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Fusion Protein:ACY1-BAP1

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: ACY1-BAP1
	FusionPDB ID: 1916
	FusionGDB2.0 ID: 1916
		Hgene	Tgene
	Gene symbol	ACY1	BAP1
	Gene ID	95	9223
	Gene name	aminoacylase 1	membrane associated guanylate kinase, WW and PDZ domain containing 1
	Synonyms	ACY-1\|ACY1D\|HEL-S-5	AIP-3\|AIP3\|BAIAP1\|BAP-1\|BAP1\|MAGI-1\|MAGI-1b\|Magi1d\|TNRC19\|WWP3
	Cytomap	3p21.2	3p14.1
	Type of gene	protein-coding	protein-coding
	Description	aminoacylase-1N-acyl-L-amino-acid amidohydrolaseacylaseepididymis secretory protein Li 5	membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1BAI1-associated protein 1WW domain-containing protein 3atrophin-1-interacting protein 3membrane-associated guanylate kinase inverted 1trinucleotide repeat-containing gene 19
	Modification date	20200313	20200313
	UniProtAcc	Q03154 Main function of 5'-partner protein: FUNCTION: Involved in the hydrolysis of N-acylated or N-acetylated amino acids (except L-aspartate). {ECO:0000269\|PubMed:12933810}.	Q8IXM2 Main function of 5'-partner protein: FUNCTION: Component of chromatin complexes such as the MLL1/MLL and NURF complexes.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000404366, ENST00000458031, ENST00000476351, ENST00000476854, ENST00000494103, ENST00000468068,	ENST00000296288, ENST00000460680,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	1 X 1 X 1=1	5 X 5 X 2=50
	# samples	1	5
	** MAII score	log2(1/1*10)=3.32192809488736	log2(5/50*10)=0
Fusion gene context	PubMed: ACY1 [Title/Abstract] AND BAP1 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: ACY1 [Title/Abstract] AND BAP1 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	ACY1(52021640)-BAP1(52441476), # samples:2
Anticipated loss of major functional domain due to fusion event.	ACY1-BAP1 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. ACY1-BAP1 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
Tgene	BAP1	GO:0022409	positive regulation of cell-cell adhesion	20298433

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr3:52021640/chr3:52441476)
- 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 ACY1 (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 BAP1 (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)
ENST00000458031	ACY1	chr3	52021640	+	ENST00000460680	BAP1	chr3	52441476	-	4512	1422	231	3236	1001
ENST00000458031	ACY1	chr3	52021640	+	ENST00000296288	BAP1	chr3	52441476	-	4445	1422	231	3182	983
ENST00000494103	ACY1	chr3	52021640	+	ENST00000460680	BAP1	chr3	52441476	-	3960	870	165	2684	839
ENST00000494103	ACY1	chr3	52021640	+	ENST00000296288	BAP1	chr3	52441476	-	3893	870	165	2630	821
ENST00000476854	ACY1	chr3	52021640	+	ENST00000460680	BAP1	chr3	52441476	-	3981	891	165	2705	846
ENST00000476854	ACY1	chr3	52021640	+	ENST00000296288	BAP1	chr3	52441476	-	3914	891	165	2651	828
ENST00000476351	ACY1	chr3	52021640	+	ENST00000460680	BAP1	chr3	52441476	-	4071	981	165	2795	876
ENST00000476351	ACY1	chr3	52021640	+	ENST00000296288	BAP1	chr3	52441476	-	4004	981	165	2741	858
ENST00000404366	ACY1	chr3	52021640	+	ENST00000460680	BAP1	chr3	52441476	-	4157	1067	146	2881	911
ENST00000404366	ACY1	chr3	52021640	+	ENST00000296288	BAP1	chr3	52441476	-	4090	1067	146	2827	893

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
ENST00000458031	ENST00000460680	ACY1	chr3	52021640	+	BAP1	chr3	52441476	-	0.004395626	0.9956044
ENST00000458031	ENST00000296288	ACY1	chr3	52021640	+	BAP1	chr3	52441476	-	0.004037257	0.9959628
ENST00000494103	ENST00000460680	ACY1	chr3	52021640	+	BAP1	chr3	52441476	-	0.012677126	0.98732287
ENST00000494103	ENST00000296288	ACY1	chr3	52021640	+	BAP1	chr3	52441476	-	0.013093281	0.98690665
ENST00000476854	ENST00000460680	ACY1	chr3	52021640	+	BAP1	chr3	52441476	-	0.013475177	0.9865248
ENST00000476854	ENST00000296288	ACY1	chr3	52021640	+	BAP1	chr3	52441476	-	0.014417702	0.9855823
ENST00000476351	ENST00000460680	ACY1	chr3	52021640	+	BAP1	chr3	52441476	-	0.008514651	0.9914854
ENST00000476351	ENST00000296288	ACY1	chr3	52021640	+	BAP1	chr3	52441476	-	0.008284329	0.9917157
ENST00000404366	ENST00000460680	ACY1	chr3	52021640	+	BAP1	chr3	52441476	-	0.006538075	0.99346197
ENST00000404366	ENST00000296288	ACY1	chr3	52021640	+	BAP1	chr3	52441476	-	0.007768508	0.9922315

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 ACY1-BAP1

+/-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
ACY1	chr3	52021640	BAP1	chr3	52441476	1067	307	QAAGEGVTLEFAQSKGYAIGNAPELA
ACY1	chr3	52021640	BAP1	chr3	52441476	1422	397	QAAGEGVTLEFAQSKGYAIGNAPELA
ACY1	chr3	52021640	BAP1	chr3	52441476	870	235	QAAGEGVTLEFAQSKGYAIGNAPELA
ACY1	chr3	52021640	BAP1	chr3	52441476	891	242	QAAGEGVTLEFAQSKGYAIGNAPELA
ACY1	chr3	52021640	BAP1	chr3	52441476	981	272	QAAGEGVTLEFAQSKGYAIGNAPELA

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Potential FusionNeoAntigen Information of ACY1-BAP1 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.

ACY1-BAP1_52021640_52441476.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)
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B13:02	AQSKGYAI	0.985	0.8863	11	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B18:01	LEFAQSKGY	0.9972	0.8607	8	17
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B44:03	LEFAQSKGY	0.997	0.9739	8	17
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B51:02	FAQSKGYAI	0.9915	0.7074	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B08:01	FAQSKGYAI	0.9899	0.5441	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B08:09	FAQSKGYAI	0.9897	0.7078	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B47:01	LEFAQSKGY	0.9466	0.5832	8	17
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-A30:08	VTLEFAQSK	0.918	0.7263	6	15
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B51:01	FAQSKGYAI	0.9006	0.6999	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B35:04	FAQSKGYAI	0.8818	0.9807	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B35:02	FAQSKGYAI	0.8818	0.9807	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B15:03	LEFAQSKGY	0.1807	0.6966	8	17
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B50:01	LEFAQSKGYA	0.6969	0.7351	8	18
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B44:03	TLEFAQSKGY	0.4826	0.9833	7	17
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B18:01	TLEFAQSKGY	0.256	0.9309	7	17
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B15:17	VTLEFAQSKGY	0.994	0.8361	6	17
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B44:03	VTLEFAQSKGY	0.7321	0.9725	6	17
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-C03:07	FAQSKGYAI	0.9993	0.9878	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-C12:12	FAQSKGYAI	0.9974	0.8992	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-C15:06	FAQSKGYAI	0.9974	0.9563	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-C06:03	FAQSKGYAI	0.9963	0.9939	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-C12:04	FAQSKGYAI	0.9956	0.9955	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-C04:06	FAQSKGYAI	0.9955	0.9465	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-C03:19	FAQSKGYAI	0.9953	0.9833	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-C03:08	FAQSKGYAI	0.9908	0.8989	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-C08:04	FAQSKGYAI	0.9787	0.9841	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-C08:13	FAQSKGYAI	0.9787	0.9841	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-C01:17	FAQSKGYAI	0.963	0.9621	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-C02:06	FAQSKGYAI	0.9443	0.9775	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B78:01	FAQSKGYAI	0.9229	0.9056	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B51:07	FAQSKGYAI	0.9005	0.9658	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B35:12	FAQSKGYAI	0.8818	0.9807	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-C08:03	FAQSKGYAI	0.8811	0.9925	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B14:03	FAQSKGYAI	0.8693	0.8082	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-C03:14	FAQSKGYAI	0.6749	0.9916	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-C01:30	FAQSKGYAI	0.624	0.9627	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B44:09	TLEFAQSKGY	0.6687	0.5361	7	17
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B44:09	VTLEFAQSKGY	0.9044	0.5595	6	17
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-C03:05	FAQSKGYAI	0.999	0.9077	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-C03:17	FAQSKGYAI	0.9989	0.9593	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B18:04	LEFAQSKGY	0.9982	0.8722	8	17
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-C03:67	FAQSKGYAI	0.9981	0.9779	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B18:07	LEFAQSKGY	0.9977	0.822	8	17
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B18:08	LEFAQSKGY	0.9976	0.802	8	17
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-C15:05	FAQSKGYAI	0.9973	0.966	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B18:05	LEFAQSKGY	0.9972	0.8607	8	17
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B44:07	LEFAQSKGY	0.997	0.9739	8	17
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B44:26	LEFAQSKGY	0.997	0.9739	8	17
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B44:13	LEFAQSKGY	0.997	0.9739	8	17
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-C15:02	FAQSKGYAI	0.9966	0.937	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-C12:03	FAQSKGYAI	0.9961	0.9785	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-C03:03	FAQSKGYAI	0.9961	0.9852	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-C03:04	FAQSKGYAI	0.9961	0.9852	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B18:06	LEFAQSKGY	0.9956	0.8702	8	17
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B18:03	LEFAQSKGY	0.9951	0.8503	8	17
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-C03:02	FAQSKGYAI	0.9946	0.9653	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-C12:02	FAQSKGYAI	0.9943	0.9765	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B08:18	FAQSKGYAI	0.9899	0.5441	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-C03:06	FAQSKGYAI	0.9845	0.9862	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-C16:04	FAQSKGYAI	0.9819	0.9792	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B35:22	FAQSKGYAI	0.9804	0.6083	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B51:05	FAQSKGYAI	0.9801	0.5088	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-C01:02	FAQSKGYAI	0.9748	0.9609	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-C01:03	FAQSKGYAI	0.9715	0.9476	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B08:12	FAQSKGYAI	0.9548	0.6705	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-C16:02	FAQSKGYAI	0.9385	0.9893	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-C02:10	FAQSKGYAI	0.9353	0.9813	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-C02:02	FAQSKGYAI	0.9353	0.9813	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-C07:04	FAQSKGYAI	0.9329	0.9733	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B78:02	FAQSKGYAI	0.9228	0.9129	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-C16:01	FAQSKGYAI	0.9177	0.9749	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-A30:01	VTLEFAQSK	0.9113	0.8755	6	15
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B51:14	FAQSKGYAI	0.8948	0.6988	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B35:09	FAQSKGYAI	0.8818	0.9807	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-C08:01	FAQSKGYAI	0.8811	0.9925	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B18:11	LEFAQSKGY	0.8782	0.8397	8	17
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B35:13	FAQSKGYAI	0.8552	0.9285	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B51:09	FAQSKGYAI	0.8475	0.6667	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B15:12	LEFAQSKGY	0.8464	0.7731	8	17
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B51:21	FAQSKGYAI	0.8315	0.6484	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B07:13	FAQSKGYAI	0.8185	0.8023	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B51:06	FAQSKGYAI	0.7885	0.6737	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B51:29	FAQSKGYAI	0.759	0.5072	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B35:28	LEFAQSKGY	0.7136	0.8688	8	17
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-C17:01	FAQSKGYAI	0.6845	0.9838	10	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B35:20	LEFAQSKGY	0.6072	0.8775	8	17
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B15:53	LEFAQSKGY	0.546	0.7891	8	17
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B48:02	LEFAQSKGY	0.1549	0.8556	8	17
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B15:54	LEFAQSKGY	0.1326	0.7473	8	17
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B15:53	TLEFAQSKGY	0.9329	0.791	7	17
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B50:04	LEFAQSKGYA	0.6969	0.7351	8	18
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B50:05	LEFAQSKGYA	0.6969	0.7351	8	18
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B18:11	TLEFAQSKGY	0.4961	0.924	7	17
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B44:07	TLEFAQSKGY	0.4826	0.9833	7	17
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B44:13	TLEFAQSKGY	0.4826	0.9833	7	17
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B44:26	TLEFAQSKGY	0.4826	0.9833	7	17
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B18:05	TLEFAQSKGY	0.256	0.9309	7	17
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B44:07	VTLEFAQSKGY	0.7321	0.9725	6	17
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B44:13	VTLEFAQSKGY	0.7321	0.9725	6	17
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	HLA-B44:26	VTLEFAQSKGY	0.7321	0.9725	6	17

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Potential FusionNeoAntigen Information of ACY1-BAP1 in HLA II

ACY1-BAP1_52021640_52441476.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)
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0103	TLEFAQSKGYAIGNA	7	22
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0109	TLEFAQSKGYAIGNA	7	22
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0109	VTLEFAQSKGYAIGN	6	21
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0113	TLEFAQSKGYAIGNA	7	22
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0113	VTLEFAQSKGYAIGN	6	21
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0115	TLEFAQSKGYAIGNA	7	22
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0115	VTLEFAQSKGYAIGN	6	21
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0117	TLEFAQSKGYAIGNA	7	22
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0117	VTLEFAQSKGYAIGN	6	21
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0121	TLEFAQSKGYAIGNA	7	22
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0121	VTLEFAQSKGYAIGN	6	21
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0701	TLEFAQSKGYAIGNA	7	22
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0701	VTLEFAQSKGYAIGN	6	21
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0701	GVTLEFAQSKGYAIG	5	20
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0701	LEFAQSKGYAIGNAP	8	23
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0701	EGVTLEFAQSKGYAI	4	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0703	TLEFAQSKGYAIGNA	7	22
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0703	VTLEFAQSKGYAIGN	6	21
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0703	GVTLEFAQSKGYAIG	5	20
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0703	LEFAQSKGYAIGNAP	8	23
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0703	EGVTLEFAQSKGYAI	4	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0704	TLEFAQSKGYAIGNA	7	22
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0704	VTLEFAQSKGYAIGN	6	21
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0704	GVTLEFAQSKGYAIG	5	20
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0704	LEFAQSKGYAIGNAP	8	23
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0704	EGVTLEFAQSKGYAI	4	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0705	TLEFAQSKGYAIGNA	7	22
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0705	VTLEFAQSKGYAIGN	6	21
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0705	GVTLEFAQSKGYAIG	5	20
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0705	LEFAQSKGYAIGNAP	8	23
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0705	EGVTLEFAQSKGYAI	4	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0706	TLEFAQSKGYAIGNA	7	22
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0706	VTLEFAQSKGYAIGN	6	21
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0706	GVTLEFAQSKGYAIG	5	20
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0706	LEFAQSKGYAIGNAP	8	23
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0707	TLEFAQSKGYAIGNA	7	22
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0707	VTLEFAQSKGYAIGN	6	21
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0707	GVTLEFAQSKGYAIG	5	20
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0707	LEFAQSKGYAIGNAP	8	23
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0707	EGVTLEFAQSKGYAI	4	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0708	TLEFAQSKGYAIGNA	7	22
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0708	VTLEFAQSKGYAIGN	6	21
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0708	GVTLEFAQSKGYAIG	5	20
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0708	LEFAQSKGYAIGNAP	8	23
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0708	EGVTLEFAQSKGYAI	4	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0709	TLEFAQSKGYAIGNA	7	22
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0709	VTLEFAQSKGYAIGN	6	21
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0709	GVTLEFAQSKGYAIG	5	20
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0709	LEFAQSKGYAIGNAP	8	23
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0709	EGVTLEFAQSKGYAI	4	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0711	TLEFAQSKGYAIGNA	7	22
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0711	VTLEFAQSKGYAIGN	6	21
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0711	GVTLEFAQSKGYAIG	5	20
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0711	LEFAQSKGYAIGNAP	8	23
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0711	EGVTLEFAQSKGYAI	4	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0712	TLEFAQSKGYAIGNA	7	22
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0712	VTLEFAQSKGYAIGN	6	21
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0712	GVTLEFAQSKGYAIG	5	20
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0712	LEFAQSKGYAIGNAP	8	23
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0712	EGVTLEFAQSKGYAI	4	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0713	TLEFAQSKGYAIGNA	7	22
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0713	VTLEFAQSKGYAIGN	6	21
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0713	GVTLEFAQSKGYAIG	5	20
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0713	LEFAQSKGYAIGNAP	8	23
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0713	EGVTLEFAQSKGYAI	4	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0714	TLEFAQSKGYAIGNA	7	22
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0714	VTLEFAQSKGYAIGN	6	21
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0714	GVTLEFAQSKGYAIG	5	20
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0714	LEFAQSKGYAIGNAP	8	23
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0714	EGVTLEFAQSKGYAI	4	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0715	TLEFAQSKGYAIGNA	7	22
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0715	VTLEFAQSKGYAIGN	6	21
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0715	GVTLEFAQSKGYAIG	5	20
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0715	LEFAQSKGYAIGNAP	8	23
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0715	EGVTLEFAQSKGYAI	4	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0716	TLEFAQSKGYAIGNA	7	22
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0716	VTLEFAQSKGYAIGN	6	21
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0716	GVTLEFAQSKGYAIG	5	20
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0716	LEFAQSKGYAIGNAP	8	23
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0716	EGVTLEFAQSKGYAI	4	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0717	TLEFAQSKGYAIGNA	7	22
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0717	VTLEFAQSKGYAIGN	6	21
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0717	GVTLEFAQSKGYAIG	5	20
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0717	LEFAQSKGYAIGNAP	8	23
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0717	EGVTLEFAQSKGYAI	4	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0719	TLEFAQSKGYAIGNA	7	22
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0719	VTLEFAQSKGYAIGN	6	21
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0719	GVTLEFAQSKGYAIG	5	20
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0719	LEFAQSKGYAIGNAP	8	23
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0719	EGVTLEFAQSKGYAI	4	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0819	TLEFAQSKGYAIGNA	7	22
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0819	VTLEFAQSKGYAIGN	6	21
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0825	TLEFAQSKGYAIGNA	7	22
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0834	TLEFAQSKGYAIGNA	7	22
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0901	TLEFAQSKGYAIGNA	7	22
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0901	VTLEFAQSKGYAIGN	6	21
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0901	GVTLEFAQSKGYAIG	5	20
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0901	LEFAQSKGYAIGNAP	8	23
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0901	EGVTLEFAQSKGYAI	4	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0902	TLEFAQSKGYAIGNA	7	22
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0902	VTLEFAQSKGYAIGN	6	21
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0902	GVTLEFAQSKGYAIG	5	20
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0903	TLEFAQSKGYAIGNA	7	22
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0903	VTLEFAQSKGYAIGN	6	21
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0903	GVTLEFAQSKGYAIG	5	20
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0903	LEFAQSKGYAIGNAP	8	23
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0904	TLEFAQSKGYAIGNA	7	22
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0904	VTLEFAQSKGYAIGN	6	21
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0904	GVTLEFAQSKGYAIG	5	20
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0904	LEFAQSKGYAIGNAP	8	23
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0904	EGVTLEFAQSKGYAI	4	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0905	TLEFAQSKGYAIGNA	7	22
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0905	VTLEFAQSKGYAIGN	6	21
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0905	GVTLEFAQSKGYAIG	5	20
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0905	LEFAQSKGYAIGNAP	8	23
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0905	EGVTLEFAQSKGYAI	4	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0906	GVTLEFAQSKGYAIG	5	20
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0906	VTLEFAQSKGYAIGN	6	21
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0906	TLEFAQSKGYAIGNA	7	22
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0907	TLEFAQSKGYAIGNA	7	22
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0907	VTLEFAQSKGYAIGN	6	21
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0907	GVTLEFAQSKGYAIG	5	20
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0907	LEFAQSKGYAIGNAP	8	23
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0907	EGVTLEFAQSKGYAI	4	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0908	TLEFAQSKGYAIGNA	7	22
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0908	VTLEFAQSKGYAIGN	6	21
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0908	GVTLEFAQSKGYAIG	5	20
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0909	TLEFAQSKGYAIGNA	7	22
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0909	VTLEFAQSKGYAIGN	6	21
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0909	GVTLEFAQSKGYAIG	5	20
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0909	LEFAQSKGYAIGNAP	8	23
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-0909	EGVTLEFAQSKGYAI	4	19
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-1448	TLEFAQSKGYAIGNA	7	22
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-1468	TLEFAQSKGYAIGNA	7	22
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-1493	TLEFAQSKGYAIGNA	7	22
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-1511	TLEFAQSKGYAIGNA	7	22
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-1515	TLEFAQSKGYAIGNA	7	22
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-1527	TLEFAQSKGYAIGNA	7	22
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-1529	TLEFAQSKGYAIGNA	7	22
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-1529	VTLEFAQSKGYAIGN	6	21
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-1530	TLEFAQSKGYAIGNA	7	22
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-1534	TLEFAQSKGYAIGNA	7	22
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-1601	TLEFAQSKGYAIGNA	7	22
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-1602	TLEFAQSKGYAIGNA	7	22
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-1603	TLEFAQSKGYAIGNA	7	22
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-1604	TLEFAQSKGYAIGNA	7	22
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-1605	TLEFAQSKGYAIGNA	7	22
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-1607	TLEFAQSKGYAIGNA	7	22
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-1608	TLEFAQSKGYAIGNA	7	22
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-1609	TLEFAQSKGYAIGNA	7	22
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-1610	TLEFAQSKGYAIGNA	7	22
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-1611	TLEFAQSKGYAIGNA	7	22
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-1612	TLEFAQSKGYAIGNA	7	22
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-1612	VTLEFAQSKGYAIGN	6	21
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-1614	TLEFAQSKGYAIGNA	7	22
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-1614	VTLEFAQSKGYAIGN	6	21
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB1-1616	TLEFAQSKGYAIGNA	7	22
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB5-0112	TLEFAQSKGYAIGNA	7	22
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB5-0112	VTLEFAQSKGYAIGN	6	21
ACY1-BAP1	chr3	52021640	chr3	52441476	1067	DRB5-0112	GVTLEFAQSKGYAIG	5	20

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Fusion breakpoint peptide structures of ACY1-BAP1

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
10318	VTLEFAQSKGYAIG	ACY1	BAP1	chr3	52021640	chr3	52441476	1067

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of ACY1-BAP1

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	10318	VTLEFAQSKGYAIG	-7.15543	-7.26883
HLA-B14:02	3BVN	10318	VTLEFAQSKGYAIG	-4.77435	-5.80965
HLA-B52:01	3W39	10318	VTLEFAQSKGYAIG	-6.80875	-6.92215
HLA-B52:01	3W39	10318	VTLEFAQSKGYAIG	-4.20386	-5.23916
HLA-A11:01	4UQ2	10318	VTLEFAQSKGYAIG	-7.5194	-8.5547
HLA-A11:01	4UQ2	10318	VTLEFAQSKGYAIG	-6.9601	-7.0735
HLA-A24:02	5HGA	10318	VTLEFAQSKGYAIG	-7.52403	-7.63743
HLA-A24:02	5HGA	10318	VTLEFAQSKGYAIG	-5.82433	-6.85963
HLA-B27:05	6PYJ	10318	VTLEFAQSKGYAIG	-3.28285	-4.31815
HLA-B44:05	3DX8	10318	VTLEFAQSKGYAIG	-5.91172	-6.94702
HLA-B44:05	3DX8	10318	VTLEFAQSKGYAIG	-4.24346	-4.35686
HLA-B35:01	1A1N	10318	VTLEFAQSKGYAIG	-5.9251	-6.0385
HLA-B35:01	1A1N	10318	VTLEFAQSKGYAIG	-4.80237	-5.83767

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Vaccine Design for the FusionNeoAntigens of ACY1-BAP1

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
ACY1-BAP1	chr3	52021640	chr3	52441476	10	19	FAQSKGYAI	TTTGCTCAGAGCAAAGGATATGCGATT
ACY1-BAP1	chr3	52021640	chr3	52441476	11	19	AQSKGYAI	GCTCAGAGCAAAGGATATGCGATT
ACY1-BAP1	chr3	52021640	chr3	52441476	6	15	VTLEFAQSK	GTCACCCTAGAGTTTGCTCAGAGCAAA
ACY1-BAP1	chr3	52021640	chr3	52441476	6	17	VTLEFAQSKGY	GTCACCCTAGAGTTTGCTCAGAGCAAAGGATAT
ACY1-BAP1	chr3	52021640	chr3	52441476	7	17	TLEFAQSKGY	ACCCTAGAGTTTGCTCAGAGCAAAGGATAT
ACY1-BAP1	chr3	52021640	chr3	52441476	8	17	LEFAQSKGY	CTAGAGTTTGCTCAGAGCAAAGGATAT
ACY1-BAP1	chr3	52021640	chr3	52441476	8	18	LEFAQSKGYA	CTAGAGTTTGCTCAGAGCAAAGGATATGCG

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
ACY1-BAP1	chr3	52021640	chr3	52441476	4	19	EGVTLEFAQSKGYAI	GAGGGGGTCACCCTAGAGTTTGCTCAGAGCAAAGGATATGCGATT
ACY1-BAP1	chr3	52021640	chr3	52441476	5	20	GVTLEFAQSKGYAIG	GGGGTCACCCTAGAGTTTGCTCAGAGCAAAGGATATGCGATTGGC
ACY1-BAP1	chr3	52021640	chr3	52441476	6	21	VTLEFAQSKGYAIGN	GTCACCCTAGAGTTTGCTCAGAGCAAAGGATATGCGATTGGCAAT
ACY1-BAP1	chr3	52021640	chr3	52441476	7	22	TLEFAQSKGYAIGNA	ACCCTAGAGTTTGCTCAGAGCAAAGGATATGCGATTGGCAATGCC
ACY1-BAP1	chr3	52021640	chr3	52441476	8	23	LEFAQSKGYAIGNAP	CTAGAGTTTGCTCAGAGCAAAGGATATGCGATTGGCAATGCCCCG

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Information of the samples that have these potential fusion neoantigens of ACY1-BAP1

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
MESO	ACY1-BAP1	chr3	52021640	ENST00000404366	chr3	52441476	ENST00000296288	TCGA-LK-A4O5-01A

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Potential target of CAR-T therapy development for ACY1-BAP1

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 ACY1-BAP1

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 ACY1-BAP1

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)