, ENST00000575977,	ENST00000358430,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	28 X 9 X 15=3780	4 X 4 X 2=32
	# samples	42	4
	** MAII score	log2(42/3780*10)=-3.16992500144231 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(4/32*10)=0.321928094887362 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0
Fusion gene context	PubMed: YWHAE [Title/Abstract] AND TXLNB [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: YWHAE [Title/Abstract] AND TXLNB [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	YWHAE(1303341)-TXLNB(139569046), # samples:2
Anticipated loss of major functional domain due to fusion event.

* 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	YWHAE	GO:0000165	MAPK cascade	12917326
Hgene	YWHAE	GO:0034605	cellular response to heat	12917326
Hgene	YWHAE	GO:0046827	positive regulation of protein export from nucleus	12917326
Hgene	YWHAE	GO:0051480	regulation of cytosolic calcium ion concentration	18029012
Hgene	YWHAE	GO:0060306	regulation of membrane repolarization	11953308
Hgene	YWHAE	GO:1901016	regulation of potassium ion transmembrane transporter activity	11953308
Hgene	YWHAE	GO:1901020	negative regulation of calcium ion transmembrane transporter activity	18029012
Hgene	YWHAE	GO:1902309	negative regulation of peptidyl-serine dephosphorylation	11953308
Hgene	YWHAE	GO:1905913	negative regulation of calcium ion export across plasma membrane	18029012

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr17:1303341/chr6:139569046)
- 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 YWHAE (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 TXLNB (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)
ENST00000264335	YWHAE	chr17	1303341	-	ENST00000358430	TXLNB	chr6	139569046	-	3775	332	248	1309	353
ENST00000573026	YWHAE	chr17	1303341	-	ENST00000358430	TXLNB	chr6	139569046	-	3578	135	51	1112	353
ENST00000575977	YWHAE	chr17	1303341	-	ENST00000358430	TXLNB	chr6	139569046	-	3611	168	84	1145	353

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
ENST00000264335	ENST00000358430	YWHAE	chr17	1303341	-	TXLNB	chr6	139569046	-	0.001061149	0.99893886
ENST00000573026	ENST00000358430	YWHAE	chr17	1303341	-	TXLNB	chr6	139569046	-	0.001070652	0.9989293
ENST00000575977	ENST00000358430	YWHAE	chr17	1303341	-	TXLNB	chr6	139569046	-	0.001046439	0.9989536

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 YWHAE-TXLNB

+/-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
YWHAE	chr17	1303341	TXLNB	chr6	139569046	135	28	TRRSWPSRLSDTTLTLYSGRFEEFQS
YWHAE	chr17	1303341	TXLNB	chr6	139569046	168	28	TRRSWPSRLSDTTLTLYSGRFEEFQS
YWHAE	chr17	1303341	TXLNB	chr6	139569046	332	28	TRRSWPSRLSDTTLTLYSGRFEEFQS

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Potential FusionNeoAntigen Information of YWHAE-TXLNB 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.

YWHAE-TXLNB_1303341_139569046.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)
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B39:24	SRLSDTTL	0.9994	0.5052	6	14
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-A02:11	RLSDTTLTL	0.9955	0.5784	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-A02:60	RLSDTTLTL	0.9954	0.5619	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-A02:30	RLSDTTLTL	0.9954	0.547	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-A02:67	RLSDTTLTL	0.9954	0.547	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-A02:24	RLSDTTLTL	0.9954	0.547	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-A02:13	RLSDTTLTL	0.9952	0.7661	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-A02:04	RLSDTTLTL	0.9941	0.6224	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-A02:21	RLSDTTLTL	0.9939	0.6508	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-A02:17	RLSDTTLTL	0.9938	0.5804	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-A02:27	RLSDTTLTL	0.9935	0.6178	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-A02:16	RLSDTTLTL	0.9915	0.5509	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-A02:38	RLSDTTLTL	0.9898	0.7627	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B15:01	RLSDTTLTL	0.9881	0.8227	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-A02:19	RLSDTTLTL	0.9816	0.5376	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-A02:35	RLSDTTLTL	0.9581	0.5506	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-A32:13	RLSDTTLTL	0.9568	0.9683	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-A02:29	RLSDTTLTL	0.9423	0.5491	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B35:08	LSDTTLTLY	0.9303	0.6911	8	17
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B15:17	LSDTTLTLY	0.9121	0.7521	8	17
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-A02:20	RLSDTTLTL	0.89	0.5504	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-A24:14	RLSDTTLTL	0.8428	0.5444	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-A30:08	RLSDTTLTL	0.8087	0.8806	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B15:25	RLSDTTLTL	0.7991	0.8436	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B48:01	RLSDTTLTL	0.5479	0.5745	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B39:13	RLSDTTLTL	0.2452	0.9237	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B13:02	RLSDTTLTL	0.2351	0.5498	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B13:01	RLSDTTLTL	0.1996	0.9884	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B27:05	SRLSDTTLTL	1	0.8251	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B27:02	SRLSDTTLTL	1	0.5473	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B27:04	SRLSDTTLTL	0.9999	0.7509	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B15:01	RLSDTTLTLY	0.9998	0.832	7	17
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B39:24	SRLSDTTLTL	0.9992	0.5327	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B39:01	SRLSDTTLTL	0.9988	0.9159	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B39:06	SRLSDTTLTL	0.9988	0.7589	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B38:02	SRLSDTTLTL	0.9981	0.9813	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B15:25	RLSDTTLTLY	0.9981	0.8743	7	17
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B38:01	SRLSDTTLTL	0.9978	0.9843	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B15:02	RLSDTTLTLY	0.9914	0.9139	7	17
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B15:10	SRLSDTTLTL	0.9705	0.6437	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B35:03	WPSRLSDTTL	0.9616	0.8761	4	14
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B15:37	SRLSDTTLTL	0.8676	0.6768	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B35:04	WPSRLSDTTL	0.8415	0.9443	4	14
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B35:02	WPSRLSDTTL	0.8415	0.9443	4	14
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-A02:22	SRLSDTTLTL	0.8184	0.5623	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-A32:13	RLSDTTLTLY	0.7555	0.9301	7	17
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-A02:35	SRLSDTTLTL	0.68	0.6518	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-A02:27	SRLSDTTLTL	0.6695	0.6154	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-A02:04	SRLSDTTLTL	0.6674	0.5391	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-A02:38	SRLSDTTLTL	0.6559	0.703	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-A02:16	SRLSDTTLTL	0.6528	0.527	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-A02:13	SRLSDTTLTL	0.6415	0.7374	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-A02:60	SRLSDTTLTL	0.6317	0.5878	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-A02:30	SRLSDTTLTL	0.6271	0.6545	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-A02:24	SRLSDTTLTL	0.6271	0.6545	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-A02:67	SRLSDTTLTL	0.6271	0.6545	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-A02:19	SRLSDTTLTL	0.5367	0.5095	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-A02:29	SRLSDTTLTL	0.5309	0.65	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-A02:20	SRLSDTTLTL	0.5179	0.6528	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B27:05	SRLSDTTLTLY	1	0.8868	6	17
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B27:02	SRLSDTTLTLY	1	0.6014	6	17
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B27:04	SRLSDTTLTLY	1	0.7422	6	17
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C05:09	LSDTTLTL	1	0.912	8	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C04:07	LSDTTLTL	1	0.8635	8	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C04:10	LSDTTLTL	1	0.8636	8	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C08:15	LSDTTLTL	1	0.9759	8	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C03:19	LSDTTLTL	0.9998	0.981	8	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C15:06	LSDTTLTL	0.9998	0.924	8	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C04:06	LSDTTLTL	0.9997	0.8097	8	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C08:04	LSDTTLTL	0.999	0.9337	8	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C08:13	LSDTTLTL	0.999	0.9337	8	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B39:12	SRLSDTTL	0.9982	0.8701	6	14
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C04:14	LSDTTLTL	0.9965	0.8316	8	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C08:03	LSDTTLTL	0.9648	0.9825	8	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C05:09	RLSDTTLTL	0.9995	0.9391	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C04:10	RLSDTTLTL	0.9989	0.9328	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C04:07	RLSDTTLTL	0.9988	0.9533	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C08:15	RLSDTTLTL	0.9974	0.9936	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-A02:07	RLSDTTLTL	0.9958	0.5689	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-A02:01	RLSDTTLTL	0.9954	0.547	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C15:04	RLSDTTLTL	0.9947	0.9479	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C15:06	RLSDTTLTL	0.9918	0.9513	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C01:17	RLSDTTLTL	0.9905	0.9492	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C04:06	RLSDTTLTL	0.9889	0.9462	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C04:14	RLSDTTLTL	0.9851	0.9736	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B15:04	RLSDTTLTL	0.9838	0.8563	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C05:09	LSDTTLTLY	0.983	0.828	8	17
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B15:07	RLSDTTLTL	0.9797	0.7268	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C03:19	RLSDTTLTL	0.9615	0.9864	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C02:06	RLSDTTLTL	0.9566	0.9345	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C03:08	RLSDTTLTL	0.9463	0.8819	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C08:04	RLSDTTLTL	0.9453	0.9732	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C08:13	RLSDTTLTL	0.9453	0.9732	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C07:13	RLSDTTLTL	0.934	0.9499	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B73:01	SRLSDTTLT	0.9269	0.5669	6	15
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C03:07	RLSDTTLTL	0.9206	0.9623	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C07:29	RLSDTTLTL	0.9069	0.9263	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C03:14	RLSDTTLTL	0.8785	0.9765	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C07:05	RLSDTTLTL	0.8709	0.9701	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C01:30	RLSDTTLTL	0.8589	0.9589	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C08:15	LSDTTLTLY	0.8501	0.9376	8	17
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C07:67	RLSDTTLTL	0.7915	0.9418	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C07:80	RLSDTTLTL	0.7915	0.9418	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C07:27	RLSDTTLTL	0.7909	0.9441	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C07:10	RLSDTTLTL	0.7786	0.9675	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C07:19	RLSDTTLTL	0.7695	0.8006	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C08:03	RLSDTTLTL	0.7683	0.9951	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C07:46	RLSDTTLTL	0.7467	0.8986	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B39:08	RLSDTTLTL	0.7224	0.9279	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C15:04	LSDTTLTLY	0.7072	0.831	8	17
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C07:95	RLSDTTLTL	0.6762	0.7571	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B15:05	RLSDTTLTL	0.2374	0.8111	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B27:14	SRLSDTTLTL	1	0.7945	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C07:05	SRLSDTTLTL	0.9996	0.9658	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C07:95	SRLSDTTLTL	0.9994	0.8111	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C07:13	SRLSDTTLTL	0.9993	0.9481	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C07:29	SRLSDTTLTL	0.9993	0.956	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C07:27	SRLSDTTLTL	0.9993	0.9631	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B15:07	RLSDTTLTLY	0.9992	0.6726	7	17
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B39:09	SRLSDTTLTL	0.9987	0.6842	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B39:12	SRLSDTTLTL	0.9986	0.9215	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B27:03	SRLSDTTLTL	0.9984	0.8584	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B39:05	SRLSDTTLTL	0.9979	0.8981	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B15:04	RLSDTTLTLY	0.9971	0.8798	7	17
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C07:67	SRLSDTTLTL	0.9958	0.9498	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C07:80	SRLSDTTLTL	0.9958	0.9498	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C07:19	SRLSDTTLTL	0.9943	0.8409	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C07:46	SRLSDTTLTL	0.9931	0.9054	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C07:10	SRLSDTTLTL	0.9924	0.9697	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B15:21	RLSDTTLTLY	0.9913	0.8286	7	17
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C12:16	SRLSDTTLTL	0.9835	0.9735	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B07:12	WPSRLSDTTL	0.9834	0.6523	4	14
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B73:01	SRLSDTTLTL	0.9813	0.6224	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B15:05	RLSDTTLTLY	0.9609	0.7972	7	17
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B15:31	RLSDTTLTLY	0.9244	0.8121	7	17
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B35:12	WPSRLSDTTL	0.8415	0.9443	4	14
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B39:10	WPSRLSDTTL	0.8334	0.9163	4	14
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-A02:01	SRLSDTTLTL	0.6271	0.6545	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B27:14	SRLSDTTLTLY	0.9999	0.7959	6	17
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B27:03	SRLSDTTLTLY	0.9998	0.9105	6	17
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C04:01	LSDTTLTL	1	0.8635	8	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C18:01	LSDTTLTL	1	0.8722	8	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C01:03	LSDTTLTL	1	0.9314	8	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C08:02	LSDTTLTL	1	0.9759	8	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C05:01	LSDTTLTL	1	0.912	8	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C04:03	LSDTTLTL	1	0.8704	8	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C15:05	LSDTTLTL	0.9997	0.8796	8	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C03:06	LSDTTLTL	0.9986	0.9776	8	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C17:01	LSDTTLTL	0.984	0.7791	8	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C08:01	LSDTTLTL	0.9648	0.9825	8	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B07:13	LSDTTLTL	0.3504	0.7095	8	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C04:03	RLSDTTLTL	0.9995	0.964	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C05:01	RLSDTTLTL	0.9995	0.9391	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C04:01	RLSDTTLTL	0.9988	0.9533	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C18:01	RLSDTTLTL	0.9979	0.9491	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C08:02	RLSDTTLTL	0.9974	0.9936	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-A02:03	RLSDTTLTL	0.9972	0.6356	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C06:06	RLSDTTLTL	0.9968	0.9879	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C01:03	RLSDTTLTL	0.9954	0.9608	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C15:09	RLSDTTLTL	0.9947	0.9479	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-A02:14	RLSDTTLTL	0.9941	0.5901	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-A02:06	RLSDTTLTL	0.9939	0.6508	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C01:02	RLSDTTLTL	0.9921	0.9483	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C15:02	RLSDTTLTL	0.9909	0.9465	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C15:05	RLSDTTLTL	0.9906	0.9616	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B15:27	RLSDTTLTL	0.99	0.8391	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B15:50	RLSDTTLTL	0.9888	0.8613	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B15:33	RLSDTTLTL	0.9881	0.8227	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B15:34	RLSDTTLTL	0.9881	0.8227	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B15:125	RLSDTTLTL	0.9881	0.8227	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C04:04	RLSDTTLTL	0.9873	0.9567	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B15:135	RLSDTTLTL	0.9871	0.828	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-A32:01	RLSDTTLTL	0.985	0.9758	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B15:24	RLSDTTLTL	0.9849	0.8921	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C04:03	LSDTTLTLY	0.9834	0.6643	8	17
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C05:01	LSDTTLTLY	0.983	0.828	8	17
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B15:73	RLSDTTLTL	0.9588	0.8604	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C03:04	RLSDTTLTL	0.9422	0.9811	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C03:03	RLSDTTLTL	0.9422	0.9811	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C03:06	RLSDTTLTL	0.922	0.9808	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C03:67	RLSDTTLTL	0.9077	0.9701	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C06:08	RLSDTTLTL	0.9	0.9767	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C07:04	RLSDTTLTL	0.8926	0.9763	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B15:30	RLSDTTLTL	0.8841	0.8326	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C03:05	RLSDTTLTL	0.8515	0.9102	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C08:02	LSDTTLTLY	0.8501	0.9376	8	17
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B15:39	RLSDTTLTL	0.8429	0.7587	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C17:01	RLSDTTLTL	0.8365	0.9278	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B57:04	LSDTTLTLY	0.8163	0.5954	8	17
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C07:02	RLSDTTLTL	0.7915	0.9418	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C08:01	RLSDTTLTL	0.7683	0.9951	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C03:02	LSDTTLTLY	0.7385	0.9083	8	17
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B07:13	RLSDTTLTL	0.7354	0.827	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C07:01	RLSDTTLTL	0.713	0.7316	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C07:17	RLSDTTLTL	0.709	0.9572	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C15:09	LSDTTLTLY	0.7072	0.831	8	17
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B39:11	RLSDTTLTL	0.6713	0.87	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B39:02	RLSDTTLTL	0.3735	0.9206	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B35:13	RLSDTTLTL	0.3569	0.8492	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B15:20	RLSDTTLTL	0.2488	0.8707	7	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C16:02	LSDTTLTLY	0.1013	0.9852	8	17
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C12:02	LSDTTLTLY	0.0164	0.9575	8	17
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C02:10	LSDTTLTLY	0.0085	0.9324	8	17
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C02:02	LSDTTLTLY	0.0085	0.9324	8	17
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B15:12	RLSDTTLTLY	0.9999	0.8652	7	17
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B27:06	SRLSDTTLTL	0.9999	0.7395	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B27:09	SRLSDTTLTL	0.9999	0.8349	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B27:08	SRLSDTTLTL	0.9999	0.7369	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B27:10	SRLSDTTLTL	0.9999	0.8427	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B15:125	RLSDTTLTLY	0.9998	0.832	7	17
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B15:33	RLSDTTLTLY	0.9998	0.832	7	17
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B15:135	RLSDTTLTLY	0.9998	0.8517	7	17
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B15:50	RLSDTTLTLY	0.9998	0.8769	7	17
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B15:27	RLSDTTLTLY	0.9998	0.8333	7	17
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B15:34	RLSDTTLTLY	0.9998	0.832	7	17
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C07:01	SRLSDTTLTL	0.9995	0.7852	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B15:35	RLSDTTLTLY	0.9994	0.8251	7	17
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B15:24	RLSDTTLTLY	0.9992	0.9023	7	17
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B39:31	SRLSDTTLTL	0.9991	0.9181	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C06:08	SRLSDTTLTL	0.9988	0.9724	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B15:39	RLSDTTLTLY	0.9981	0.7493	7	17
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B38:05	SRLSDTTLTL	0.9978	0.9843	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C07:02	SRLSDTTLTL	0.9958	0.9498	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C06:06	SRLSDTTLTL	0.9934	0.9891	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C07:22	SRLSDTTLTL	0.9928	0.8282	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C07:04	SRLSDTTLTL	0.9879	0.9603	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C06:17	SRLSDTTLTL	0.9787	0.9915	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-C06:02	SRLSDTTLTL	0.9787	0.9915	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B15:20	RLSDTTLTLY	0.9649	0.8981	7	17
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B15:09	SRLSDTTLTL	0.9454	0.6879	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B35:28	RLSDTTLTLY	0.9447	0.9031	7	17
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-A32:01	RLSDTTLTLY	0.9229	0.941	7	17
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B15:73	SRLSDTTLTL	0.9139	0.8171	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B35:09	WPSRLSDTTL	0.8415	0.9443	4	14
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B15:30	SRLSDTTLTL	0.8375	0.822	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B67:01	WPSRLSDTTL	0.8342	0.7546	4	14
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-A02:03	SRLSDTTLTL	0.7761	0.6965	6	16
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B27:08	SRLSDTTLTLY	1	0.7478	6	17
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B27:10	SRLSDTTLTLY	1	0.8615	6	17
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	HLA-B27:09	SRLSDTTLTLY	0.9987	0.8627	6	17

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Potential FusionNeoAntigen Information of YWHAE-TXLNB in HLA II

YWHAE-TXLNB_1303341_139569046.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)
YWHAE-TXLNB	chr17	1303341	chr6	139569046	332	DRB1-1512	DTTLTLYSGRFEEFQ	10	25

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Fusion breakpoint peptide structures of YWHAE-TXLNB

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
8968	SRLSDTTLTLYSGR	YWHAE	TXLNB	chr17	1303341	chr6	139569046	332

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of YWHAE-TXLNB

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	8968	SRLSDTTLTLYSGR	-7.15543	-7.26883
HLA-B14:02	3BVN	8968	SRLSDTTLTLYSGR	-4.77435	-5.80965
HLA-B52:01	3W39	8968	SRLSDTTLTLYSGR	-6.80875	-6.92215
HLA-B52:01	3W39	8968	SRLSDTTLTLYSGR	-4.20386	-5.23916
HLA-A11:01	4UQ2	8968	SRLSDTTLTLYSGR	-7.5194	-8.5547
HLA-A11:01	4UQ2	8968	SRLSDTTLTLYSGR	-6.9601	-7.0735
HLA-A24:02	5HGA	8968	SRLSDTTLTLYSGR	-7.52403	-7.63743
HLA-A24:02	5HGA	8968	SRLSDTTLTLYSGR	-5.82433	-6.85963
HLA-B27:05	6PYJ	8968	SRLSDTTLTLYSGR	-3.28285	-4.31815
HLA-B44:05	3DX8	8968	SRLSDTTLTLYSGR	-5.91172	-6.94702
HLA-B44:05	3DX8	8968	SRLSDTTLTLYSGR	-4.24346	-4.35686

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Vaccine Design for the FusionNeoAntigens of YWHAE-TXLNB

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
YWHAE-TXLNB	chr17	1303341	chr6	139569046	4	14	WPSRLSDTTL	TGGCCGAGCAGGCTGAGCGATACGACGCTC
YWHAE-TXLNB	chr17	1303341	chr6	139569046	6	14	SRLSDTTL	AGCAGGCTGAGCGATACGACGCTC
YWHAE-TXLNB	chr17	1303341	chr6	139569046	6	15	SRLSDTTLT	AGCAGGCTGAGCGATACGACGCTCACT
YWHAE-TXLNB	chr17	1303341	chr6	139569046	6	16	SRLSDTTLTL	AGCAGGCTGAGCGATACGACGCTCACTCTC
YWHAE-TXLNB	chr17	1303341	chr6	139569046	6	17	SRLSDTTLTLY	AGCAGGCTGAGCGATACGACGCTCACTCTCTAC
YWHAE-TXLNB	chr17	1303341	chr6	139569046	7	16	RLSDTTLTL	AGGCTGAGCGATACGACGCTCACTCTC
YWHAE-TXLNB	chr17	1303341	chr6	139569046	7	17	RLSDTTLTLY	AGGCTGAGCGATACGACGCTCACTCTCTAC
YWHAE-TXLNB	chr17	1303341	chr6	139569046	8	16	LSDTTLTL	CTGAGCGATACGACGCTCACTCTC
YWHAE-TXLNB	chr17	1303341	chr6	139569046	8	17	LSDTTLTLY	CTGAGCGATACGACGCTCACTCTCTAC

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
YWHAE-TXLNB	chr17	1303341	chr6	139569046	10	25	DTTLTLYSGRFEEFQ	GATACGACGCTCACTCTCTACTCAGGAAGGTTTGAAGAATTCCAG

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Information of the samples that have these potential fusion neoantigens of YWHAE-TXLNB

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
SKCM	YWHAE-TXLNB	chr17	1303341	ENST00000264335	chr6	139569046	ENST00000358430	TCGA-EB-A6L9-06A

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Potential target of CAR-T therapy development for YWHAE-TXLNB

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 YWHAE-TXLNB

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 YWHAE-TXLNB

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
Hgene	YWHAE	C0036341	Schizophrenia	4	PSYGENET
Hgene	YWHAE	C0005586	Bipolar Disorder	2	PSYGENET
Hgene	YWHAE	C0206630	Endometrial Stromal Sarcoma	2	ORPHANET
Hgene	YWHAE	C0027627	Neoplasm Metastasis	1	CTD_human
Hgene	YWHAE	C0265219	Miller Dieker syndrome	1	ORPHANET
Hgene	YWHAE	C0334488	Clear cell sarcoma of kidney	1	ORPHANET
Hgene	YWHAE	C2750748	Chromosome 17p13.3 Duplication Syndrome	1	ORPHANET
Hgene	YWHAE	C4707092	Distal 17p13.3 microdeletion syndrome	1	ORPHANET

	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)