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Fusion Protein:EPT1-CCNI

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: EPT1-CCNI
	FusionPDB ID: 27121
	FusionGDB2.0 ID: 27121
		Hgene	Tgene
	Gene symbol	EPT1	CCNI
	Gene ID	85465	10983
	Gene name	selenoprotein I	cyclin I
	Synonyms	EPT1\|SELI\|SEPI\|SPG81	CCNI1\|CYC1\|CYI
	Cytomap	2p23.3	4q21.1
	Type of gene	protein-coding	protein-coding
	Description	ethanolaminephosphotransferase 1ethanolaminephosphotransferase 1 (CDP-ethanolamine-specific)hEPT1	cyclin-Icyclin ITI
	Modification date	20200313	20200327
	UniProtAcc	.	Q6ZMN8 Main function of 5'-partner protein:
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000260585, ENST00000462301,	ENST00000504697, ENST00000237654, ENST00000537948,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	3 X 3 X 3=27	17 X 12 X 5=1020
	# samples	3	19
	** MAII score	log2(3/27*10)=0.15200309344505 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0	log2(19/1020*10)=-2.42449782852791 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: EPT1 [Title/Abstract] AND CCNI [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: EPT1 [Title/Abstract] AND CCNI [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	EPT1(26596497)-CCNI(77976533), # samples:1
Anticipated loss of major functional domain due to fusion event.

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

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

Partner	Gene	GO ID	GO term	PubMed ID
Hgene	EPT1	GO:0006646	phosphatidylethanolamine biosynthetic process	17132865

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr2:26596497/chr4:77976533)
- 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 EPT1 (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 CCNI (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)

ENST00000260585

EPT1

chr2

26596497

ENST00000237654

CCNI

chr4

77976533

2428

692

119

1366

415

ENST00000260585

EPT1

chr2

26596497

ENST00000537948

CCNI

chr4

77976533

1451

692

119

1366

415

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
ENST00000260585	ENST00000237654	EPT1	chr2	26596497	+	CCNI	chr4	77976533	-	0.001059077	0.9989409
ENST00000260585	ENST00000537948	EPT1	chr2	26596497	+	CCNI	chr4	77976533	-	0.003936804	0.9960632

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 EPT1-CCNI

+/-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
EPT1	chr2	26596497	CCNI	chr4	77976533	692	191	ILFLPWGYDISQVFHAIAVSTRPQLL

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Potential FusionNeoAntigen Information of EPT1-CCNI 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.

EPT1-CCNI_26596497_77976533.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)
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B52:01	ISQVFHAI	0.9988	0.7642	9	17
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B35:01	WGYDISQVF	0.9934	0.8533	5	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B35:05	WGYDISQVF	0.9932	0.6136	5	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B39:06	SQVFHAIAV	0.9887	0.8956	10	19
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B48:01	SQVFHAIAV	0.9886	0.7159	10	19
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B14:02	SQVFHAIAV	0.9876	0.8882	10	19
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B14:01	SQVFHAIAV	0.9876	0.8882	10	19
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B39:24	SQVFHAIAV	0.979	0.7457	10	19
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B15:03	WGYDISQVF	0.9637	0.7994	5	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-A02:21	SQVFHAIAV	0.952	0.7035	10	19
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B13:02	SQVFHAIAV	0.9313	0.9345	10	19
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B39:01	SQVFHAIAV	0.8294	0.9224	10	19
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B13:01	SQVFHAIAV	0.809	0.9924	10	19
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B39:13	SQVFHAIAV	0.7612	0.9423	10	19
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B52:01	WGYDISQVF	0.7072	0.9795	5	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B08:09	DISQVFHAI	0.6269	0.5602	8	17
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B52:01	SQVFHAIAV	0.2143	0.9796	10	19
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-A24:25	PWGYDISQVF	0.9985	0.5115	4	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-A24:20	PWGYDISQVF	0.9982	0.5108	4	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-A24:15	PWGYDISQVF	0.9982	0.5243	4	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-A31:02	VFHAIAVSTR	0.9831	0.7988	12	22
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B35:01	LPWGYDISQVF	0.9997	0.8262	3	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B35:05	LPWGYDISQVF	0.9992	0.6494	3	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B35:08	LPWGYDISQVF	0.9988	0.8347	3	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B53:01	LPWGYDISQVF	0.9987	0.5473	3	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B35:03	LPWGYDISQVF	0.9986	0.8548	3	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B51:01	LPWGYDISQVF	0.9974	0.5632	3	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B35:04	LPWGYDISQVF	0.9947	0.9663	3	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B35:02	LPWGYDISQVF	0.9947	0.9663	3	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B51:02	LPWGYDISQVF	0.9942	0.5634	3	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B81:01	LPWGYDISQVF	0.9783	0.6695	3	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-C04:07	GYDISQVF	0.9997	0.8127	6	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-C04:10	GYDISQVF	0.9997	0.8185	6	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-C04:14	GYDISQVF	0.987	0.7879	6	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-C03:19	WGYDISQVF	0.9947	0.988	5	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B15:21	WGYDISQVF	0.994	0.875	5	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B40:06	YDISQVFHA	0.9925	0.6395	7	16
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B15:31	WGYDISQVF	0.9921	0.8595	5	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B51:07	DISQVFHAI	0.9914	0.5757	8	17
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-A02:05	SQVFHAIAV	0.9792	0.6217	10	19
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-C03:07	WGYDISQVF	0.9661	0.9783	5	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B15:04	SQVFHAIAV	0.86	0.976	10	19
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-C03:14	WGYDISQVF	0.8522	0.9706	5	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B39:09	SQVFHAIAV	0.7983	0.783	10	19
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-C12:12	WGYDISQVF	0.7906	0.9106	5	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B48:03	SQVFHAIAV	0.79	0.7141	10	19
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B39:05	SQVFHAIAV	0.7289	0.9149	10	19
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B51:07	WGYDISQVF	0.6618	0.964	5	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B51:07	SQVFHAIAV	0.1415	0.9662	10	19
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-A24:02	PWGYDISQVF	0.9982	0.5108	4	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B35:12	LPWGYDISQVF	0.9947	0.9663	3	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-C04:01	GYDISQVF	0.9997	0.8127	6	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-C18:01	GYDISQVF	0.9995	0.7975	6	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-C14:03	GYDISQVF	0.9866	0.9285	6	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-C14:02	GYDISQVF	0.9866	0.9285	6	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-C04:04	GYDISQVF	0.9848	0.7957	6	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-C03:02	WGYDISQVF	0.9985	0.9441	5	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-C03:03	WGYDISQVF	0.9981	0.9868	5	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-C03:04	WGYDISQVF	0.9981	0.9868	5	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-C03:67	WGYDISQVF	0.9957	0.9815	5	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-C03:05	WGYDISQVF	0.9951	0.9185	5	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B35:23	WGYDISQVF	0.9938	0.8462	5	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B35:77	WGYDISQVF	0.9934	0.8533	5	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B35:11	WGYDISQVF	0.9932	0.8806	5	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B35:17	WGYDISQVF	0.9928	0.782	5	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B35:30	WGYDISQVF	0.9928	0.782	5	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-A25:01	DISQVFHAI	0.9925	0.8469	8	17
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B40:40	SQVFHAIAV	0.9917	0.5049	10	19
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B35:20	WGYDISQVF	0.9905	0.936	5	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-C03:17	WGYDISQVF	0.9893	0.9535	5	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B35:28	WGYDISQVF	0.9892	0.9316	5	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B15:11	WGYDISQVF	0.9788	0.8306	5	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B15:08	WGYDISQVF	0.9763	0.8224	5	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B35:43	WGYDISQVF	0.9759	0.8237	5	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B35:24	WGYDISQVF	0.9669	0.8503	5	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-A02:14	SQVFHAIAV	0.9523	0.6516	10	19
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-A02:06	SQVFHAIAV	0.952	0.7035	10	19
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-A69:01	DISQVFHAI	0.9512	0.5456	8	17
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-C16:04	WGYDISQVF	0.9461	0.9694	5	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B15:73	SQVFHAIAV	0.9277	0.9685	10	19
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-C12:02	WGYDISQVF	0.8584	0.9343	5	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B15:30	SQVFHAIAV	0.8497	0.9329	10	19
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B39:02	SQVFHAIAV	0.84	0.9355	10	19
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-C07:17	WGYDISQVF	0.838	0.9411	5	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-C12:03	WGYDISQVF	0.8334	0.9584	5	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B40:12	SQVFHAIAV	0.79	0.7141	10	19
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B18:04	WGYDISQVF	0.7639	0.8807	5	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-C16:01	WGYDISQVF	0.7413	0.9787	5	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B40:21	SQVFHAIAV	0.6921	0.7207	10	19
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B18:07	WGYDISQVF	0.6207	0.7833	5	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B08:12	DISQVFHAI	0.5922	0.5478	8	17
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-C02:10	WGYDISQVF	0.5849	0.9593	5	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-C02:02	WGYDISQVF	0.5849	0.9593	5	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B15:09	SQVFHAIAV	0.4348	0.8452	10	19
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B48:05	SQVFHAIAV	0.3142	0.5798	10	19
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B35:24	LPWGYDISQVF	0.9998	0.8426	3	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B35:23	LPWGYDISQVF	0.9997	0.8535	3	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B35:77	LPWGYDISQVF	0.9997	0.8262	3	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B35:20	LPWGYDISQVF	0.9995	0.9222	3	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B35:30	LPWGYDISQVF	0.9993	0.7767	3	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B35:17	LPWGYDISQVF	0.9993	0.7767	3	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B53:02	LPWGYDISQVF	0.9991	0.538	3	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B35:11	LPWGYDISQVF	0.9984	0.8847	3	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B35:22	LPWGYDISQVF	0.9981	0.6086	3	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B51:14	LPWGYDISQVF	0.9978	0.5495	3	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B51:21	LPWGYDISQVF	0.9976	0.5556	3	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B51:06	LPWGYDISQVF	0.9975	0.5606	3	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B51:09	LPWGYDISQVF	0.9973	0.5358	3	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B35:43	LPWGYDISQVF	0.9966	0.8489	3	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B15:13	LPWGYDISQVF	0.9964	0.8389	3	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B15:08	LPWGYDISQVF	0.9963	0.8454	3	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B15:11	LPWGYDISQVF	0.9959	0.8499	3	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B55:04	LPWGYDISQVF	0.9952	0.7032	3	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B35:09	LPWGYDISQVF	0.9947	0.9663	3	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B18:07	LPWGYDISQVF	0.9808	0.7706	3	14
EPT1-CCNI	chr2	26596497	chr4	77976533	692	HLA-B67:01	LPWGYDISQVF	0.9685	0.9053	3	14

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Potential FusionNeoAntigen Information of EPT1-CCNI in HLA II

EPT1-CCNI_26596497_77976533.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)
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB1-0902	ISQVFHAIAVSTRPQ	9	24
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB1-1117	QVFHAIAVSTRPQLL	11	26
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB1-1152	QVFHAIAVSTRPQLL	11	26
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB1-1401	QVFHAIAVSTRPQLL	11	26
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB1-1404	QVFHAIAVSTRPQLL	11	26
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB1-1405	QVFHAIAVSTRPQLL	11	26
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB1-1407	QVFHAIAVSTRPQLL	11	26
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB1-1408	QVFHAIAVSTRPQLL	11	26
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB1-1418	QVFHAIAVSTRPQLL	11	26
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB1-1423	QVFHAIAVSTRPQLL	11	26
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB1-1426	QVFHAIAVSTRPQLL	11	26
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB1-1428	QVFHAIAVSTRPQLL	11	26
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB1-1432	QVFHAIAVSTRPQLL	11	26
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB1-1435	QVFHAIAVSTRPQLL	11	26
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB1-1438	QVFHAIAVSTRPQLL	11	26
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB1-1443	QVFHAIAVSTRPQLL	11	26
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB1-1445	QVFHAIAVSTRPQLL	11	26
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB1-1446	ISQVFHAIAVSTRPQ	9	24
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB1-1447	ISQVFHAIAVSTRPQ	9	24
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB1-1450	QVFHAIAVSTRPQLL	11	26
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB1-1454	QVFHAIAVSTRPQLL	11	26
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB1-1455	QVFHAIAVSTRPQLL	11	26
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB1-1456	QVFHAIAVSTRPQLL	11	26
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB1-1458	QVFHAIAVSTRPQLL	11	26
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB1-1459	QVFHAIAVSTRPQLL	11	26
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB1-1460	QVFHAIAVSTRPQLL	11	26
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB1-1461	QVFHAIAVSTRPQLL	11	26
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB1-1462	QVFHAIAVSTRPQLL	11	26
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB1-1464	QVFHAIAVSTRPQLL	11	26
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB1-1470	QVFHAIAVSTRPQLL	11	26
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB1-1471	QVFHAIAVSTRPQLL	11	26
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB1-1472	QVFHAIAVSTRPQLL	11	26
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB1-1475	QVFHAIAVSTRPQLL	11	26
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB1-1482	QVFHAIAVSTRPQLL	11	26
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB1-1482	SQVFHAIAVSTRPQL	10	25
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB1-1486	QVFHAIAVSTRPQLL	11	26
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB1-1487	QVFHAIAVSTRPQLL	11	26
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB1-1488	QVFHAIAVSTRPQLL	11	26
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB1-1490	QVFHAIAVSTRPQLL	11	26
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB1-1491	QVFHAIAVSTRPQLL	11	26
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB1-1495	QVFHAIAVSTRPQLL	11	26
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB1-1496	QVFHAIAVSTRPQLL	11	26
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB1-1497	QVFHAIAVSTRPQLL	11	26
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB1-1499	QVFHAIAVSTRPQLL	11	26
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB1-1499	SQVFHAIAVSTRPQL	10	25
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB5-0101	ISQVFHAIAVSTRPQ	9	24
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB5-0101	SQVFHAIAVSTRPQL	10	25
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB5-0101	DISQVFHAIAVSTRP	8	23
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB5-0102	ISQVFHAIAVSTRPQ	9	24
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB5-0102	SQVFHAIAVSTRPQL	10	25
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB5-0103	ISQVFHAIAVSTRPQ	9	24
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB5-0104	ISQVFHAIAVSTRPQ	9	24
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB5-0104	SQVFHAIAVSTRPQL	10	25
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB5-0104	DISQVFHAIAVSTRP	8	23
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB5-0105	ISQVFHAIAVSTRPQ	9	24
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB5-0105	SQVFHAIAVSTRPQL	10	25
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB5-0105	DISQVFHAIAVSTRP	8	23
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB5-0108N	ISQVFHAIAVSTRPQ	9	24
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB5-0108N	SQVFHAIAVSTRPQL	10	25
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB5-0111	ISQVFHAIAVSTRPQ	9	24
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB5-0111	SQVFHAIAVSTRPQL	10	25
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB5-0112	ISQVFHAIAVSTRPQ	9	24
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB5-0112	SQVFHAIAVSTRPQL	10	25
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB5-0112	DISQVFHAIAVSTRP	8	23
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB5-0113	ISQVFHAIAVSTRPQ	9	24
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB5-0113	SQVFHAIAVSTRPQL	10	25
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB5-0113	DISQVFHAIAVSTRP	8	23
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB5-0114	ISQVFHAIAVSTRPQ	9	24
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB5-0114	SQVFHAIAVSTRPQL	10	25
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB5-0114	DISQVFHAIAVSTRP	8	23
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB5-0203	ISQVFHAIAVSTRPQ	9	24
EPT1-CCNI	chr2	26596497	chr4	77976533	692	DRB5-0203	SQVFHAIAVSTRPQL	10	25

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Fusion breakpoint peptide structures of EPT1-CCNI

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
3245	GYDISQVFHAIAVS	EPT1	CCNI	chr2	26596497	chr4	77976533	692

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of EPT1-CCNI

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	3245	GYDISQVFHAIAVS	-7.9962	-8.1096
HLA-B14:02	3BVN	3245	GYDISQVFHAIAVS	-5.70842	-6.74372
HLA-B52:01	3W39	3245	GYDISQVFHAIAVS	-6.83737	-6.95077
HLA-B52:01	3W39	3245	GYDISQVFHAIAVS	-4.4836	-5.5189
HLA-A11:01	4UQ2	3245	GYDISQVFHAIAVS	-10.0067	-10.1201
HLA-A11:01	4UQ2	3245	GYDISQVFHAIAVS	-9.03915	-10.0745
HLA-A24:02	5HGA	3245	GYDISQVFHAIAVS	-6.56204	-6.67544
HLA-A24:02	5HGA	3245	GYDISQVFHAIAVS	-5.42271	-6.45801
HLA-B44:05	3DX8	3245	GYDISQVFHAIAVS	-7.85648	-8.89178
HLA-B44:05	3DX8	3245	GYDISQVFHAIAVS	-5.3978	-5.5112
HLA-A02:01	6TDR	3245	GYDISQVFHAIAVS	-3.37154	-4.40684

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Vaccine Design for the FusionNeoAntigens of EPT1-CCNI

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
EPT1-CCNI	chr2	26596497	chr4	77976533	10	19	SQVFHAIAV	AGCCAGGTGTTCCATGCCATTGCAGTG
EPT1-CCNI	chr2	26596497	chr4	77976533	12	22	VFHAIAVSTR	GTGTTCCATGCCATTGCAGTGTCAACTAGG
EPT1-CCNI	chr2	26596497	chr4	77976533	3	14	LPWGYDISQVF	CTGCCATGGGGATATGACATTAGCCAGGTGTTC
EPT1-CCNI	chr2	26596497	chr4	77976533	4	14	PWGYDISQVF	CCATGGGGATATGACATTAGCCAGGTGTTC
EPT1-CCNI	chr2	26596497	chr4	77976533	5	14	WGYDISQVF	TGGGGATATGACATTAGCCAGGTGTTC
EPT1-CCNI	chr2	26596497	chr4	77976533	6	14	GYDISQVF	GGATATGACATTAGCCAGGTGTTC
EPT1-CCNI	chr2	26596497	chr4	77976533	7	16	YDISQVFHA	TATGACATTAGCCAGGTGTTCCATGCC
EPT1-CCNI	chr2	26596497	chr4	77976533	8	17	DISQVFHAI	GACATTAGCCAGGTGTTCCATGCCATT
EPT1-CCNI	chr2	26596497	chr4	77976533	9	17	ISQVFHAI	ATTAGCCAGGTGTTCCATGCCATT

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
EPT1-CCNI	chr2	26596497	chr4	77976533	10	25	SQVFHAIAVSTRPQL	AGCCAGGTGTTCCATGCCATTGCAGTGTCAACTAGGCCTCAGTTA
EPT1-CCNI	chr2	26596497	chr4	77976533	11	26	QVFHAIAVSTRPQLL	CAGGTGTTCCATGCCATTGCAGTGTCAACTAGGCCTCAGTTACTT
EPT1-CCNI	chr2	26596497	chr4	77976533	8	23	DISQVFHAIAVSTRP	GACATTAGCCAGGTGTTCCATGCCATTGCAGTGTCAACTAGGCCT
EPT1-CCNI	chr2	26596497	chr4	77976533	9	24	ISQVFHAIAVSTRPQ	ATTAGCCAGGTGTTCCATGCCATTGCAGTGTCAACTAGGCCTCAG

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Information of the samples that have these potential fusion neoantigens of EPT1-CCNI

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	EPT1-CCNI	chr2	26596497	ENST00000260585	chr4	77976533	ENST00000237654	TCGA-CG-5717-01A

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Potential target of CAR-T therapy development for EPT1-CCNI

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

Hgene

EPT1

chr2:26596497

chr4:77976533

ENST00000260585

123_145

191

398.0

Transmembrane

Helical

Hgene

EPT1

chr2:26596497

chr4:77976533

ENST00000260585

150_172

191

398.0

Transmembrane

Helical

Hgene

EPT1

chr2:26596497

chr4:77976533

ENST00000260585

47_69

191

398.0

Transmembrane

Helical

Hgene

EPT1

chr2:26596497

chr4:77976533

ENST00000260585

84_103

191

398.0

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 EPT1-CCNI

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 EPT1-CCNI

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)