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Fusion Protein:BANP-SLC9A3R2

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: BANP-SLC9A3R2
	FusionPDB ID: 8964
	FusionGDB2.0 ID: 8964
		Hgene	Tgene
	Gene symbol	BANP	SLC9A3R2
	Gene ID	54971	9351
	Gene name	BTG3 associated nuclear protein	SLC9A3 regulator 2
	Synonyms	BEND1\|SMAR1\|SMARBP1	E3KARP\|NHE3RF2\|NHERF-2\|NHERF2\|OCTS2\|SIP-1\|SIP1\|TKA-1
	Cytomap	16q24.2	16p13.3
	Type of gene	protein-coding	protein-coding
	Description	protein BANPBEN domain-containing protein 1scaffold/matrix-associated region-1-binding protein	Na(+)/H(+) exchange regulatory cofactor NHE-RF2NHE3 kinase A regulatory protein E3KARPNHE3 regulatory factor 2SRY-interacting protein 1sodium/hydrogen exchanger 3 kinase A regulatory proteinsolute carrier family 9 (sodium/hydrogen exchanger), isoform
	Modification date	20200315	20200313
	UniProtAcc	Q8N9N5 Main function of 5'-partner protein: FUNCTION: Controls V(D)J recombination during T-cell development by repressing T-cell receptor (TCR) beta enhancer function. Binds to scaffold/matrix attachment region beta (S/MARbeta), an ATC-rich DNA sequence located upstream of the TCR beta enhancer. Represses cyclin D1 transcription by recruiting HDAC1 to its promoter, thereby diminishing H3K9ac, H3S10ph and H4K8ac levels. Promotes TP53 'Ser-15' phosphorylation and nuclear accumulation, which causes cell cycle arrest (By similarity). {ECO:0000250, ECO:0000269\|PubMed:16166625}.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000481948, ENST00000286122, ENST00000355022, ENST00000355163, ENST00000393207, ENST00000393208, ENST00000479780, ENST00000538234,	ENST00000424542, ENST00000432365, ENST00000563587, ENST00000565086, ENST00000566198,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	8 X 7 X 8=448	2 X 2 X 2=8
	# samples	8	2
	** MAII score	log2(8/448*10)=-2.48542682717024 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(2/8*10)=1.32192809488736
Fusion gene context	PubMed: BANP [Title/Abstract] AND SLC9A3R2 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: BANP [Title/Abstract] AND SLC9A3R2 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	BANP(88105818)-SLC9A3R2(2086325), # samples:1
Anticipated loss of major functional domain due to fusion event.	BANP-SLC9A3R2 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. BANP-SLC9A3R2 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. BANP-SLC9A3R2 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. BANP-SLC9A3R2 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

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr16:88105818/chr16:2086325)
- 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 BANP (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 SLC9A3R2 (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)
ENST00000286122	BANP	chr16	88105818	+	ENST00000424542	SLC9A3R2	chr16	2086325	+	3282	1640	152	2239	695
ENST00000286122	BANP	chr16	88105818	+	ENST00000432365	SLC9A3R2	chr16	2086325	+	2712	1640	152	2206	684
ENST00000286122	BANP	chr16	88105818	+	ENST00000563587	SLC9A3R2	chr16	2086325	+	2421	1640	152	2239	695
ENST00000355163	BANP	chr16	88105818	+	ENST00000424542	SLC9A3R2	chr16	2086325	+	3216	1574	152	2173	673
ENST00000355163	BANP	chr16	88105818	+	ENST00000432365	SLC9A3R2	chr16	2086325	+	2646	1574	152	2140	662
ENST00000355163	BANP	chr16	88105818	+	ENST00000563587	SLC9A3R2	chr16	2086325	+	2355	1574	152	2173	673
ENST00000479780	BANP	chr16	88105818	+	ENST00000424542	SLC9A3R2	chr16	2086325	+	3121	1479	150	2078	642
ENST00000479780	BANP	chr16	88105818	+	ENST00000432365	SLC9A3R2	chr16	2086325	+	2551	1479	150	2045	631
ENST00000479780	BANP	chr16	88105818	+	ENST00000563587	SLC9A3R2	chr16	2086325	+	2260	1479	150	2078	642
ENST00000393208	BANP	chr16	88105818	+	ENST00000424542	SLC9A3R2	chr16	2086325	+	3196	1554	150	2153	667
ENST00000393208	BANP	chr16	88105818	+	ENST00000432365	SLC9A3R2	chr16	2086325	+	2626	1554	150	2120	656
ENST00000393208	BANP	chr16	88105818	+	ENST00000563587	SLC9A3R2	chr16	2086325	+	2335	1554	150	2153	667
ENST00000355022	BANP	chr16	88105818	+	ENST00000424542	SLC9A3R2	chr16	2086325	+	3077	1435	97	2034	645
ENST00000355022	BANP	chr16	88105818	+	ENST00000432365	SLC9A3R2	chr16	2086325	+	2507	1435	97	2001	634
ENST00000355022	BANP	chr16	88105818	+	ENST00000563587	SLC9A3R2	chr16	2086325	+	2216	1435	97	2034	645
ENST00000538234	BANP	chr16	88105818	+	ENST00000424542	SLC9A3R2	chr16	2086325	+	3288	1646	191	2245	684
ENST00000538234	BANP	chr16	88105818	+	ENST00000432365	SLC9A3R2	chr16	2086325	+	2718	1646	191	2212	673
ENST00000538234	BANP	chr16	88105818	+	ENST00000563587	SLC9A3R2	chr16	2086325	+	2427	1646	191	2245	684
ENST00000393207	BANP	chr16	88105818	+	ENST00000424542	SLC9A3R2	chr16	2086325	+	3351	1709	221	2308	695
ENST00000393207	BANP	chr16	88105818	+	ENST00000432365	SLC9A3R2	chr16	2086325	+	2781	1709	221	2275	684
ENST00000393207	BANP	chr16	88105818	+	ENST00000563587	SLC9A3R2	chr16	2086325	+	2490	1709	221	2308	695

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
ENST00000286122	ENST00000424542	BANP	chr16	88105818	+	SLC9A3R2	chr16	2086325	+	0.015629878	0.9843701
ENST00000286122	ENST00000432365	BANP	chr16	88105818	+	SLC9A3R2	chr16	2086325	+	0.02121502	0.978785
ENST00000286122	ENST00000563587	BANP	chr16	88105818	+	SLC9A3R2	chr16	2086325	+	0.022538584	0.9774614
ENST00000355163	ENST00000424542	BANP	chr16	88105818	+	SLC9A3R2	chr16	2086325	+	0.01965415	0.9803459
ENST00000355163	ENST00000432365	BANP	chr16	88105818	+	SLC9A3R2	chr16	2086325	+	0.027371159	0.9726289
ENST00000355163	ENST00000563587	BANP	chr16	88105818	+	SLC9A3R2	chr16	2086325	+	0.03167496	0.9683251
ENST00000479780	ENST00000424542	BANP	chr16	88105818	+	SLC9A3R2	chr16	2086325	+	0.016754514	0.9832455
ENST00000479780	ENST00000432365	BANP	chr16	88105818	+	SLC9A3R2	chr16	2086325	+	0.022149986	0.9778501
ENST00000479780	ENST00000563587	BANP	chr16	88105818	+	SLC9A3R2	chr16	2086325	+	0.025635896	0.97436404
ENST00000393208	ENST00000424542	BANP	chr16	88105818	+	SLC9A3R2	chr16	2086325	+	0.017160013	0.98284
ENST00000393208	ENST00000432365	BANP	chr16	88105818	+	SLC9A3R2	chr16	2086325	+	0.022946227	0.9770537
ENST00000393208	ENST00000563587	BANP	chr16	88105818	+	SLC9A3R2	chr16	2086325	+	0.026225602	0.97377443
ENST00000355022	ENST00000424542	BANP	chr16	88105818	+	SLC9A3R2	chr16	2086325	+	0.014231026	0.985769
ENST00000355022	ENST00000432365	BANP	chr16	88105818	+	SLC9A3R2	chr16	2086325	+	0.019571984	0.98042804
ENST00000355022	ENST00000563587	BANP	chr16	88105818	+	SLC9A3R2	chr16	2086325	+	0.023545144	0.9764548
ENST00000538234	ENST00000424542	BANP	chr16	88105818	+	SLC9A3R2	chr16	2086325	+	0.012941775	0.9870582
ENST00000538234	ENST00000432365	BANP	chr16	88105818	+	SLC9A3R2	chr16	2086325	+	0.017436028	0.9825639
ENST00000538234	ENST00000563587	BANP	chr16	88105818	+	SLC9A3R2	chr16	2086325	+	0.022413593	0.9775864
ENST00000393207	ENST00000424542	BANP	chr16	88105818	+	SLC9A3R2	chr16	2086325	+	0.013994262	0.9860058
ENST00000393207	ENST00000432365	BANP	chr16	88105818	+	SLC9A3R2	chr16	2086325	+	0.018671852	0.9813281
ENST00000393207	ENST00000563587	BANP	chr16	88105818	+	SLC9A3R2	chr16	2086325	+	0.020941	0.97905904

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 BANP-SLC9A3R2

+/-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
BANP	chr16	88105818	SLC9A3R2	chr16	2086325	1435	104	VTNKQHSPIQVPMVAGSPLGATQTCN
BANP	chr16	88105818	SLC9A3R2	chr16	2086325	1479	104	VTNKQHSPIQVPMVAGSPLGATQTCN
BANP	chr16	88105818	SLC9A3R2	chr16	2086325	1554	104	VTNKQHSPIQVPMVAGSPLGATQTCN
BANP	chr16	88105818	SLC9A3R2	chr16	2086325	1574	110	VTNKQHSPIQVPMVAGSPLGATQTCN
BANP	chr16	88105818	SLC9A3R2	chr16	2086325	1640	96	VTNKQHSPIQVPMVAGSPLGATQTCN
BANP	chr16	88105818	SLC9A3R2	chr16	2086325	1646	104	VTNKQHSPIQVPMVAGSPLGATQTCN
BANP	chr16	88105818	SLC9A3R2	chr16	2086325	1709	96	VTNKQHSPIQVPMVAGSPLGATQTCN

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Potential FusionNeoAntigen Information of BANP-SLC9A3R2 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.

BANP-SLC9A3R2_88105818_2086325.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)
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B35:03	VPMVAGSPL	0.9929	0.8041	10	19
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B56:01	SPIQVPMVA	0.992	0.6482	6	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B07:05	SPIQVPMVA	0.9869	0.5951	6	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B07:02	SPIQVPMVA	0.9854	0.6255	6	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B35:01	VPMVAGSPL	0.9814	0.8395	10	19
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B35:08	VPMVAGSPL	0.98	0.7753	10	19
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B35:02	VPMVAGSPL	0.9718	0.9392	10	19
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B35:04	VPMVAGSPL	0.9718	0.9392	10	19
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B35:03	SPIQVPMVA	0.9377	0.6779	6	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B35:05	VPMVAGSPL	0.9301	0.566	10	19
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B39:06	SPIQVPMVA	0.9052	0.9744	6	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B35:02	SPIQVPMVA	0.8841	0.9453	6	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B35:04	SPIQVPMVA	0.8841	0.9453	6	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B35:01	SPIQVPMVA	0.8825	0.6764	6	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B35:05	SPIQVPMVA	0.8537	0.5768	6	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B08:09	SPIQVPMVA	0.6083	0.9137	6	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B82:01	SPIQVPMVA	0.5581	0.6495	6	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B81:01	SPIQVPMVA	0.5382	0.7773	6	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B39:06	QHSPIQVPMV	0.997	0.9763	4	14
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B38:01	QHSPIQVPMV	0.996	0.9938	4	14
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B38:02	QHSPIQVPMV	0.9956	0.9937	4	14
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B56:01	HSPIQVPMVA	0.9322	0.7696	5	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B55:01	HSPIQVPMVA	0.8971	0.5394	5	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B56:01	SPIQVPMVAG	0.8132	0.5044	6	16
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B81:01	QVPMVAGSPL	0.7281	0.6512	9	19
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B82:01	QVPMVAGSPL	0.4576	0.6458	9	19
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B39:06	QHSPIQVPMVA	0.9978	0.9897	4	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B56:01	VPMVAGSPLGA	0.9974	0.7647	10	21
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B55:01	VPMVAGSPLGA	0.9962	0.5148	10	21
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B55:01	QHSPIQVPMVA	0.996	0.8195	4	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B56:01	QHSPIQVPMVA	0.9944	0.9501	4	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B81:01	IQVPMVAGSPL	0.9686	0.6109	8	19
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B13:02	KQHSPIQVPMV	0.9556	0.9811	3	14
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B51:07	SPIQVPMV	0.9948	0.8716	6	14
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B78:01	SPIQVPMV	0.9943	0.6228	6	14
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B51:08	SPIQVPMV	0.9887	0.64	6	14
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B54:01	SPIQVPMV	0.9641	0.633	6	14
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B54:01	SPIQVPMVA	0.997	0.8866	6	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B07:12	VPMVAGSPL	0.9887	0.5651	10	19
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B07:12	SPIQVPMVA	0.9718	0.6978	6	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B35:12	VPMVAGSPL	0.9718	0.9392	10	19
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B39:10	VPMVAGSPL	0.9453	0.893	10	19
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B07:04	SPIQVPMVA	0.9201	0.622	6	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B56:04	SPIQVPMVA	0.9037	0.7217	6	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B42:02	VPMVAGSPL	0.8858	0.6373	10	19
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B35:12	SPIQVPMVA	0.8841	0.9453	6	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B78:01	SPIQVPMVA	0.8782	0.8057	6	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-C01:17	HSPIQVPMV	0.8559	0.9719	5	14
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B78:01	VPMVAGSPL	0.8458	0.5451	10	19
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B42:02	SPIQVPMVA	0.8352	0.813	6	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B42:01	VPMVAGSPL	0.8347	0.6284	10	19
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-C01:30	HSPIQVPMV	0.7331	0.9868	5	14
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B42:01	SPIQVPMVA	0.722	0.8071	6	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B39:10	SPIQVPMVA	0.5983	0.9595	6	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B39:05	QHSPIQVPMV	0.9944	0.977	4	14
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B54:01	HSPIQVPMVA	0.9713	0.9166	5	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B07:12	QVPMVAGSPL	0.9677	0.5446	9	19
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B56:04	HSPIQVPMVA	0.7151	0.8356	5	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B42:01	QVPMVAGSPL	0.6708	0.8042	9	19
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B78:01	HSPIQVPMVA	0.5876	0.7859	5	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B54:01	VPMVAGSPLGA	0.9996	0.8888	10	21
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B54:01	QHSPIQVPMVA	0.9913	0.9713	4	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B78:02	SPIQVPMV	0.9964	0.7302	6	14
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B51:21	SPIQVPMV	0.9937	0.6265	6	14
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B51:29	SPIQVPMV	0.9916	0.53	6	14
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B51:09	SPIQVPMV	0.9911	0.5134	6	14
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B59:01	SPIQVPMV	0.9592	0.5478	6	14
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B35:13	VPMVAGSPL	0.992	0.8087	10	19
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B55:02	SPIQVPMVA	0.9915	0.7545	6	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B07:22	SPIQVPMVA	0.9854	0.6255	6	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B07:09	SPIQVPMVA	0.9851	0.6217	6	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-A68:02	MVAGSPLGA	0.9841	0.7232	12	21
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B35:77	VPMVAGSPL	0.9814	0.8395	10	19
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B35:23	VPMVAGSPL	0.9796	0.8388	10	19
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B59:01	SPIQVPMVA	0.9752	0.8103	6	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B35:09	VPMVAGSPL	0.9718	0.9392	10	19
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B56:05	SPIQVPMVA	0.9701	0.6739	6	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B35:24	VPMVAGSPL	0.946	0.8318	10	19
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B67:01	VPMVAGSPL	0.9444	0.7757	10	19
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B35:30	VPMVAGSPL	0.9344	0.7392	10	19
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B35:17	VPMVAGSPL	0.9344	0.7392	10	19
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B35:11	VPMVAGSPL	0.9186	0.8529	10	19
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B55:04	SPIQVPMVA	0.9141	0.7339	6	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B35:22	SPIQVPMVA	0.9116	0.6836	6	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B56:02	SPIQVPMVA	0.9037	0.7217	6	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-C01:03	HSPIQVPMV	0.8881	0.9707	5	14
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B35:23	SPIQVPMVA	0.8854	0.7223	6	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B35:09	SPIQVPMVA	0.8841	0.9453	6	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B35:77	SPIQVPMVA	0.8825	0.6764	6	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B78:02	VPMVAGSPL	0.8662	0.6078	10	19
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B35:17	SPIQVPMVA	0.8606	0.6343	6	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B35:30	SPIQVPMVA	0.8606	0.6343	6	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-C01:02	HSPIQVPMV	0.8559	0.9735	5	14
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B78:02	SPIQVPMVA	0.8495	0.8714	6	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B51:14	SPIQVPMVA	0.8093	0.6073	6	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B51:13	SPIQVPMVA	0.803	0.6573	6	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B35:11	SPIQVPMVA	0.7884	0.7687	6	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B51:09	SPIQVPMVA	0.7836	0.7248	6	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B51:21	SPIQVPMVA	0.7604	0.7173	6	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B07:26	SPIQVPMVA	0.748	0.5133	6	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B67:01	SPIQVPMVA	0.7346	0.9715	6	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B35:24	SPIQVPMVA	0.577	0.7498	6	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B82:02	SPIQVPMVA	0.5581	0.6495	6	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B18:07	SPIQVPMVA	0.0517	0.7817	6	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B35:43	VPMVAGSPL	0.0424	0.8145	10	19
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B35:43	SPIQVPMVA	0.0102	0.8111	6	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B38:05	QHSPIQVPMV	0.996	0.9938	4	14
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B55:02	HSPIQVPMVA	0.9369	0.8007	5	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B55:02	SPIQVPMVAG	0.8711	0.6094	6	16
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B55:04	QVPMVAGSPL	0.7396	0.5237	9	19
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B56:02	HSPIQVPMVA	0.7151	0.8356	5	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B56:05	HSPIQVPMVA	0.7035	0.6732	5	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B67:01	QVPMVAGSPL	0.6563	0.9187	9	19
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B78:02	HSPIQVPMVA	0.6365	0.8536	5	15
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B82:02	QVPMVAGSPL	0.4576	0.6458	9	19
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B55:02	VPMVAGSPLGA	0.9986	0.7416	10	21
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	1640	HLA-B55:02	QHSPIQVPMVA	0.9976	0.9344	4	15

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Potential FusionNeoAntigen Information of BANP-SLC9A3R2 in HLA II

Potential FusionNeoAntigen Information
* We used NetMHCIIpan v4.1 (%rank<0.5).

Fusion gene

Hchr

Hbp

Tgene

Tchr

Tbp

HLA II

FusionNeoAntigen peptide

Neoantigen start (at BP 13)

Neoantigen end (at BP 13)

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Fusion breakpoint peptide structures of BANP-SLC9A3R2

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
8882	SPIQVPMVAGSPLG	BANP	SLC9A3R2	chr16	88105818	chr16	2086325	1640

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of BANP-SLC9A3R2

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	8882	SPIQVPMVAGSPLG	-8.55667	-8.74867
HLA-B14:02	3BVN	8882	SPIQVPMVAGSPLG	-3.49457	-4.25557
HLA-B52:01	3W39	8882	SPIQVPMVAGSPLG	-7.26725	-7.45925
HLA-B52:01	3W39	8882	SPIQVPMVAGSPLG	-4.01461	-4.77561
HLA-A24:02	5HGA	8882	SPIQVPMVAGSPLG	-7.65911	-8.42011
HLA-A24:02	5HGA	8882	SPIQVPMVAGSPLG	-7.10204	-7.29404
HLA-B44:05	3DX8	8882	SPIQVPMVAGSPLG	-7.5556	-8.3166
HLA-B44:05	3DX8	8882	SPIQVPMVAGSPLG	-2.76159	-2.95359

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Vaccine Design for the FusionNeoAntigens of BANP-SLC9A3R2

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
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	10	19	VPMVAGSPL	GGGGCACAGGATGTCAGTGGGCCCCTG
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	10	21	VPMVAGSPLGA	GGGGCACAGGATGTCAGTGGGCCCCTGAGGGAG
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	12	21	MVAGSPLGA	CAGGATGTCAGTGGGCCCCTGAGGGAG
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	3	14	KQHSPIQVPMV	CCAGTGAGTGACCACACGGCCGGGGCACAGGAT
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	4	14	QHSPIQVPMV	GTGAGTGACCACACGGCCGGGGCACAGGAT
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	4	15	QHSPIQVPMVA	GTGAGTGACCACACGGCCGGGGCACAGGATGTC
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	5	14	HSPIQVPMV	AGTGACCACACGGCCGGGGCACAGGAT
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	5	15	HSPIQVPMVA	AGTGACCACACGGCCGGGGCACAGGATGTC
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	6	14	SPIQVPMV	GACCACACGGCCGGGGCACAGGAT
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	6	15	SPIQVPMVA	GACCACACGGCCGGGGCACAGGATGTC
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	6	16	SPIQVPMVAG	GACCACACGGCCGGGGCACAGGATGTCAGT
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	8	19	IQVPMVAGSPL	ACGGCCGGGGCACAGGATGTCAGTGGGCCCCTG
BANP-SLC9A3R2	chr16	88105818	chr16	2086325	9	19	QVPMVAGSPL	GCCGGGGCACAGGATGTCAGTGGGCCCCTG

mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.

Fusion gene

Hchr

Hbp

Tchr

Tbp

Start in +/-13AA

End in +/-13AA

FusionNeoAntigen peptide

FusionNEoAntigen RNA sequence

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Information of the samples that have these potential fusion neoantigens of BANP-SLC9A3R2

These samples were reported as having these fusion breakpoints. For individual breakpoints, we checked the open reading frames considering multiple gene isoforms and chose the in-frame fusion genes only. Then, we made fusion protein sequences and predicted the fusion neoantigens. These fusion-positive samples may have these potential fusion neoantigens.

Cancer type	Fusion gene	Hchr	Hbp	Henst	Tchr	Tbp	Tenst	Sample
STAD	BANP-SLC9A3R2	chr16	88105818	ENST00000286122	chr16	2086325	ENST00000424542	TCGA-IN-7808-01A

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Potential target of CAR-T therapy development for BANP-SLC9A3R2

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 BANP-SLC9A3R2

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 BANP-SLC9A3R2

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)