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Fusion Protein:EPS15-TRABD2B

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: EPS15-TRABD2B
	FusionPDB ID: 27092
	FusionGDB2.0 ID: 27092
		Hgene	Tgene
	Gene symbol	EPS15	TRABD2B
	Gene ID	2060	388630
	Gene name	epidermal growth factor receptor pathway substrate 15	TraB domain containing 2B
	Synonyms	AF-1P\|AF1P\|MLLT5	TIKI2
	Cytomap	1p32.3	1p33
	Type of gene	protein-coding	protein-coding
	Description	epidermal growth factor receptor substrate 15ALL1 fused gene from chromosome 1protein AF-1p	metalloprotease TIKI2TRAB domain-containing protein 2BUPF0632 protein Aheart, kidney and adipose-enriched transmembrane protein homolog
	Modification date	20200313	20200313
	UniProtAcc	Q9UBC2 Main function of 5'-partner protein: FUNCTION: Seems to be a constitutive component of clathrin-coated pits that is required for receptor-mediated endocytosis. Involved in endocytosis of integrin beta-1 (ITGB1) and transferrin receptor (TFR); internalization of ITGB1 as DAB2-dependent cargo but not TFR seems to require association with DAB2. {ECO:0000269\|PubMed:22648170, ECO:0000269\|PubMed:9407958}.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000371730, ENST00000371733, ENST00000396122, ENST00000493793,	ENST00000435576, ENST00000606738,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	17 X 13 X 11=2431	6 X 4 X 4=96
	# samples	17	6
	** MAII score	log2(17/2431*10)=-3.83794324189103 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(6/96*10)=-0.678071905112638 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: EPS15 [Title/Abstract] AND TRABD2B [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: EPS15 [Title/Abstract] AND TRABD2B [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	EPS15(51984871)-TRABD2B(48267291), # samples:2
Anticipated loss of major functional domain due to fusion event.	EPS15-TRABD2B 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. EPS15-TRABD2B seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.

* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner	Gene	GO ID	GO term	PubMed ID
Hgene	EPS15	GO:0048268	clathrin coat assembly	12807910
Tgene	TRABD2B	GO:0006508	proteolysis	22726442
Tgene	TRABD2B	GO:0030178	negative regulation of Wnt signaling pathway	22726442
Tgene	TRABD2B	GO:0031334	positive regulation of protein complex assembly	22726442
Tgene	TRABD2B	GO:1904808	positive regulation of protein oxidation	22726442

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr1:51984871/chr1:48267291)
- 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 EPS15 (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 TRABD2B (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)
ENST00000371730	EPS15	chr1	51984871	-	ENST00000606738	TRABD2B	chr1	48267291	-	6305	43	10	930	306
ENST00000371733	EPS15	chr1	51984871	-	ENST00000606738	TRABD2B	chr1	48267291	-	6392	130	13	1017	334

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
ENST00000371730	ENST00000606738	EPS15	chr1	51984871	-	TRABD2B	chr1	48267291	-	0.0080614	0.99193853
ENST00000371733	ENST00000606738	EPS15	chr1	51984871	-	TRABD2B	chr1	48267291	-	0.008471802	0.99152815

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 EPS15-TRABD2B

+/-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
EPS15	chr1	51984871	TRABD2B	chr1	48267291	130	34	PLHDGNTMAAAAQLSLTQVLFALNQT

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Potential FusionNeoAntigen Information of EPS15-TRABD2B 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.

EPS15-TRABD2B_51984871_48267291.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)
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B13:02	AQLSLTQV	0.9881	0.8497	11	19
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B52:01	AQLSLTQV	0.8233	0.9817	11	19
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B48:01	AQLSLTQVL	0.9974	0.6364	11	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B35:08	MAAAAQLSL	0.993	0.9145	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B35:03	MAAAAQLSL	0.992	0.9109	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:01	AQLSLTQVL	0.991	0.8172	11	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B39:24	AQLSLTQVL	0.9905	0.5353	11	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B35:01	MAAAAQLSL	0.9842	0.9105	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:17	MAAAAQLSL	0.9748	0.8914	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B35:04	MAAAAQLSL	0.9717	0.9748	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B35:02	MAAAAQLSL	0.9717	0.9748	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B35:05	MAAAAQLSL	0.9662	0.7276	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B39:01	AQLSLTQVL	0.959	0.904	11	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:16	MAAAAQLSL	0.9582	0.7978	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:02	QLSLTQVLF	0.8919	0.8888	12	21
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B39:13	AQLSLTQVL	0.8882	0.9178	11	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B13:02	AQLSLTQVL	0.8804	0.7499	11	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-A32:13	QLSLTQVLF	0.8707	0.8895	12	21
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-A02:21	AQLSLTQVL	0.8675	0.7367	11	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B38:02	AQLSLTQVL	0.8503	0.9538	11	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B52:01	AAQLSLTQV	0.8472	0.9803	10	19
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B38:01	AQLSLTQVL	0.8444	0.9424	11	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B13:01	AQLSLTQVL	0.8351	0.9832	11	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B47:01	AQLSLTQVL	0.8021	0.5721	11	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:03	AQLSLTQVL	0.7795	0.7482	11	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:25	AQLSLTQVL	0.7348	0.8625	11	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:10	AQLSLTQVL	0.7328	0.5188	11	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:37	AQLSLTQVL	0.4356	0.5387	11	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B13:01	QLSLTQVLF	0.0806	0.9736	12	21
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B52:01	AQLSLTQVL	0.0354	0.9757	11	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:01	AQLSLTQVLF	0.9991	0.7118	11	21
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:25	AQLSLTQVLF	0.9587	0.7965	11	21
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:03	AQLSLTQVLF	0.9319	0.6415	11	21
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B13:01	AQLSLTQVLF	0.8646	0.9755	11	21
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B48:01	AAQLSLTQVL	0.8584	0.6858	10	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B13:02	AAQLSLTQVL	0.4741	0.776	10	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B13:01	AAQLSLTQVL	0.4166	0.9781	10	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B48:01	AAAQLSLTQVL	0.9166	0.7067	9	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-C03:19	AAAAQLSL	0.9999	0.9936	8	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-C03:19	MAAAAQLSL	0.9998	0.9859	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-C03:08	MAAAAQLSL	0.9998	0.8914	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-C03:07	MAAAAQLSL	0.9998	0.95	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-C15:04	MAAAAQLSL	0.9997	0.812	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-C15:06	MAAAAQLSL	0.9995	0.8369	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-C04:06	MAAAAQLSL	0.9988	0.8849	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-C12:12	MAAAAQLSL	0.9971	0.9436	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-C06:03	MAAAAQLSL	0.9965	0.9789	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-C12:04	MAAAAQLSL	0.9964	0.9719	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-C08:04	MAAAAQLSL	0.996	0.9108	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-C08:13	MAAAAQLSL	0.996	0.9108	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:21	MAAAAQLSL	0.9946	0.9005	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-C03:14	MAAAAQLSL	0.9917	0.9664	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-C01:17	MAAAAQLSL	0.9914	0.953	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-C08:03	MAAAAQLSL	0.9903	0.9786	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-C01:30	MAAAAQLSL	0.9855	0.9555	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-C02:06	MAAAAQLSL	0.9787	0.8781	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B35:12	MAAAAQLSL	0.9717	0.9748	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B39:09	AQLSLTQVL	0.9661	0.6828	11	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B39:12	AQLSLTQVL	0.9511	0.9058	11	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-C02:06	AAQLSLTQV	0.9435	0.951	10	19
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:04	AQLSLTQVL	0.9288	0.8391	11	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B39:10	MAAAAQLSL	0.9236	0.9149	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B78:01	MAAAAQLSL	0.9234	0.5751	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:07	AQLSLTQVL	0.9203	0.7482	11	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-A02:05	AQLSLTQVL	0.9157	0.6287	11	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B39:08	AQLSLTQVL	0.9025	0.9028	11	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B39:05	AQLSLTQVL	0.8397	0.8948	11	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:05	QLSLTQVLF	0.6478	0.7699	12	21
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:31	QLSLTQVLF	0.646	0.779	12	21
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B14:03	AQLSLTQVL	0.5669	0.7973	11	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:05	AQLSLTQVL	0.3046	0.8476	11	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:07	AQLSLTQVLF	0.9964	0.5406	11	21
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:04	AQLSLTQVLF	0.992	0.7363	11	21
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:05	AQLSLTQVLF	0.8907	0.7857	11	21
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B48:03	AAQLSLTQVL	0.5539	0.5149	10	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B48:03	AAAQLSLTQVL	0.6644	0.5778	9	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-C16:01	AAAAQLSL	0.9599	0.9826	8	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B07:13	AAAAQLSL	0.9385	0.888	8	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-C03:03	MAAAAQLSL	0.9998	0.9879	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-C03:04	MAAAAQLSL	0.9998	0.9879	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-C15:09	MAAAAQLSL	0.9997	0.812	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-C03:67	MAAAAQLSL	0.9997	0.9822	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-C03:05	MAAAAQLSL	0.9996	0.9282	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-C03:02	MAAAAQLSL	0.9996	0.9738	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-C03:17	MAAAAQLSL	0.9995	0.9754	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-C15:05	MAAAAQLSL	0.9993	0.8236	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-C15:02	MAAAAQLSL	0.9992	0.7945	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-C12:02	MAAAAQLSL	0.9989	0.9457	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-C15:02	AAQLSLTQV	0.9986	0.8619	10	19
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-C16:04	MAAAAQLSL	0.9981	0.9671	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-C15:05	AAQLSLTQV	0.998	0.8882	10	19
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-C12:03	MAAAAQLSL	0.9978	0.9541	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B27:06	AQLSLTQVL	0.996	0.6297	11	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B35:11	MAAAAQLSL	0.9947	0.8929	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-C03:06	MAAAAQLSL	0.9943	0.9897	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-C16:01	MAAAAQLSL	0.9928	0.9574	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-C01:02	MAAAAQLSL	0.9922	0.95	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B35:13	MAAAAQLSL	0.9921	0.9165	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:125	AQLSLTQVL	0.991	0.8172	11	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:33	AQLSLTQVL	0.991	0.8172	11	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:34	AQLSLTQVL	0.991	0.8172	11	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-C16:02	MAAAAQLSL	0.9908	0.9787	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:27	AQLSLTQVL	0.9908	0.8261	11	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:135	AQLSLTQVL	0.9905	0.8227	11	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-C08:01	MAAAAQLSL	0.9903	0.9786	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-C01:03	MAAAAQLSL	0.9883	0.9321	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:24	AQLSLTQVL	0.9877	0.8188	11	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B27:09	AQLSLTQVL	0.9866	0.7744	11	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-A68:02	NTMAAAAQL	0.986	0.8604	5	14
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B35:23	MAAAAQLSL	0.985	0.8885	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B35:77	MAAAAQLSL	0.9842	0.9105	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:50	AQLSLTQVL	0.9824	0.8423	11	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-C02:02	MAAAAQLSL	0.9757	0.9169	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-C02:10	MAAAAQLSL	0.9757	0.9169	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B35:09	MAAAAQLSL	0.9717	0.9748	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-A69:01	NTMAAAAQL	0.9712	0.8531	5	14
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B39:02	AQLSLTQVL	0.9705	0.9202	11	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B35:17	MAAAAQLSL	0.967	0.8085	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B35:30	MAAAAQLSL	0.967	0.8085	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:24	QLSLTQVLF	0.965	0.7099	12	21
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B39:31	AQLSLTQVL	0.961	0.9022	11	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:73	AQLSLTQVL	0.9554	0.9161	11	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:11	MAAAAQLSL	0.9525	0.7733	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:08	MAAAAQLSL	0.952	0.7804	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B07:13	MAAAAQLSL	0.9416	0.803	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B35:43	MAAAAQLSL	0.9414	0.7829	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B78:02	MAAAAQLSL	0.9385	0.6492	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:12	QLSLTQVLF	0.9372	0.688	12	21
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B67:01	MAAAAQLSL	0.9296	0.7308	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:30	MAAAAQLSL	0.9285	0.8861	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-A32:01	QLSLTQVLF	0.9267	0.9354	12	21
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:35	AQLSLTQVL	0.903	0.8102	11	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-C17:01	MAAAAQLSL	0.898	0.8474	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:30	AQLSLTQVL	0.888	0.8918	11	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:68	AQLSLTQVL	0.8805	0.687	11	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B35:24	MAAAAQLSL	0.8723	0.8771	7	16
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-A02:14	AQLSLTQVL	0.8702	0.6719	11	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-A02:06	AQLSLTQVL	0.8675	0.7367	11	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:53	AQLSLTQVL	0.8644	0.7896	11	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:54	AQLSLTQVL	0.856	0.7752	11	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B38:05	AQLSLTQVL	0.8444	0.9424	11	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:13	QLSLTQVLF	0.8242	0.6017	12	21
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:12	AQLSLTQVL	0.8179	0.7962	11	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B39:11	AQLSLTQVL	0.8121	0.8851	11	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:39	AQLSLTQVL	0.736	0.7952	11	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:20	QLSLTQVLF	0.6726	0.8613	12	21
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B48:02	AQLSLTQVL	0.6704	0.9046	11	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:09	AQLSLTQVL	0.5589	0.859	11	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B35:13	AQLSLTQVL	0.472	0.8631	11	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:20	AQLSLTQVL	0.3143	0.8774	11	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B35:28	AQLSLTQVL	0.3078	0.9285	11	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B07:13	AAQLSLTQV	0.2863	0.8055	10	19
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:125	AQLSLTQVLF	0.9991	0.7118	11	21
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:33	AQLSLTQVLF	0.9991	0.7118	11	21
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:34	AQLSLTQVLF	0.9991	0.7118	11	21
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:135	AQLSLTQVLF	0.9991	0.7291	11	21
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:27	AQLSLTQVLF	0.999	0.7318	11	21
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:50	AQLSLTQVLF	0.9987	0.8032	11	21
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:24	AQLSLTQVLF	0.9984	0.7545	11	21
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:53	AQLSLTQVLF	0.9962	0.6742	11	21
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:35	AQLSLTQVLF	0.9949	0.6539	11	21
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:12	AQLSLTQVLF	0.9946	0.7297	11	21
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:54	AQLSLTQVLF	0.9914	0.649	11	21
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:73	AQLSLTQVLF	0.9744	0.8284	11	21
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:39	AQLSLTQVLF	0.9635	0.7105	11	21
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:30	AQLSLTQVLF	0.94	0.847	11	21
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:30	AAQLSLTQVL	0.9019	0.8876	10	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B48:02	AQLSLTQVLF	0.8883	0.9171	11	21
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:73	AAQLSLTQVL	0.8878	0.9118	10	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B15:20	AQLSLTQVLF	0.8861	0.8441	11	21
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B35:28	AQLSLTQVLF	0.8645	0.9369	11	21
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B40:12	AAQLSLTQVL	0.5539	0.5149	10	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B40:21	AAQLSLTQVL	0.3582	0.6231	10	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B40:21	AAAQLSLTQVL	0.6701	0.7204	9	20
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	HLA-B40:12	AAAQLSLTQVL	0.6644	0.5778	9	20

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Potential FusionNeoAntigen Information of EPS15-TRABD2B in HLA II

EPS15-TRABD2B_51984871_48267291.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)
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	DRB1-0906	DGNTMAAAAQLSLTQ	3	18
EPS15-TRABD2B	chr1	51984871	chr1	48267291	130	DRB1-0906	GNTMAAAAQLSLTQV	4	19

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Fusion breakpoint peptide structures of EPS15-TRABD2B

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
9501	TMAAAAQLSLTQVL	EPS15	TRABD2B	chr1	51984871	chr1	48267291	130

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of EPS15-TRABD2B

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	9501	TMAAAAQLSLTQVL	-7.9962	-8.1096
HLA-B14:02	3BVN	9501	TMAAAAQLSLTQVL	-5.70842	-6.74372
HLA-B52:01	3W39	9501	TMAAAAQLSLTQVL	-6.83737	-6.95077
HLA-B52:01	3W39	9501	TMAAAAQLSLTQVL	-4.4836	-5.5189
HLA-A11:01	4UQ2	9501	TMAAAAQLSLTQVL	-10.0067	-10.1201
HLA-A11:01	4UQ2	9501	TMAAAAQLSLTQVL	-9.03915	-10.0745
HLA-A24:02	5HGA	9501	TMAAAAQLSLTQVL	-6.56204	-6.67544
HLA-A24:02	5HGA	9501	TMAAAAQLSLTQVL	-5.42271	-6.45801
HLA-B44:05	3DX8	9501	TMAAAAQLSLTQVL	-7.85648	-8.89178
HLA-B44:05	3DX8	9501	TMAAAAQLSLTQVL	-5.3978	-5.5112
HLA-A02:01	6TDR	9501	TMAAAAQLSLTQVL	-3.37154	-4.40684

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Vaccine Design for the FusionNeoAntigens of EPS15-TRABD2B

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
EPS15-TRABD2B	chr1	51984871	chr1	48267291	10	19	AAQLSLTQV	CTGACACAGGTGCTGTTTGCCCTGAAC
EPS15-TRABD2B	chr1	51984871	chr1	48267291	10	20	AAQLSLTQVL	CTGACACAGGTGCTGTTTGCCCTGAACCAA
EPS15-TRABD2B	chr1	51984871	chr1	48267291	11	19	AQLSLTQV	ACACAGGTGCTGTTTGCCCTGAAC
EPS15-TRABD2B	chr1	51984871	chr1	48267291	11	20	AQLSLTQVL	ACACAGGTGCTGTTTGCCCTGAACCAA
EPS15-TRABD2B	chr1	51984871	chr1	48267291	11	21	AQLSLTQVLF	ACACAGGTGCTGTTTGCCCTGAACCAAACC
EPS15-TRABD2B	chr1	51984871	chr1	48267291	12	21	QLSLTQVLF	CAGGTGCTGTTTGCCCTGAACCAAACC
EPS15-TRABD2B	chr1	51984871	chr1	48267291	5	14	NTMAAAAQL	GCGGCCCAGCTCTCTCTGACACAGGTG
EPS15-TRABD2B	chr1	51984871	chr1	48267291	7	16	MAAAAQLSL	CAGCTCTCTCTGACACAGGTGCTGTTT
EPS15-TRABD2B	chr1	51984871	chr1	48267291	8	16	AAAAQLSL	CTCTCTCTGACACAGGTGCTGTTT
EPS15-TRABD2B	chr1	51984871	chr1	48267291	9	20	AAAQLSLTQVL	TCTCTGACACAGGTGCTGTTTGCCCTGAACCAA

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
EPS15-TRABD2B	chr1	51984871	chr1	48267291	3	18	DGNTMAAAAQLSLTQ	GCTGCGGCGGCCCAGCTCTCTCTGACACAGGTGCTGTTTGCCCTG
EPS15-TRABD2B	chr1	51984871	chr1	48267291	4	19	GNTMAAAAQLSLTQV	GCGGCGGCCCAGCTCTCTCTGACACAGGTGCTGTTTGCCCTGAAC

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Information of the samples that have these potential fusion neoantigens of EPS15-TRABD2B

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
GBM	EPS15-TRABD2B	chr1	51984871	ENST00000371733	chr1	48267291	ENST00000606738	TCGA-16-1045-01B

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Potential target of CAR-T therapy development for EPS15-TRABD2B

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

Tgene

TRABD2B

chr1:51984871

chr1:48267291

ENST00000606738

495_515

518.0

Transmembrane

Helical

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 EPS15-TRABD2B

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 EPS15-TRABD2B

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)