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Fusion Protein:ATG4B-SEC23IP

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: ATG4B-SEC23IP
	FusionPDB ID: 7568
	FusionGDB2.0 ID: 7568
		Hgene	Tgene
	Gene symbol	ATG4B	SEC23IP
	Gene ID	23192	11196
	Gene name	autophagy related 4B cysteine peptidase	SEC23 interacting protein
	Synonyms	APG4B\|AUTL1	MSTP053\|P125\|P125A
	Cytomap	2q37.3	10q26.11-q26.12
	Type of gene	protein-coding	protein-coding
	Description	cysteine protease ATG4BAPG4 autophagy 4 homolog BATG4 autophagy related 4 homolog BAUT-like 1 cysteine endopeptidaseautophagin-1autophagy-related cysteine endopeptidase 1autophagy-related protein 4 homolog BhAPG4B	SEC23-interacting protein
	Modification date	20200329	20200313
	UniProtAcc	Q9Y4P1 Main function of 5'-partner protein: FUNCTION: Cysteine protease required for the cytoplasm to vacuole transport (Cvt) and autophagy. Cleaves the C-terminal amino acid of ATG8 family proteins MAP1LC3, GABARAPL1, GABARAPL2 and GABARAP, to reveal a C-terminal glycine. Exposure of the glycine at the C-terminus is essential for ATG8 proteins conjugation to phosphatidylethanolamine (PE) and insertion to membranes, which is necessary for autophagy. Has also an activity of delipidating enzyme for the PE-conjugated forms. {ECO:0000269\|PubMed:15169837, ECO:0000269\|PubMed:15187094, ECO:0000269\|PubMed:17347651, ECO:0000269\|PubMed:19322194, ECO:0000269\|PubMed:21177865, ECO:0000269\|PubMed:22302004}.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000396411, ENST00000402096, ENST00000404914, ENST00000405546, ENST00000474739, ENST00000491867,	ENST00000475542, ENST00000369075, ENST00000543134,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	5 X 4 X 4=80	7 X 9 X 4=252
	# samples	4	7
	** MAII score	log2(4/80*10)=-1 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(7/252*10)=-1.84799690655495 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: ATG4B [Title/Abstract] AND SEC23IP [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: ATG4B [Title/Abstract] AND SEC23IP [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	ATG4B(242606253)-SEC23IP(121678956), # samples:1
Anticipated loss of major functional domain due to fusion event.	ATG4B-SEC23IP 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. ATG4B-SEC23IP 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. ATG4B-SEC23IP 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. ATG4B-SEC23IP 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	ATG4B	GO:0006508	proteolysis	15169837\|18387192
Hgene	ATG4B	GO:0006914	autophagy	18387192
Hgene	ATG4B	GO:0051697	protein delipidation	25327288

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr2:242606253/chr10:121678956)
- 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 ATG4B (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 SEC23IP (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)
ENST00000405546	ATG4B	chr2	242606253	+	ENST00000369075	SEC23IP	chr10	121678956	+	3946	1234	238	2364	708
ENST00000405546	ATG4B	chr2	242606253	+	ENST00000543134	SEC23IP	chr10	121678956	+	2534	1234	238	2364	708
ENST00000402096	ATG4B	chr2	242606253	+	ENST00000369075	SEC23IP	chr10	121678956	+	3547	835	103	1965	620
ENST00000402096	ATG4B	chr2	242606253	+	ENST00000543134	SEC23IP	chr10	121678956	+	2135	835	103	1965	620
ENST00000404914	ATG4B	chr2	242606253	+	ENST00000369075	SEC23IP	chr10	121678956	+	3547	835	103	1965	620
ENST00000404914	ATG4B	chr2	242606253	+	ENST00000543134	SEC23IP	chr10	121678956	+	2135	835	103	1965	620
ENST00000396411	ATG4B	chr2	242606253	+	ENST00000369075	SEC23IP	chr10	121678956	+	3529	817	307	1947	546
ENST00000396411	ATG4B	chr2	242606253	+	ENST00000543134	SEC23IP	chr10	121678956	+	2117	817	307	1947	546
ENST00000474739	ATG4B	chr2	242606253	+	ENST00000369075	SEC23IP	chr10	121678956	+	3557	845	59	1975	638
ENST00000474739	ATG4B	chr2	242606253	+	ENST00000543134	SEC23IP	chr10	121678956	+	2145	845	59	1975	638

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
ENST00000405546	ENST00000369075	ATG4B	chr2	242606253	+	SEC23IP	chr10	121678956	+	0.000955339	0.9990446
ENST00000405546	ENST00000543134	ATG4B	chr2	242606253	+	SEC23IP	chr10	121678956	+	0.004703462	0.99529654
ENST00000402096	ENST00000369075	ATG4B	chr2	242606253	+	SEC23IP	chr10	121678956	+	0.00026999	0.99973005
ENST00000402096	ENST00000543134	ATG4B	chr2	242606253	+	SEC23IP	chr10	121678956	+	0.001046493	0.99895346
ENST00000404914	ENST00000369075	ATG4B	chr2	242606253	+	SEC23IP	chr10	121678956	+	0.00026999	0.99973005
ENST00000404914	ENST00000543134	ATG4B	chr2	242606253	+	SEC23IP	chr10	121678956	+	0.001046493	0.99895346
ENST00000396411	ENST00000369075	ATG4B	chr2	242606253	+	SEC23IP	chr10	121678956	+	0.001102364	0.99889755
ENST00000396411	ENST00000543134	ATG4B	chr2	242606253	+	SEC23IP	chr10	121678956	+	0.003071028	0.996929
ENST00000474739	ENST00000369075	ATG4B	chr2	242606253	+	SEC23IP	chr10	121678956	+	0.000599043	0.999401
ENST00000474739	ENST00000543134	ATG4B	chr2	242606253	+	SEC23IP	chr10	121678956	+	0.002178749	0.9978212

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 ATG4B-SEC23IP

+/-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
ATG4B	chr2	242606253	SEC23IP	chr10	121678956	1234	330	LGLTDINEAYVETLKMPEEPKLTLDE
ATG4B	chr2	242606253	SEC23IP	chr10	121678956	817	168	LGLTDINEAYVETLKMPEEPKLTLDE
ATG4B	chr2	242606253	SEC23IP	chr10	121678956	835	242	LGLTDINEAYVETLKMPEEPKLTLDE
ATG4B	chr2	242606253	SEC23IP	chr10	121678956	845	260	LGLTDINEAYVETLKMPEEPKLTLDE

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Potential FusionNeoAntigen Information of ATG4B-SEC23IP 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.

ATG4B-SEC23IP_242606253_121678956.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)
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-B18:01	NEAYVETL	0.9972	0.9398	6	14
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-B39:13	NEAYVETL	0.9376	0.911	6	14
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-B35:08	EAYVETLKM	0.9973	0.8685	7	16
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-B35:01	EAYVETLKM	0.9831	0.9128	7	16
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-B35:03	EAYVETLKM	0.9719	0.9297	7	16
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-B35:05	EAYVETLKM	0.8779	0.6344	7	16
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-B52:01	EAYVETLKM	0.8741	0.8361	7	16
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-B35:02	EAYVETLKM	0.7648	0.926	7	16
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-B35:04	EAYVETLKM	0.7648	0.926	7	16
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-A02:67	TLKMPEEPKL	0.5605	0.5186	12	22
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-A02:30	TLKMPEEPKL	0.5605	0.5186	12	22
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-A02:24	TLKMPEEPKL	0.5605	0.5186	12	22
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-A02:04	TLKMPEEPKL	0.5302	0.5711	12	22
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-A02:29	TLKMPEEPKL	0.4728	0.5127	12	22
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-A02:20	TLKMPEEPKL	0.4389	0.5233	12	22
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-B39:08	NEAYVETL	0.974	0.7707	6	14
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-C03:19	EAYVETLKM	0.9971	0.9892	7	16
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-C03:07	EAYVETLKM	0.9958	0.9852	7	16
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-C03:08	EAYVETLKM	0.9937	0.8834	7	16
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-B15:21	EAYVETLKM	0.9921	0.9221	7	16
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-B51:07	EAYVETLKM	0.8782	0.7742	7	16
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-C12:12	EAYVETLKM	0.8238	0.9576	7	16
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-C12:04	EAYVETLKM	0.7734	0.9956	7	16
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-B35:12	EAYVETLKM	0.7648	0.926	7	16
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-C06:03	EAYVETLKM	0.7646	0.9953	7	16
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-A02:01	TLKMPEEPKL	0.5605	0.5186	12	22
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-B40:04	NEAYVETL	0.9997	0.6744	6	14
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-B18:04	NEAYVETL	0.9974	0.9455	6	14
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-B18:05	NEAYVETL	0.9972	0.9398	6	14
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-B18:08	NEAYVETL	0.9969	0.8874	6	14
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-B18:06	NEAYVETL	0.9959	0.9451	6	14
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-B18:03	NEAYVETL	0.9959	0.9357	6	14
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-B41:03	NEAYVETL	0.9708	0.551	6	14
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-B18:11	NEAYVETL	0.9684	0.9028	6	14
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-B39:11	NEAYVETL	0.9636	0.7588	6	14
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-B39:31	NEAYVETL	0.9613	0.9561	6	14
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-B39:02	NEAYVETL	0.9605	0.9203	6	14
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-C14:03	AYVETLKM	0.8972	0.9658	8	16
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-C14:02	AYVETLKM	0.8972	0.9658	8	16
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-C03:03	EAYVETLKM	0.9988	0.9874	7	16
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-C03:04	EAYVETLKM	0.9988	0.9874	7	16
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-C03:02	EAYVETLKM	0.9985	0.9718	7	16
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-A25:01	EAYVETLKM	0.9971	0.8582	7	16
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-B35:11	EAYVETLKM	0.9924	0.915	7	16
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-B35:77	EAYVETLKM	0.9831	0.9128	7	16
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-B35:23	EAYVETLKM	0.981	0.8911	7	16
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-B35:20	EAYVETLKM	0.9809	0.9387	7	16
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-C16:04	EAYVETLKM	0.9698	0.9898	7	16
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-B35:13	EAYVETLKM	0.9602	0.9339	7	16
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-B35:24	EAYVETLKM	0.9317	0.8836	7	16
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-C03:06	EAYVETLKM	0.9147	0.9878	7	16
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-B78:02	EAYVETLKM	0.8986	0.5538	7	16
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-B35:30	EAYVETLKM	0.8916	0.798	7	16
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-B35:17	EAYVETLKM	0.8916	0.798	7	16
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-C12:02	EAYVETLKM	0.8466	0.9782	7	16
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-C12:03	EAYVETLKM	0.8378	0.9884	7	16
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-B35:09	EAYVETLKM	0.7648	0.926	7	16
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-B15:11	EAYVETLKM	0.6249	0.8388	7	16
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-B15:08	EAYVETLKM	0.6219	0.8526	7	16
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-B35:43	EAYVETLKM	0.6152	0.8554	7	16
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	HLA-B18:07	EAYVETLKM	0.2745	0.8522	7	16

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Potential FusionNeoAntigen Information of ATG4B-SEC23IP in HLA II

ATG4B-SEC23IP_242606253_121678956.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)
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0801	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0801	INEAYVETLKMPEEP	5	20
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0801	EAYVETLKMPEEPKL	7	22
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0801	DINEAYVETLKMPEE	4	19
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0803	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0803	INEAYVETLKMPEEP	5	20
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0803	EAYVETLKMPEEPKL	7	22
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0803	DINEAYVETLKMPEE	4	19
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0805	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0805	INEAYVETLKMPEEP	5	20
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0805	DINEAYVETLKMPEE	4	19
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0805	EAYVETLKMPEEPKL	7	22
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0807	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0808	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0808	INEAYVETLKMPEEP	5	20
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0811	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0811	INEAYVETLKMPEEP	5	20
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0814	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0814	INEAYVETLKMPEEP	5	20
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0814	EAYVETLKMPEEPKL	7	22
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0814	DINEAYVETLKMPEE	4	19
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0816	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0816	INEAYVETLKMPEEP	5	20
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0816	EAYVETLKMPEEPKL	7	22
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0816	DINEAYVETLKMPEE	4	19
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0818	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0818	INEAYVETLKMPEEP	5	20
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0818	DINEAYVETLKMPEE	4	19
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0818	EAYVETLKMPEEPKL	7	22
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0823	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0823	INEAYVETLKMPEEP	5	20
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0823	EAYVETLKMPEEPKL	7	22
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0823	DINEAYVETLKMPEE	4	19
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0826	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0826	INEAYVETLKMPEEP	5	20
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0826	EAYVETLKMPEEPKL	7	22
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0826	DINEAYVETLKMPEE	4	19
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0827	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0827	INEAYVETLKMPEEP	5	20
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0827	EAYVETLKMPEEPKL	7	22
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0827	DINEAYVETLKMPEE	4	19
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0829	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0829	INEAYVETLKMPEEP	5	20
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0829	DINEAYVETLKMPEE	4	19
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0829	EAYVETLKMPEEPKL	7	22
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0832	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0833	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0833	INEAYVETLKMPEEP	5	20
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0833	EAYVETLKMPEEPKL	7	22
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0833	DINEAYVETLKMPEE	4	19
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0835	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0835	INEAYVETLKMPEEP	5	20
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0835	EAYVETLKMPEEPKL	7	22
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0835	DINEAYVETLKMPEE	4	19
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0836	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0836	INEAYVETLKMPEEP	5	20
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0836	EAYVETLKMPEEPKL	7	22
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0836	DINEAYVETLKMPEE	4	19
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0837	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0837	INEAYVETLKMPEEP	5	20
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0838	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0838	INEAYVETLKMPEEP	5	20
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0838	EAYVETLKMPEEPKL	7	22
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0838	DINEAYVETLKMPEE	4	19
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0839	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0839	INEAYVETLKMPEEP	5	20
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0839	EAYVETLKMPEEPKL	7	22
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0839	DINEAYVETLKMPEE	4	19
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0840	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0840	INEAYVETLKMPEEP	5	20
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0840	DINEAYVETLKMPEE	4	19
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-0840	EAYVETLKMPEEPKL	7	22
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1108	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1119	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1131	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1153	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1173	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1180	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1187	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1193	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1303	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1303	INEAYVETLKMPEEP	5	20
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1303	DINEAYVETLKMPEE	4	19
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1303	EAYVETLKMPEEPKL	7	22
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-13100	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-13100	INEAYVETLKMPEEP	5	20
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-13101	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-13101	INEAYVETLKMPEEP	5	20
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-13101	EAYVETLKMPEEPKL	7	22
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-13101	DINEAYVETLKMPEE	4	19
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1310	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1310	INEAYVETLKMPEEP	5	20
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1310	EAYVETLKMPEEPKL	7	22
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1310	DINEAYVETLKMPEE	4	19
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1312	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1312	INEAYVETLKMPEEP	5	20
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1312	DINEAYVETLKMPEE	4	19
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1312	EAYVETLKMPEEPKL	7	22
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1313	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1313	INEAYVETLKMPEEP	5	20
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1313	EAYVETLKMPEEPKL	7	22
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1313	DINEAYVETLKMPEE	4	19
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1321	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1321	INEAYVETLKMPEEP	5	20
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1321	EAYVETLKMPEEPKL	7	22
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1321	DINEAYVETLKMPEE	4	19
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1330	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1330	INEAYVETLKMPEEP	5	20
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1330	DINEAYVETLKMPEE	4	19
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1330	EAYVETLKMPEEPKL	7	22
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1333	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1333	INEAYVETLKMPEEP	5	20
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1333	EAYVETLKMPEEPKL	7	22
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1337	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1338	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1338	INEAYVETLKMPEEP	5	20
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1346	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1346	INEAYVETLKMPEEP	5	20
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1349	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1349	INEAYVETLKMPEEP	5	20
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1349	EAYVETLKMPEEPKL	7	22
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1349	DINEAYVETLKMPEE	4	19
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1355	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1355	INEAYVETLKMPEEP	5	20
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1355	EAYVETLKMPEEPKL	7	22
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1355	DINEAYVETLKMPEE	4	19
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1356	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1360	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1365	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1365	INEAYVETLKMPEEP	5	20
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1366	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1366	INEAYVETLKMPEEP	5	20
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1366	EAYVETLKMPEEPKL	7	22
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1366	DINEAYVETLKMPEE	4	19
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1382	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1388	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1388	INEAYVETLKMPEEP	5	20
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1388	EAYVETLKMPEEPKL	7	22
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1388	DINEAYVETLKMPEE	4	19
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1390	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1390	INEAYVETLKMPEEP	5	20
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1390	DINEAYVETLKMPEE	4	19
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1390	EAYVETLKMPEEPKL	7	22
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1395	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1395	INEAYVETLKMPEEP	5	20
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1395	DINEAYVETLKMPEE	4	19
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1395	EAYVETLKMPEEPKL	7	22
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1407	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1413	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1413	INEAYVETLKMPEEP	5	20
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1414	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1422	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1422	INEAYVETLKMPEEP	5	20
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1425	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1425	INEAYVETLKMPEEP	5	20
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1436	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1442	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1444	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1451	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1453	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1453	INEAYVETLKMPEEP	5	20
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1463	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1463	INEAYVETLKMPEEP	5	20
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1468	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1469	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1469	INEAYVETLKMPEEP	5	20
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1485	NEAYVETLKMPEEPK	6	21
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1485	INEAYVETLKMPEEP	5	20
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	817	DRB1-1485	EAYVETLKMPEEPKL	7	22

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Fusion breakpoint peptide structures of ATG4B-SEC23IP

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
6125	NEAYVETLKMPEEP	ATG4B	SEC23IP	chr2	242606253	chr10	121678956	817

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of ATG4B-SEC23IP

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	6125	NEAYVETLKMPEEP	-6.6891	-6.8025
HLA-B14:02	3BVN	6125	NEAYVETLKMPEEP	-3.95973	-4.99503
HLA-B52:01	3W39	6125	NEAYVETLKMPEEP	-6.08758	-6.20098
HLA-B52:01	3W39	6125	NEAYVETLKMPEEP	-3.48594	-4.52124
HLA-A11:01	4UQ2	6125	NEAYVETLKMPEEP	-6.93079	-7.04419
HLA-A24:02	5HGA	6125	NEAYVETLKMPEEP	-8.12692	-8.24032
HLA-A24:02	5HGA	6125	NEAYVETLKMPEEP	-5.7285	-6.7638
HLA-B44:05	3DX8	6125	NEAYVETLKMPEEP	-6.06119	-6.17459
HLA-B44:05	3DX8	6125	NEAYVETLKMPEEP	-3.26873	-4.30403

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Vaccine Design for the FusionNeoAntigens of ATG4B-SEC23IP

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
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	12	22	TLKMPEEPKL	AAGATGCCTGAAGAGCCAAAGCTGACTTTG
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	6	14	NEAYVETL	GCCTACGTGGAGACGCTGAAGATG
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	7	16	EAYVETLKM	TACGTGGAGACGCTGAAGATGCCTGAA
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	8	16	AYVETLKM	GTGGAGACGCTGAAGATGCCTGAA

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
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	4	19	DINEAYVETLKMPEE	AACGAGGCCTACGTGGAGACGCTGAAGATGCCTGAAGAGCCAAAG
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	5	20	INEAYVETLKMPEEP	GAGGCCTACGTGGAGACGCTGAAGATGCCTGAAGAGCCAAAGCTG
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	6	21	NEAYVETLKMPEEPK	GCCTACGTGGAGACGCTGAAGATGCCTGAAGAGCCAAAGCTGACT
ATG4B-SEC23IP	chr2	242606253	chr10	121678956	7	22	EAYVETLKMPEEPKL	TACGTGGAGACGCTGAAGATGCCTGAAGAGCCAAAGCTGACTTTG

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Information of the samples that have these potential fusion neoantigens of ATG4B-SEC23IP

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	ATG4B-SEC23IP	chr2	242606253	ENST00000396411	chr10	121678956	ENST00000369075	TCGA-BR-8058-01A

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Potential target of CAR-T therapy development for ATG4B-SEC23IP

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 ATG4B-SEC23IP

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 ATG4B-SEC23IP

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)