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Fusion Protein:EPB41-HGSNAT

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: EPB41-HGSNAT
	FusionPDB ID: 26800
	FusionGDB2.0 ID: 26800
		Hgene	Tgene
	Gene symbol	EPB41	HGSNAT
	Gene ID	2035	138050
	Gene name	erythrocyte membrane protein band 4.1	heparan-alpha-glucosaminide N-acetyltransferase
	Synonyms	4.1R\|EL1\|HE	HGNAT\|MPS3C\|RP73\|TMEM76
	Cytomap	1p35.3	8p11.21-p11.1
	Type of gene	protein-coding	protein-coding
	Description	protein 4.1EPB4.1P4.1band 4.1elliptocytosis 1, RH-linkederythrocyte surface protein band 4.1	heparan-alpha-glucosaminide N-acetyltransferasetransmembrane protein 76
	Modification date	20200320	20200313
	UniProtAcc	Q9HCM4 Main function of 5'-partner protein: FUNCTION: Plays a role in the formation and organization of tight junctions during the establishment of polarity in epithelial cells. {ECO:0000269\|PubMed:17920587}.	Q68CP4 Main function of 5'-partner protein: FUNCTION: Lysosomal acetyltransferase that acetylates the non-reducing terminal alpha-glucosamine residue of intralysosomal heparin or heparan sulfate, converting it into a substrate for luminal alpha-N-acetyl glucosaminidase. {ECO:0000269\|PubMed:16960811, ECO:0000269\|PubMed:17033958, ECO:0000269\|PubMed:19823584, ECO:0000269\|PubMed:20650889}.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000343067, ENST00000349460, ENST00000356093, ENST00000373797, ENST00000373798, ENST00000373800, ENST00000398863, ENST00000347529, ENST00000460378,	ENST00000297798, ENST00000521576, ENST00000379644, ENST00000458501,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	18 X 16 X 9=2592	12 X 13 X 4=624
	# samples	20	13
	** MAII score	log2(20/2592*10)=-3.6959938131099 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(13/624*10)=-2.26303440583379 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: EPB41 [Title/Abstract] AND HGSNAT [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: EPB41 [Title/Abstract] AND HGSNAT [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	EPB41(29323831)-HGSNAT(43013718), # samples:3
Anticipated loss of major functional domain due to fusion event.	EPB41-HGSNAT 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. EPB41-HGSNAT 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. EPB41-HGSNAT 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. EPB41-HGSNAT 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	EPB41	GO:0032092	positive regulation of protein binding	3693401
Tgene	HGSNAT	GO:0007041	lysosomal transport	20650889
Tgene	HGSNAT	GO:0051259	protein complex oligomerization	20650889

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr1:29323831/chr8:43013718)
- 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 EPB41 (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 HGSNAT (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)
ENST00000356093	EPB41	chr1	29323831	+	ENST00000458501	HGSNAT	chr8	43013718	+	5844	913	7	2586	859
ENST00000356093	EPB41	chr1	29323831	+	ENST00000379644	HGSNAT	chr8	43013718	+	5873	913	7	2586	859
ENST00000398863	EPB41	chr1	29323831	+	ENST00000458501	HGSNAT	chr8	43013718	+	5844	913	7	2586	859
ENST00000398863	EPB41	chr1	29323831	+	ENST00000379644	HGSNAT	chr8	43013718	+	5873	913	7	2586	859
ENST00000343067	EPB41	chr1	29323831	+	ENST00000458501	HGSNAT	chr8	43013718	+	5844	913	7	2586	859
ENST00000343067	EPB41	chr1	29323831	+	ENST00000379644	HGSNAT	chr8	43013718	+	5873	913	7	2586	859
ENST00000349460	EPB41	chr1	29323831	+	ENST00000458501	HGSNAT	chr8	43013718	+	5891	960	606	2633	675
ENST00000349460	EPB41	chr1	29323831	+	ENST00000379644	HGSNAT	chr8	43013718	+	5920	960	606	2633	675
ENST00000373800	EPB41	chr1	29323831	+	ENST00000458501	HGSNAT	chr8	43013718	+	5874	943	589	2616	675
ENST00000373800	EPB41	chr1	29323831	+	ENST00000379644	HGSNAT	chr8	43013718	+	5903	943	589	2616	675
ENST00000373798	EPB41	chr1	29323831	+	ENST00000458501	HGSNAT	chr8	43013718	+	5821	890	104	2563	819
ENST00000373798	EPB41	chr1	29323831	+	ENST00000379644	HGSNAT	chr8	43013718	+	5850	890	104	2563	819
ENST00000373797	EPB41	chr1	29323831	+	ENST00000458501	HGSNAT	chr8	43013718	+	5914	983	44	2656	870
ENST00000373797	EPB41	chr1	29323831	+	ENST00000379644	HGSNAT	chr8	43013718	+	5943	983	44	2656	870
ENST00000356093	EPB41	chr1	29323831	+	ENST00000458501	HGSNAT	chr8	43013717	+	5844	913	7	2586	859
ENST00000356093	EPB41	chr1	29323831	+	ENST00000379644	HGSNAT	chr8	43013717	+	5873	913	7	2586	859
ENST00000398863	EPB41	chr1	29323831	+	ENST00000458501	HGSNAT	chr8	43013717	+	5844	913	7	2586	859
ENST00000398863	EPB41	chr1	29323831	+	ENST00000379644	HGSNAT	chr8	43013717	+	5873	913	7	2586	859
ENST00000343067	EPB41	chr1	29323831	+	ENST00000458501	HGSNAT	chr8	43013717	+	5844	913	7	2586	859
ENST00000343067	EPB41	chr1	29323831	+	ENST00000379644	HGSNAT	chr8	43013717	+	5873	913	7	2586	859
ENST00000349460	EPB41	chr1	29323831	+	ENST00000458501	HGSNAT	chr8	43013717	+	5891	960	606	2633	675
ENST00000349460	EPB41	chr1	29323831	+	ENST00000379644	HGSNAT	chr8	43013717	+	5920	960	606	2633	675
ENST00000373800	EPB41	chr1	29323831	+	ENST00000458501	HGSNAT	chr8	43013717	+	5874	943	589	2616	675
ENST00000373800	EPB41	chr1	29323831	+	ENST00000379644	HGSNAT	chr8	43013717	+	5903	943	589	2616	675
ENST00000373798	EPB41	chr1	29323831	+	ENST00000458501	HGSNAT	chr8	43013717	+	5821	890	104	2563	819
ENST00000373798	EPB41	chr1	29323831	+	ENST00000379644	HGSNAT	chr8	43013717	+	5850	890	104	2563	819
ENST00000373797	EPB41	chr1	29323831	+	ENST00000458501	HGSNAT	chr8	43013717	+	5914	983	44	2656	870
ENST00000373797	EPB41	chr1	29323831	+	ENST00000379644	HGSNAT	chr8	43013717	+	5943	983	44	2656	870

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
ENST00000356093	ENST00000458501	EPB41	chr1	29323831	+	HGSNAT	chr8	43013718	+	0.000225265	0.99977475
ENST00000356093	ENST00000379644	EPB41	chr1	29323831	+	HGSNAT	chr8	43013718	+	0.000228459	0.99977154
ENST00000398863	ENST00000458501	EPB41	chr1	29323831	+	HGSNAT	chr8	43013718	+	0.000225265	0.99977475
ENST00000398863	ENST00000379644	EPB41	chr1	29323831	+	HGSNAT	chr8	43013718	+	0.000228459	0.99977154
ENST00000343067	ENST00000458501	EPB41	chr1	29323831	+	HGSNAT	chr8	43013718	+	0.000225265	0.99977475
ENST00000343067	ENST00000379644	EPB41	chr1	29323831	+	HGSNAT	chr8	43013718	+	0.000228459	0.99977154
ENST00000349460	ENST00000458501	EPB41	chr1	29323831	+	HGSNAT	chr8	43013718	+	0.000870006	0.9991301
ENST00000349460	ENST00000379644	EPB41	chr1	29323831	+	HGSNAT	chr8	43013718	+	0.000880135	0.9991198
ENST00000373800	ENST00000458501	EPB41	chr1	29323831	+	HGSNAT	chr8	43013718	+	0.000837143	0.9991629
ENST00000373800	ENST00000379644	EPB41	chr1	29323831	+	HGSNAT	chr8	43013718	+	0.000844828	0.99915516
ENST00000373798	ENST00000458501	EPB41	chr1	29323831	+	HGSNAT	chr8	43013718	+	0.000239288	0.9997607
ENST00000373798	ENST00000379644	EPB41	chr1	29323831	+	HGSNAT	chr8	43013718	+	0.000242251	0.9997577
ENST00000373797	ENST00000458501	EPB41	chr1	29323831	+	HGSNAT	chr8	43013718	+	0.000252757	0.9997472
ENST00000373797	ENST00000379644	EPB41	chr1	29323831	+	HGSNAT	chr8	43013718	+	0.000255741	0.99974424
ENST00000356093	ENST00000458501	EPB41	chr1	29323831	+	HGSNAT	chr8	43013717	+	0.000225265	0.99977475
ENST00000356093	ENST00000379644	EPB41	chr1	29323831	+	HGSNAT	chr8	43013717	+	0.000228459	0.99977154
ENST00000398863	ENST00000458501	EPB41	chr1	29323831	+	HGSNAT	chr8	43013717	+	0.000225265	0.99977475
ENST00000398863	ENST00000379644	EPB41	chr1	29323831	+	HGSNAT	chr8	43013717	+	0.000228459	0.99977154
ENST00000343067	ENST00000458501	EPB41	chr1	29323831	+	HGSNAT	chr8	43013717	+	0.000225265	0.99977475
ENST00000343067	ENST00000379644	EPB41	chr1	29323831	+	HGSNAT	chr8	43013717	+	0.000228459	0.99977154
ENST00000349460	ENST00000458501	EPB41	chr1	29323831	+	HGSNAT	chr8	43013717	+	0.000870006	0.9991301
ENST00000349460	ENST00000379644	EPB41	chr1	29323831	+	HGSNAT	chr8	43013717	+	0.000880135	0.9991198
ENST00000373800	ENST00000458501	EPB41	chr1	29323831	+	HGSNAT	chr8	43013717	+	0.000837143	0.9991629
ENST00000373800	ENST00000379644	EPB41	chr1	29323831	+	HGSNAT	chr8	43013717	+	0.000844828	0.99915516
ENST00000373798	ENST00000458501	EPB41	chr1	29323831	+	HGSNAT	chr8	43013717	+	0.000239288	0.9997607
ENST00000373798	ENST00000379644	EPB41	chr1	29323831	+	HGSNAT	chr8	43013717	+	0.000242251	0.9997577
ENST00000373797	ENST00000458501	EPB41	chr1	29323831	+	HGSNAT	chr8	43013717	+	0.000252757	0.9997472
ENST00000373797	ENST00000379644	EPB41	chr1	29323831	+	HGSNAT	chr8	43013717	+	0.000255741	0.99974424

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 EPB41-HGSNAT

+/-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
EPB41	chr1	29323831	HGSNAT	chr8	43013717	890	262	YFGLAIWDNATSKCLFQVLVNVPQSP
EPB41	chr1	29323831	HGSNAT	chr8	43013717	913	302	YFGLAIWDNATSKCLFQVLVNVPQSP
EPB41	chr1	29323831	HGSNAT	chr8	43013717	943	118	YFGLAIWDNATSKCLFQVLVNVPQSP
EPB41	chr1	29323831	HGSNAT	chr8	43013717	960	118	YFGLAIWDNATSKCLFQVLVNVPQSP
EPB41	chr1	29323831	HGSNAT	chr8	43013717	983	313	YFGLAIWDNATSKCLFQVLVNVPQSP
EPB41	chr1	29323831	HGSNAT	chr8	43013718	890	262	YFGLAIWDNATSKCLFQVLVNVPQSP
EPB41	chr1	29323831	HGSNAT	chr8	43013718	913	302	YFGLAIWDNATSKCLFQVLVNVPQSP
EPB41	chr1	29323831	HGSNAT	chr8	43013718	943	118	YFGLAIWDNATSKCLFQVLVNVPQSP
EPB41	chr1	29323831	HGSNAT	chr8	43013718	960	118	YFGLAIWDNATSKCLFQVLVNVPQSP
EPB41	chr1	29323831	HGSNAT	chr8	43013718	983	313	YFGLAIWDNATSKCLFQVLVNVPQSP

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Potential FusionNeoAntigen Information of EPB41-HGSNAT 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.

EPB41-HGSNAT_29323831_43013717.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)
EPB41-HGSNAT	chr1	29323831	chr8	43013717	913	HLA-A02:60	KCLFQVLVNV	0.8889	0.7948	12	22
EPB41-HGSNAT	chr1	29323831	chr8	43013717	913	HLA-A02:24	KCLFQVLVNV	0.8807	0.7855	12	22
EPB41-HGSNAT	chr1	29323831	chr8	43013717	913	HLA-A02:67	KCLFQVLVNV	0.8807	0.7855	12	22
EPB41-HGSNAT	chr1	29323831	chr8	43013717	913	HLA-A02:30	KCLFQVLVNV	0.8807	0.7855	12	22
EPB41-HGSNAT	chr1	29323831	chr8	43013717	913	HLA-A02:11	KCLFQVLVNV	0.8769	0.8075	12	22
EPB41-HGSNAT	chr1	29323831	chr8	43013717	913	HLA-A02:04	KCLFQVLVNV	0.862	0.887	12	22
EPB41-HGSNAT	chr1	29323831	chr8	43013717	913	HLA-A02:16	KCLFQVLVNV	0.8493	0.7605	12	22
EPB41-HGSNAT	chr1	29323831	chr8	43013717	913	HLA-A02:35	KCLFQVLVNV	0.7767	0.8072	12	22
EPB41-HGSNAT	chr1	29323831	chr8	43013717	913	HLA-A02:29	KCLFQVLVNV	0.7734	0.7847	12	22
EPB41-HGSNAT	chr1	29323831	chr8	43013717	913	HLA-A02:20	KCLFQVLVNV	0.7676	0.7943	12	22
EPB41-HGSNAT	chr1	29323831	chr8	43013717	913	HLA-A24:15	IWDNATSKCLF	0.9995	0.5972	5	16
EPB41-HGSNAT	chr1	29323831	chr8	43013717	913	HLA-A24:25	IWDNATSKCLF	0.9995	0.6101	5	16
EPB41-HGSNAT	chr1	29323831	chr8	43013717	913	HLA-A24:20	IWDNATSKCLF	0.9995	0.6087	5	16
EPB41-HGSNAT	chr1	29323831	chr8	43013717	913	HLA-A24:31	IWDNATSKCLF	0.9993	0.5689	5	16
EPB41-HGSNAT	chr1	29323831	chr8	43013717	913	HLA-A24:17	IWDNATSKCLF	0.9992	0.6716	5	16
EPB41-HGSNAT	chr1	29323831	chr8	43013717	913	HLA-A24:14	IWDNATSKCLF	0.9835	0.5993	5	16
EPB41-HGSNAT	chr1	29323831	chr8	43013717	913	HLA-C04:10	IWDNATSKC	0.9734	0.7867	5	14
EPB41-HGSNAT	chr1	29323831	chr8	43013717	913	HLA-C04:07	IWDNATSKC	0.9698	0.7942	5	14
EPB41-HGSNAT	chr1	29323831	chr8	43013717	913	HLA-C04:14	IWDNATSKC	0.3413	0.7867	5	14
EPB41-HGSNAT	chr1	29323831	chr8	43013717	913	HLA-C04:10	IWDNATSKCL	0.9994	0.815	5	15
EPB41-HGSNAT	chr1	29323831	chr8	43013717	913	HLA-C04:07	IWDNATSKCL	0.9993	0.8325	5	15
EPB41-HGSNAT	chr1	29323831	chr8	43013717	913	HLA-C04:14	IWDNATSKCL	0.9135	0.8168	5	15
EPB41-HGSNAT	chr1	29323831	chr8	43013717	913	HLA-A02:01	KCLFQVLVNV	0.8807	0.7855	12	22
EPB41-HGSNAT	chr1	29323831	chr8	43013717	913	HLA-C04:10	IWDNATSKCLF	1	0.8384	5	16
EPB41-HGSNAT	chr1	29323831	chr8	43013717	913	HLA-C04:07	IWDNATSKCLF	1	0.8443	5	16
EPB41-HGSNAT	chr1	29323831	chr8	43013717	913	HLA-A24:02	IWDNATSKCLF	0.9995	0.6087	5	16
EPB41-HGSNAT	chr1	29323831	chr8	43013717	913	HLA-C04:14	IWDNATSKCLF	0.9982	0.8273	5	16
EPB41-HGSNAT	chr1	29323831	chr8	43013717	913	HLA-C04:01	IWDNATSKC	0.9698	0.7942	5	14
EPB41-HGSNAT	chr1	29323831	chr8	43013717	913	HLA-C18:01	IWDNATSKC	0.9492	0.7989	5	14
EPB41-HGSNAT	chr1	29323831	chr8	43013717	913	HLA-C04:04	IWDNATSKC	0.4478	0.8304	5	14
EPB41-HGSNAT	chr1	29323831	chr8	43013717	913	HLA-C04:01	IWDNATSKCL	0.9993	0.8325	5	15
EPB41-HGSNAT	chr1	29323831	chr8	43013717	913	HLA-C18:01	IWDNATSKCL	0.9984	0.8361	5	15
EPB41-HGSNAT	chr1	29323831	chr8	43013717	913	HLA-C04:04	IWDNATSKCL	0.9331	0.8921	5	15
EPB41-HGSNAT	chr1	29323831	chr8	43013717	913	HLA-C04:01	IWDNATSKCLF	1	0.8443	5	16
EPB41-HGSNAT	chr1	29323831	chr8	43013717	913	HLA-C18:01	IWDNATSKCLF	0.9999	0.8444	5	16

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Potential FusionNeoAntigen Information of EPB41-HGSNAT in HLA II

EPB41-HGSNAT_29323831_43013717.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)
EPB41-HGSNAT	chr1	29323831	chr8	43013717	913	DRB1-0443	SKCLFQVLVNVPQSP	11	26

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Fusion breakpoint peptide structures of EPB41-HGSNAT

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
10433	WDNATSKCLFQVLV	EPB41	HGSNAT	chr1	29323831	chr8	43013717	913

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of EPB41-HGSNAT

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	10433	WDNATSKCLFQVLV	-8.85616	-8.96956
HLA-B14:02	3BVN	10433	WDNATSKCLFQVLV	-5.66423	-6.69953
HLA-B52:01	3W39	10433	WDNATSKCLFQVLV	-6.49489	-6.60829
HLA-B52:01	3W39	10433	WDNATSKCLFQVLV	-3.99785	-5.03315
HLA-A11:01	4UQ2	10433	WDNATSKCLFQVLV	-4.90759	-5.94289
HLA-A24:02	5HGA	10433	WDNATSKCLFQVLV	-7.27887	-7.39227
HLA-A24:02	5HGA	10433	WDNATSKCLFQVLV	-7.11524	-8.15054
HLA-B27:05	6PYJ	10433	WDNATSKCLFQVLV	-6.11615	-6.22955
HLA-B27:05	6PYJ	10433	WDNATSKCLFQVLV	-4.78818	-5.82348
HLA-B44:05	3DX8	10433	WDNATSKCLFQVLV	-7.22602	-7.33942
HLA-B44:05	3DX8	10433	WDNATSKCLFQVLV	-4.86671	-5.90201
HLA-B35:01	1A1N	10433	WDNATSKCLFQVLV	-7.63459	-7.74799
HLA-B35:01	1A1N	10433	WDNATSKCLFQVLV	-5.22375	-6.25905

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Vaccine Design for the FusionNeoAntigens of EPB41-HGSNAT

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
EPB41-HGSNAT	chr1	29323831	chr8	43013717	12	22	KCLFQVLVNV	AAGTGCTTGTTTCAGGTTCTGGTAAACGTT
EPB41-HGSNAT	chr1	29323831	chr8	43013717	5	14	IWDNATSKC	ATTTGGGATAACGCAACCTCTAAGTGC
EPB41-HGSNAT	chr1	29323831	chr8	43013717	5	15	IWDNATSKCL	ATTTGGGATAACGCAACCTCTAAGTGCTTG
EPB41-HGSNAT	chr1	29323831	chr8	43013717	5	16	IWDNATSKCLF	ATTTGGGATAACGCAACCTCTAAGTGCTTGTTT

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
EPB41-HGSNAT	chr1	29323831	chr8	43013717	11	26	SKCLFQVLVNVPQSP	TCTAAGTGCTTGTTTCAGGTTCTGGTAAACGTTCCTCAGAGTCCA

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Information of the samples that have these potential fusion neoantigens of EPB41-HGSNAT

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
BLCA	EPB41-HGSNAT	chr1	29323831	ENST00000343067	chr8	43013717	ENST00000379644	TCGA-2F-A9KP

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Potential target of CAR-T therapy development for EPB41-HGSNAT

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

HGSNAT

chr1:29323831

chr8:43013717

ENST00000379644

191_211

636.0

Transmembrane

Helical

Tgene

HGSNAT

chr1:29323831

chr8:43013717

ENST00000379644

276_296

636.0

Transmembrane

Helical

Tgene

HGSNAT

chr1:29323831

chr8:43013717

ENST00000379644

303_323

636.0

Transmembrane

Helical

Tgene

HGSNAT

chr1:29323831

chr8:43013717

ENST00000379644

346_366

636.0

Transmembrane

Helical

Tgene

HGSNAT

chr1:29323831

chr8:43013717

ENST00000379644

375_395

636.0

Transmembrane

Helical

Tgene

HGSNAT

chr1:29323831

chr8:43013717

ENST00000379644

421_441

636.0

Transmembrane

Helical

Tgene

HGSNAT

chr1:29323831

chr8:43013717

ENST00000379644

501_521

636.0

Transmembrane

Helical

Tgene

HGSNAT

chr1:29323831

chr8:43013717

ENST00000379644

530_550

636.0

Transmembrane

Helical

Tgene

HGSNAT

chr1:29323831

chr8:43013717

ENST00000379644

565_585

636.0

Transmembrane

Helical

Tgene

HGSNAT

chr1:29323831

chr8:43013717

ENST00000379644

593_613

636.0

Transmembrane

Helical

Tgene

HGSNAT

chr1:29323831

chr8:43013717

ENST00000379644

635_655

636.0

Transmembrane

Helical

Tgene

HGSNAT

chr1:29323831

chr8:43013717

ENST00000458501

191_211

664.0

Transmembrane

Helical

Tgene

HGSNAT

chr1:29323831

chr8:43013717

ENST00000458501

276_296

664.0

Transmembrane

Helical

Tgene

HGSNAT

chr1:29323831

chr8:43013717

ENST00000458501

303_323

664.0

Transmembrane

Helical

Tgene

HGSNAT

chr1:29323831

chr8:43013717

ENST00000458501

346_366

664.0

Transmembrane

Helical

Tgene

HGSNAT

chr1:29323831

chr8:43013717

ENST00000458501

375_395

664.0

Transmembrane

Helical

Tgene

HGSNAT

chr1:29323831

chr8:43013717

ENST00000458501

421_441

664.0

Transmembrane

Helical

Tgene

HGSNAT

chr1:29323831

chr8:43013717

ENST00000458501

501_521

664.0

Transmembrane

Helical

Tgene

HGSNAT

chr1:29323831

chr8:43013717

ENST00000458501

530_550

664.0

Transmembrane

Helical

Tgene

HGSNAT

chr1:29323831

chr8:43013717

ENST00000458501

565_585

664.0

Transmembrane

Helical

Tgene

HGSNAT

chr1:29323831

chr8:43013717

ENST00000458501

593_613

664.0

Transmembrane

Helical

Tgene

HGSNAT

chr1:29323831

chr8:43013717

ENST00000458501

635_655

664.0

Transmembrane

Helical

Tgene

HGSNAT

chr1:29323831

chr8:43013718

ENST00000379644

191_211

636.0

Transmembrane

Helical

Tgene

HGSNAT

chr1:29323831

chr8:43013718

ENST00000379644

276_296

636.0

Transmembrane

Helical

Tgene

HGSNAT

chr1:29323831

chr8:43013718

ENST00000379644

303_323

636.0

Transmembrane

Helical

Tgene

HGSNAT

chr1:29323831

chr8:43013718

ENST00000379644

346_366

636.0

Transmembrane

Helical

Tgene

HGSNAT

chr1:29323831

chr8:43013718

ENST00000379644

375_395

636.0

Transmembrane

Helical

Tgene

HGSNAT

chr1:29323831

chr8:43013718

ENST00000379644

421_441

636.0

Transmembrane

Helical

Tgene

HGSNAT

chr1:29323831

chr8:43013718

ENST00000379644

501_521

636.0

Transmembrane

Helical

Tgene

HGSNAT

chr1:29323831

chr8:43013718

ENST00000379644

530_550

636.0

Transmembrane

Helical

Tgene

HGSNAT

chr1:29323831

chr8:43013718

ENST00000379644

565_585

636.0

Transmembrane

Helical

Tgene

HGSNAT

chr1:29323831

chr8:43013718

ENST00000379644

593_613

636.0

Transmembrane

Helical

Tgene

HGSNAT

chr1:29323831

chr8:43013718

ENST00000379644

635_655

636.0

Transmembrane

Helical

Tgene

HGSNAT

chr1:29323831

chr8:43013718

ENST00000458501

191_211

664.0

Transmembrane

Helical

Tgene

HGSNAT

chr1:29323831

chr8:43013718

ENST00000458501

276_296

664.0

Transmembrane

Helical

Tgene

HGSNAT

chr1:29323831

chr8:43013718

ENST00000458501

303_323

664.0

Transmembrane

Helical

Tgene

HGSNAT

chr1:29323831

chr8:43013718

ENST00000458501

346_366

664.0

Transmembrane

Helical

Tgene

HGSNAT

chr1:29323831

chr8:43013718

ENST00000458501

375_395

664.0

Transmembrane

Helical

Tgene

HGSNAT

chr1:29323831

chr8:43013718

ENST00000458501

421_441

664.0

Transmembrane

Helical

Tgene

HGSNAT

chr1:29323831

chr8:43013718

ENST00000458501

501_521

664.0

Transmembrane

Helical

Tgene

HGSNAT

chr1:29323831

chr8:43013718

ENST00000458501

530_550

664.0

Transmembrane

Helical

Tgene

HGSNAT

chr1:29323831

chr8:43013718

ENST00000458501

565_585

664.0

Transmembrane

Helical

Tgene

HGSNAT

chr1:29323831

chr8:43013718

ENST00000458501

593_613

664.0

Transmembrane

Helical

Tgene

HGSNAT

chr1:29323831

chr8:43013718

ENST00000458501

635_655

664.0

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 EPB41-HGSNAT

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 EPB41-HGSNAT

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)