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Fusion Protein:RABEP1-ZMYND15

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: RABEP1-ZMYND15
	FusionPDB ID: 71530
	FusionGDB2.0 ID: 71530
		Hgene	Tgene
	Gene symbol	RABEP1	ZMYND15
	Gene ID	9135	84225
	Gene name	rabaptin, RAB GTPase binding effector protein 1	zinc finger MYND-type containing 15
	Synonyms	RAB5EP\|RABPT5	SPGF14
	Cytomap	17p13.2	17p13.2
	Type of gene	protein-coding	protein-coding
	Description	rab GTPase-binding effector protein 1neurocrescinrabaptin-4rabaptin-5rabaptin-5alpharenal carcinoma antigen NY-REN-17	zinc finger MYND domain-containing protein 15
	Modification date	20200313	20200313
	UniProtAcc	.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000262477, ENST00000341923, ENST00000408982, ENST00000537505, ENST00000546142, ENST00000570487,	ENST00000269289, ENST00000433935, ENST00000573751, ENST00000592813,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	14 X 10 X 8=1120	2 X 2 X 2=8
	# samples	17	2
	** MAII score	log2(17/1120*10)=-2.71989208080726 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(2/8*10)=1.32192809488736
Fusion gene context	PubMed: RABEP1 [Title/Abstract] AND ZMYND15 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: RABEP1 [Title/Abstract] AND ZMYND15 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	RABEP1(5185815)-ZMYND15(4646598), # samples:2
Anticipated loss of major functional domain due to fusion event.	RABEP1-ZMYND15 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. RABEP1-ZMYND15 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. RABEP1-ZMYND15 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. RABEP1-ZMYND15 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/chr17:5185815/chr17:4646598)
- 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 RABEP1 (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 ZMYND15 (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)
ENST00000408982	RABEP1	chr17	5185815	+	ENST00000433935	ZMYND15	chr17	4646598	+	1468	258	155	1342	395
ENST00000408982	RABEP1	chr17	5185815	+	ENST00000592813	ZMYND15	chr17	4646598	+	1349	258	155	1225	356
ENST00000408982	RABEP1	chr17	5185815	+	ENST00000269289	ZMYND15	chr17	4646598	+	1346	258	155	1225	356
ENST00000408982	RABEP1	chr17	5185815	+	ENST00000573751	ZMYND15	chr17	4646598	+	1493	258	155	1366	403
ENST00000262477	RABEP1	chr17	5185815	+	ENST00000433935	ZMYND15	chr17	4646598	+	1468	258	155	1342	395
ENST00000262477	RABEP1	chr17	5185815	+	ENST00000592813	ZMYND15	chr17	4646598	+	1349	258	155	1225	356
ENST00000262477	RABEP1	chr17	5185815	+	ENST00000269289	ZMYND15	chr17	4646598	+	1346	258	155	1225	356
ENST00000262477	RABEP1	chr17	5185815	+	ENST00000573751	ZMYND15	chr17	4646598	+	1493	258	155	1366	403
ENST00000537505	RABEP1	chr17	5185815	+	ENST00000433935	ZMYND15	chr17	4646598	+	1457	247	144	1331	395
ENST00000537505	RABEP1	chr17	5185815	+	ENST00000592813	ZMYND15	chr17	4646598	+	1338	247	144	1214	356
ENST00000537505	RABEP1	chr17	5185815	+	ENST00000269289	ZMYND15	chr17	4646598	+	1335	247	144	1214	356
ENST00000537505	RABEP1	chr17	5185815	+	ENST00000573751	ZMYND15	chr17	4646598	+	1482	247	144	1355	403
ENST00000546142	RABEP1	chr17	5185815	+	ENST00000433935	ZMYND15	chr17	4646598	+	1431	221	118	1305	395
ENST00000546142	RABEP1	chr17	5185815	+	ENST00000592813	ZMYND15	chr17	4646598	+	1312	221	118	1188	356
ENST00000546142	RABEP1	chr17	5185815	+	ENST00000269289	ZMYND15	chr17	4646598	+	1309	221	118	1188	356
ENST00000546142	RABEP1	chr17	5185815	+	ENST00000573751	ZMYND15	chr17	4646598	+	1456	221	118	1329	403
ENST00000341923	RABEP1	chr17	5185815	+	ENST00000433935	ZMYND15	chr17	4646598	+	1244	34	0	1118	372
ENST00000341923	RABEP1	chr17	5185815	+	ENST00000592813	ZMYND15	chr17	4646598	+	1125	34	0	1001	333
ENST00000341923	RABEP1	chr17	5185815	+	ENST00000269289	ZMYND15	chr17	4646598	+	1122	34	0	1001	333
ENST00000341923	RABEP1	chr17	5185815	+	ENST00000573751	ZMYND15	chr17	4646598	+	1269	34	0	1142	380

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
ENST00000408982	ENST00000433935	RABEP1	chr17	5185815	+	ZMYND15	chr17	4646598	+	0.163533	0.836467
ENST00000408982	ENST00000592813	RABEP1	chr17	5185815	+	ZMYND15	chr17	4646598	+	0.2276887	0.77231133
ENST00000408982	ENST00000269289	RABEP1	chr17	5185815	+	ZMYND15	chr17	4646598	+	0.22861032	0.77138966
ENST00000408982	ENST00000573751	RABEP1	chr17	5185815	+	ZMYND15	chr17	4646598	+	0.17495121	0.8250488
ENST00000262477	ENST00000433935	RABEP1	chr17	5185815	+	ZMYND15	chr17	4646598	+	0.163533	0.836467
ENST00000262477	ENST00000592813	RABEP1	chr17	5185815	+	ZMYND15	chr17	4646598	+	0.2276887	0.77231133
ENST00000262477	ENST00000269289	RABEP1	chr17	5185815	+	ZMYND15	chr17	4646598	+	0.22861032	0.77138966
ENST00000262477	ENST00000573751	RABEP1	chr17	5185815	+	ZMYND15	chr17	4646598	+	0.17495121	0.8250488
ENST00000537505	ENST00000433935	RABEP1	chr17	5185815	+	ZMYND15	chr17	4646598	+	0.1640172	0.83598286
ENST00000537505	ENST00000592813	RABEP1	chr17	5185815	+	ZMYND15	chr17	4646598	+	0.22877733	0.77122265
ENST00000537505	ENST00000269289	RABEP1	chr17	5185815	+	ZMYND15	chr17	4646598	+	0.22890335	0.77109665
ENST00000537505	ENST00000573751	RABEP1	chr17	5185815	+	ZMYND15	chr17	4646598	+	0.17479068	0.8252094
ENST00000546142	ENST00000433935	RABEP1	chr17	5185815	+	ZMYND15	chr17	4646598	+	0.1689061	0.8310939
ENST00000546142	ENST00000592813	RABEP1	chr17	5185815	+	ZMYND15	chr17	4646598	+	0.24136773	0.75863224
ENST00000546142	ENST00000269289	RABEP1	chr17	5185815	+	ZMYND15	chr17	4646598	+	0.24160825	0.7583918
ENST00000546142	ENST00000573751	RABEP1	chr17	5185815	+	ZMYND15	chr17	4646598	+	0.18145734	0.8185426
ENST00000341923	ENST00000433935	RABEP1	chr17	5185815	+	ZMYND15	chr17	4646598	+	0.194872	0.80512804
ENST00000341923	ENST00000592813	RABEP1	chr17	5185815	+	ZMYND15	chr17	4646598	+	0.2821879	0.71781206
ENST00000341923	ENST00000269289	RABEP1	chr17	5185815	+	ZMYND15	chr17	4646598	+	0.28310412	0.7168959
ENST00000341923	ENST00000573751	RABEP1	chr17	5185815	+	ZMYND15	chr17	4646598	+	0.21415399	0.785846

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 RABEP1-ZMYND15

+/-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
RABEP1	chr17	5185815	ZMYND15	chr17	4646598	221	34	LVMAQPGPASQPDEVTSETFNKEAFL
RABEP1	chr17	5185815	ZMYND15	chr17	4646598	247	34	LVMAQPGPASQPDEVTSETFNKEAFL
RABEP1	chr17	5185815	ZMYND15	chr17	4646598	258	34	LVMAQPGPASQPDEVTSETFNKEAFL

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Potential FusionNeoAntigen Information of RABEP1-ZMYND15 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.

RABEP1-ZMYND15_5185815_4646598.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)
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B18:01	DEVTSETF	0.9991	0.9628	12	20
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B35:08	QPDEVTSET	0.483	0.9595	10	19
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B35:04	QPDEVTSET	0.3149	0.9908	10	19
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B35:02	QPDEVTSET	0.3149	0.9908	10	19
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B35:08	QPDEVTSETF	0.9763	0.958	10	20
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B35:01	QPDEVTSETF	0.9747	0.9719	10	20
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B35:05	QPDEVTSETF	0.9458	0.923	10	20
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B35:03	QPDEVTSETF	0.9186	0.9702	10	20
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B53:01	QPDEVTSETF	0.9173	0.8093	10	20
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B35:02	QPDEVTSETF	0.768	0.9897	10	20
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B35:04	QPDEVTSETF	0.768	0.9897	10	20
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B15:01	SQPDEVTSETF	1	0.9037	9	20
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B13:01	SQPDEVTSETF	0.9811	0.9508	9	20
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B35:12	QPDEVTSET	0.3149	0.9908	10	19
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B39:10	QPDEVTSET	0.1405	0.9714	10	19
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B39:10	GPASQPDEV	0.0636	0.916	6	15
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-C04:10	QPDEVTSETF	0.9997	0.7475	10	20
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-C04:07	QPDEVTSETF	0.9997	0.7822	10	20
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B07:12	QPDEVTSETF	0.9643	0.5373	10	20
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B56:04	QPDEVTSETF	0.8045	0.5525	10	20
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B35:12	QPDEVTSETF	0.768	0.9897	10	20
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B39:10	QPDEVTSETF	0.6548	0.9676	10	20
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B42:02	QPDEVTSETF	0.6403	0.7415	10	20
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B42:01	QPDEVTSETF	0.5324	0.7279	10	20
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B15:05	SQPDEVTSETF	0.9953	0.9239	9	20
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B18:04	DEVTSETF	0.9994	0.9683	12	20
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B18:07	DEVTSETF	0.9992	0.9403	12	20
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B18:05	DEVTSETF	0.9991	0.9628	12	20
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B18:06	DEVTSETF	0.999	0.9662	12	20
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B18:08	DEVTSETF	0.9987	0.9322	12	20
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B18:03	DEVTSETF	0.9985	0.959	12	20
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B18:11	DEVTSETF	0.9832	0.933	12	20
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B59:01	GPASQPDEV	0.4326	0.5173	6	15
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B35:09	QPDEVTSET	0.3149	0.9908	10	19
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B67:01	QPDEVTSET	0.2467	0.9554	10	19
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B67:01	GPASQPDEV	0.1207	0.8952	6	15
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-C04:01	QPDEVTSETF	0.9997	0.7822	10	20
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B35:77	QPDEVTSETF	0.9747	0.9719	10	20
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B35:23	QPDEVTSETF	0.9734	0.9754	10	20
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B35:17	QPDEVTSETF	0.9527	0.9587	10	20
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B35:30	QPDEVTSETF	0.9527	0.9587	10	20
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B35:11	QPDEVTSETF	0.952	0.9684	10	20
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B35:43	QPDEVTSETF	0.8572	0.9321	10	20
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B35:24	QPDEVTSETF	0.8426	0.9689	10	20
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B15:08	QPDEVTSETF	0.8351	0.9257	10	20
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B15:11	QPDEVTSETF	0.8227	0.9326	10	20
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B56:02	QPDEVTSETF	0.8045	0.5525	10	20
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B35:09	QPDEVTSETF	0.768	0.9897	10	20
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B53:02	QPDEVTSETF	0.7618	0.7946	10	20
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B35:22	QPDEVTSETF	0.7235	0.6457	10	20
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B67:01	QPDEVTSETF	0.6666	0.9443	10	20
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B51:06	QPDEVTSETF	0.476	0.6817	10	20
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B18:07	QPDEVTSETF	0.3871	0.9301	10	20
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B15:125	SQPDEVTSETF	1	0.9037	9	20
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B15:27	SQPDEVTSETF	1	0.9076	9	20
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B15:53	SQPDEVTSETF	1	0.8862	9	20
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B15:34	SQPDEVTSETF	1	0.9037	9	20
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B15:33	SQPDEVTSETF	1	0.9037	9	20
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B15:50	SQPDEVTSETF	1	0.8948	9	20
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B15:24	SQPDEVTSETF	1	0.9092	9	20
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B15:12	SQPDEVTSETF	0.9999	0.8947	9	20
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B15:73	SQPDEVTSETF	0.9997	0.8772	9	20
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B15:30	SQPDEVTSETF	0.9995	0.9422	9	20
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B15:54	SQPDEVTSETF	0.9994	0.8797	9	20
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B15:20	SQPDEVTSETF	0.9944	0.9516	9	20
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	258	HLA-B35:28	SQPDEVTSETF	0.9931	0.9643	9	20

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Potential FusionNeoAntigen Information of RABEP1-ZMYND15 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 RABEP1-ZMYND15

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
3010	GPASQPDEVTSETF	RABEP1	ZMYND15	chr17	5185815	chr17	4646598	258

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of RABEP1-ZMYND15

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	3010	GPASQPDEVTSETF	-7.9962	-8.1096
HLA-B14:02	3BVN	3010	GPASQPDEVTSETF	-5.70842	-6.74372
HLA-B52:01	3W39	3010	GPASQPDEVTSETF	-6.83737	-6.95077
HLA-B52:01	3W39	3010	GPASQPDEVTSETF	-4.4836	-5.5189
HLA-A11:01	4UQ2	3010	GPASQPDEVTSETF	-10.0067	-10.1201
HLA-A11:01	4UQ2	3010	GPASQPDEVTSETF	-9.03915	-10.0745
HLA-A24:02	5HGA	3010	GPASQPDEVTSETF	-6.56204	-6.67544
HLA-A24:02	5HGA	3010	GPASQPDEVTSETF	-5.42271	-6.45801
HLA-B44:05	3DX8	3010	GPASQPDEVTSETF	-7.85648	-8.89178
HLA-B44:05	3DX8	3010	GPASQPDEVTSETF	-5.3978	-5.5112
HLA-A02:01	6TDR	3010	GPASQPDEVTSETF	-3.37154	-4.40684

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Vaccine Design for the FusionNeoAntigens of RABEP1-ZMYND15

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
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	10	19	QPDEVTSET	AGCCTGACGAGGTGACCAGTGAAACCT
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	10	20	QPDEVTSETF	AGCCTGACGAGGTGACCAGTGAAACCTTCA
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	12	20	DEVTSETF	ACGAGGTGACCAGTGAAACCTTCA
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	6	15	GPASQPDEV	GCCCGGCTTCCCAGCCTGACGAGGTGA
RABEP1-ZMYND15	chr17	5185815	chr17	4646598	9	20	SQPDEVTSETF	CCCAGCCTGACGAGGTGACCAGTGAAACCTTCA

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 RABEP1-ZMYND15

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	RABEP1-ZMYND15	chr17	5185815	ENST00000262477	chr17	4646598	ENST00000269289	TCGA-VQ-A8PE-01A

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Potential target of CAR-T therapy development for RABEP1-ZMYND15

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 RABEP1-ZMYND15

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 RABEP1-ZMYND15

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)