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Fusion Protein:EEF2-SMARCA4

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: EEF2-SMARCA4
	FusionPDB ID: 25260
	FusionGDB2.0 ID: 25260
		Hgene	Tgene
	Gene symbol	EEF2	SMARCA4
	Gene ID	1938	6597
	Gene name	eukaryotic translation elongation factor 2	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4
	Synonyms	EEF-2\|EF-2\|EF2\|SCA26	BAF190\|BAF190A\|BRG1\|CSS4\|MRD16\|RTPS2\|SNF2\|SNF2-beta\|SNF2L4\|SNF2LB\|SWI2\|hSNF2b
	Cytomap	19p13.3	19p13.2
	Type of gene	protein-coding	protein-coding
	Description	elongation factor 2epididymis secretory sperm binding proteinpolypeptidyl-tRNA translocase	transcription activator BRG1ATP-dependent helicase SMARCA4BRG1-associated factor 190ABRM/SWI2-related gene 1SNF2-like 4brahma protein-like 1global transcription activator homologous sequencehomeotic gene regulatormitotic growth and transcription a
	Modification date	20200313	20200315
	UniProtAcc	Q96G04 Main function of 5'-partner protein: FUNCTION: Catalyzes the trimethylation of eukaryotic elongation factor 2 (EEF2) on 'Lys-525'. {ECO:0000269\|PubMed:25231979}.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000309311, ENST00000600720,	ENST00000538456, ENST00000344626, ENST00000358026, ENST00000413806, ENST00000429416, ENST00000444061, ENST00000450717, ENST00000541122, ENST00000589677, ENST00000590574,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	44 X 37 X 16=26048	20 X 28 X 15=8400
	# samples	56	32
	** MAII score	log2(56/26048*10)=-5.53960196732128 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(32/8400*10)=-4.71424551766612 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: EEF2 [Title/Abstract] AND SMARCA4 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: EEF2 [Title/Abstract] AND SMARCA4 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	EEF2(3982805)-SMARCA4(11151983), # samples:1
Anticipated loss of major functional domain due to fusion event.	EEF2-SMARCA4 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. EEF2-SMARCA4 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. EEF2-SMARCA4 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. EEF2-SMARCA4 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.

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

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

Partner	Gene	GO ID	GO term	PubMed ID
Tgene	SMARCA4	GO:0006337	nucleosome disassembly	8895581
Tgene	SMARCA4	GO:0006338	chromatin remodeling	10943845\|11726552
Tgene	SMARCA4	GO:0045892	negative regulation of transcription, DNA-templated	12065415
Tgene	SMARCA4	GO:0045944	positive regulation of transcription by RNA polymerase II	15774904\|17938176
Tgene	SMARCA4	GO:0051091	positive regulation of DNA-binding transcription factor activity	11950834\|17938176
Tgene	SMARCA4	GO:1902661	positive regulation of glucose mediated signaling pathway	22368283

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr19:3982805/chr19:11151983)
- 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 EEF2 (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 SMARCA4 (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)
ENST00000309311	EEF2	chr19	3982805	-	ENST00000358026	SMARCA4	chr19	11151983	+	1941	701	89	1474	461
ENST00000309311	EEF2	chr19	3982805	-	ENST00000344626	SMARCA4	chr19	11151983	+	1718	701	89	1474	461
ENST00000309311	EEF2	chr19	3982805	-	ENST00000429416	SMARCA4	chr19	11151983	+	1941	701	89	1474	461
ENST00000309311	EEF2	chr19	3982805	-	ENST00000541122	SMARCA4	chr19	11151983	+	1474	701	478	1473	332
ENST00000309311	EEF2	chr19	3982805	-	ENST00000589677	SMARCA4	chr19	11151983	+	1471	701	478	1470	331
ENST00000309311	EEF2	chr19	3982805	-	ENST00000444061	SMARCA4	chr19	11151983	+	1472	701	89	1471	461
ENST00000309311	EEF2	chr19	3982805	-	ENST00000590574	SMARCA4	chr19	11151983	+	1475	701	89	1474	462
ENST00000309311	EEF2	chr19	3982805	-	ENST00000413806	SMARCA4	chr19	11151983	+	1940	701	478	1473	331
ENST00000309311	EEF2	chr19	3982805	-	ENST00000450717	SMARCA4	chr19	11151983	+	1937	701	478	1470	330

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
ENST00000309311	ENST00000358026	EEF2	chr19	3982805	-	SMARCA4	chr19	11151983	+	0.004341185	0.9956589
ENST00000309311	ENST00000344626	EEF2	chr19	3982805	-	SMARCA4	chr19	11151983	+	0.005086862	0.9949131
ENST00000309311	ENST00000429416	EEF2	chr19	3982805	-	SMARCA4	chr19	11151983	+	0.004341185	0.9956589
ENST00000309311	ENST00000541122	EEF2	chr19	3982805	-	SMARCA4	chr19	11151983	+	0.014419458	0.9855805
ENST00000309311	ENST00000589677	EEF2	chr19	3982805	-	SMARCA4	chr19	11151983	+	0.016031928	0.983968
ENST00000309311	ENST00000444061	EEF2	chr19	3982805	-	SMARCA4	chr19	11151983	+	0.004027261	0.9959727
ENST00000309311	ENST00000590574	EEF2	chr19	3982805	-	SMARCA4	chr19	11151983	+	0.003726899	0.99627316
ENST00000309311	ENST00000413806	EEF2	chr19	3982805	-	SMARCA4	chr19	11151983	+	0.025827985	0.97417206
ENST00000309311	ENST00000450717	EEF2	chr19	3982805	-	SMARCA4	chr19	11151983	+	0.027561065	0.9724389

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 EEF2-SMARCA4

+/-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
EEF2	chr19	3982805	SMARCA4	chr19	11151983	701	204	YGEGESGPMGNIMAIEEGTLEEIEEE
EEF2	chr19	3982805	SMARCA4	chr19	11151983	701	74	LRRGRERPHGQHHAIEEGTLEEIEEE

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Potential FusionNeoAntigen Information of EEF2-SMARCA4 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.

EEF2-SMARCA4_3982805_11151983.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)
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B39:01	HHAIEEGTL	0.9976	0.9579	11	20
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B38:02	HHAIEEGTL	0.995	0.9806	11	20
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B38:01	HHAIEEGTL	0.9948	0.9795	11	20
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B39:24	HHAIEEGTL	0.9887	0.639	11	20
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B39:06	HHAIEEGTL	0.9881	0.8339	11	20
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B15:10	HHAIEEGTL	0.9649	0.7744	11	20
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B35:03	GPMGNIMAI	0.9572	0.9058	6	15
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B35:04	GPMGNIMAI	0.9349	0.9653	6	15
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B35:02	GPMGNIMAI	0.9349	0.9653	6	15
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B51:02	GPMGNIMAI	0.9303	0.6397	6	15
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B35:03	RPHGQHHAI	0.7985	0.6111	6	15
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B14:01	HHAIEEGTL	0.7699	0.8423	11	20
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B14:02	HHAIEEGTL	0.7699	0.8423	11	20
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B51:01	GPMGNIMAI	0.7658	0.5832	6	15
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B35:04	RPHGQHHAI	0.7525	0.7744	6	15
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B35:02	RPHGQHHAI	0.7525	0.7744	6	15
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B15:37	HHAIEEGTL	0.6419	0.7323	11	20
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B15:18	HHAIEEGTL	0.5791	0.8605	11	20
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B81:01	GPMGNIMAI	0.1615	0.6685	6	15
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B07:10	HHAIEEGTL	0.0076	0.6432	11	20
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B39:01	QHHAIEEGTL	0.9935	0.9328	10	20
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B38:02	QHHAIEEGTL	0.9866	0.9746	10	20
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B38:01	QHHAIEEGTL	0.9833	0.9734	10	20
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B39:24	QHHAIEEGTL	0.9825	0.6829	10	20
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B15:10	QHHAIEEGTL	0.9692	0.5552	10	20
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B45:01	RERPHGQHHA	0.9477	0.8289	4	14
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B50:02	RERPHGQHHA	0.9267	0.5224	4	14
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B15:37	QHHAIEEGTL	0.8079	0.5732	10	20
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B41:01	RERPHGQHHA	0.7758	0.7788	4	14
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B50:01	RERPHGQHHA	0.629	0.5536	4	14
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B48:01	GQHHAIEEGTL	0.9987	0.7879	9	20
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B45:01	GESGPMGNIMA	0.9903	0.978	3	14
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B50:01	GESGPMGNIMA	0.9567	0.8331	3	14
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B41:01	GESGPMGNIMA	0.9271	0.9871	3	14
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-C03:19	HAIEEGTL	0.9999	0.9961	12	20
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-C03:19	MAIEEGTL	0.9999	0.9904	12	20
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B39:09	HHAIEEGTL	0.9973	0.7966	11	20
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B39:12	HHAIEEGTL	0.997	0.9604	11	20
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B39:05	HHAIEEGTL	0.996	0.9521	11	20
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B73:01	ERPHGQHHA	0.9834	0.6124	5	14
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B35:12	GPMGNIMAI	0.9349	0.9653	6	15
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B07:12	GPMGNIMAI	0.8659	0.584	6	15
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B14:03	RPHGQHHAI	0.7842	0.5416	6	15
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B54:01	GPMGNIMAI	0.7732	0.5366	6	15
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B78:01	GPMGNIMAI	0.7669	0.6678	6	15
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B35:12	RPHGQHHAI	0.7525	0.7744	6	15
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B42:02	GPMGNIMAI	0.7239	0.771	6	15
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B42:01	GPMGNIMAI	0.6683	0.7654	6	15
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B39:10	GPMGNIMAI	0.5915	0.9406	6	15
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B51:08	GPMGNIMAI	0.5913	0.5777	6	15
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B39:10	RPHGQHHAI	0.5529	0.511	6	15
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B14:03	HHAIEEGTL	0.3624	0.8651	11	20
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B39:09	QHHAIEEGTL	0.9936	0.8151	10	20
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B40:06	RERPHGQHHA	0.9929	0.5693	4	14
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B39:05	QHHAIEEGTL	0.9874	0.9225	10	20
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B48:03	GQHHAIEEGTL	0.9953	0.654	9	20
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B40:06	GESGPMGNIMA	0.9883	0.9298	3	14
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-C03:03	HAIEEGTL	0.9999	0.9959	12	20
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-C03:04	HAIEEGTL	0.9999	0.9959	12	20
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-C03:04	MAIEEGTL	0.9999	0.9908	12	20
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-C03:03	MAIEEGTL	0.9999	0.9908	12	20
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-C03:06	MAIEEGTL	0.9972	0.9918	12	20
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-C03:06	HAIEEGTL	0.996	0.9963	12	20
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B35:13	MAIEEGTL	0.9609	0.9434	12	20
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B35:13	HAIEEGTL	0.9329	0.9761	12	20
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B39:31	HHAIEEGTL	0.9972	0.9584	11	20
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B38:05	HHAIEEGTL	0.9948	0.9795	11	20
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B35:22	GPMGNIMAI	0.9858	0.6	6	15
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B15:09	HHAIEEGTL	0.969	0.868	11	20
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B35:13	GPMGNIMAI	0.9568	0.9127	6	15
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B35:09	GPMGNIMAI	0.9349	0.9653	6	15
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B51:09	GPMGNIMAI	0.8299	0.6168	6	15
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B55:04	GPMGNIMAI	0.8101	0.6305	6	15
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B78:02	GPMGNIMAI	0.796	0.8223	6	15
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B35:13	RPHGQHHAI	0.794	0.6236	6	15
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B35:09	RPHGQHHAI	0.7525	0.7744	6	15
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B67:01	GPMGNIMAI	0.7233	0.9022	6	15
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B39:11	HHAIEEGTL	0.6949	0.8983	11	20
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B67:01	RPHGQHHAI	0.6732	0.5152	6	15
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B51:21	GPMGNIMAI	0.6411	0.604	6	15
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B39:02	RPHGQHHAI	0.5727	0.5678	6	15
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B51:29	GPMGNIMAI	0.5237	0.5201	6	15
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-C07:04	RPHGQHHAI	0.318	0.9014	6	15
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B39:31	QHHAIEEGTL	0.9936	0.9325	10	20
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B38:05	QHHAIEEGTL	0.9833	0.9734	10	20
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B39:11	QHHAIEEGTL	0.9408	0.8928	10	20
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B15:09	QHHAIEEGTL	0.9366	0.9193	10	20
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B55:04	SGPMGNIMAI	0.6322	0.5787	5	15
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B50:05	RERPHGQHHA	0.629	0.5536	4	14
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B50:04	RERPHGQHHA	0.629	0.5536	4	14
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B67:01	SGPMGNIMAI	0.3674	0.847	5	15
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B40:12	GQHHAIEEGTL	0.9953	0.654	9	20
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B50:04	GESGPMGNIMA	0.9567	0.8331	3	14
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	HLA-B50:05	GESGPMGNIMA	0.9567	0.8331	3	14

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Potential FusionNeoAntigen Information of EEF2-SMARCA4 in HLA II

EEF2-SMARCA4_3982805_11151983.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)
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	DRB1-1503	PMGNIMAIEEGTLEE	7	22
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	DRB1-1503	MGNIMAIEEGTLEEI	8	23
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	DRB1-1523	PMGNIMAIEEGTLEE	7	22
EEF2-SMARCA4	chr19	3982805	chr19	11151983	701	DRB1-1523	MGNIMAIEEGTLEEI	8	23

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Fusion breakpoint peptide structures of EEF2-SMARCA4

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
3025	GPMGNIMAIEEGTL	EEF2	SMARCA4	chr19	3982805	chr19	11151983	701

File name	BPseq	Hgene	Tgene	Hchr	Hbp	Tchr	Tbp	AAlen
8083	RPHGQHHAIEEGTL	EEF2	SMARCA4	chr19	3982805	chr19	11151983	701

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of EEF2-SMARCA4

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-B52:01	3W39	3025	GPMGNIMAIEEGTL	-5.87005	-5.87405
HLA-B44:05	3DX8	3025	GPMGNIMAIEEGTL	-4.94496	-4.94896
HLA-B14:02	3BVN	8083	RPHGQHHAIEEGTL	-7.15543	-7.26883
HLA-B14:02	3BVN	8083	RPHGQHHAIEEGTL	-4.77435	-5.80965
HLA-B52:01	3W39	8083	RPHGQHHAIEEGTL	-6.80875	-6.92215
HLA-B52:01	3W39	8083	RPHGQHHAIEEGTL	-4.20386	-5.23916
HLA-A11:01	4UQ2	8083	RPHGQHHAIEEGTL	-7.5194	-8.5547
HLA-A11:01	4UQ2	8083	RPHGQHHAIEEGTL	-6.9601	-7.0735
HLA-A24:02	5HGA	8083	RPHGQHHAIEEGTL	-7.52403	-7.63743
HLA-A24:02	5HGA	8083	RPHGQHHAIEEGTL	-5.82433	-6.85963
HLA-B27:05	6PYJ	8083	RPHGQHHAIEEGTL	-3.28285	-4.31815
HLA-B44:05	3DX8	8083	RPHGQHHAIEEGTL	-5.91172	-6.94702
HLA-B44:05	3DX8	8083	RPHGQHHAIEEGTL	-4.24346	-4.35686

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Vaccine Design for the FusionNeoAntigens of EEF2-SMARCA4

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
EEF2-SMARCA4	chr19	3982805	chr19	11151983	10	20	QHHAIEEGTL	AACATCATGCCATCGAGGAGGGCACGCTGG
EEF2-SMARCA4	chr19	3982805	chr19	11151983	11	20	HHAIEEGTL	ATCATGCCATCGAGGAGGGCACGCTGG
EEF2-SMARCA4	chr19	3982805	chr19	11151983	12	20	HAIEEGTL	ATGCCATCGAGGAGGGCACGCTGG
EEF2-SMARCA4	chr19	3982805	chr19	11151983	12	20	MAIEEGTL	ATGGCCATCGAGGAGGGCACGCTG
EEF2-SMARCA4	chr19	3982805	chr19	11151983	3	14	GESGPMGNIMA	GGCGAGAGCGGCCCCATGGGCAACATCATGGCC
EEF2-SMARCA4	chr19	3982805	chr19	11151983	4	14	RERPHGQHHA	GAGAGCGGCCCCATGGGCAACATCATGCCA
EEF2-SMARCA4	chr19	3982805	chr19	11151983	5	14	ERPHGQHHA	AGCGGCCCCATGGGCAACATCATGCCA
EEF2-SMARCA4	chr19	3982805	chr19	11151983	5	15	SGPMGNIMAI	AGCGGCCCCATGGGCAACATCATGGCCATC
EEF2-SMARCA4	chr19	3982805	chr19	11151983	6	15	GPMGNIMAI	GGCCCCATGGGCAACATCATGGCCATC
EEF2-SMARCA4	chr19	3982805	chr19	11151983	6	15	RPHGQHHAI	GGCCCCATGGGCAACATCATGCCATCG
EEF2-SMARCA4	chr19	3982805	chr19	11151983	9	20	GQHHAIEEGTL	GGCAACATCATGCCATCGAGGAGGGCACGCTGG

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
EEF2-SMARCA4	chr19	3982805	chr19	11151983	7	22	PMGNIMAIEEGTLEE	CCCATGGGCAACATCATGGCCATCGAGGAGGGCACGCTGGAGGAG
EEF2-SMARCA4	chr19	3982805	chr19	11151983	8	23	MGNIMAIEEGTLEEI	ATGGGCAACATCATGGCCATCGAGGAGGGCACGCTGGAGGAGATC

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Information of the samples that have these potential fusion neoantigens of EEF2-SMARCA4

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
Non-Cancer	EEF2-SMARCA4	chr19	3982805	ENST00000309311	chr19	11151983	ENST00000344626	TCGA-K1-A3PO-11A
Non-Cancer	EEF2-SMARCA4	chr19	3982805	ENST00000309311	chr19	11151983	ENST00000413806	TCGA-K1-A3PO-11A

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Potential target of CAR-T therapy development for EEF2-SMARCA4

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 EEF2-SMARCA4

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 EEF2-SMARCA4

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)