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Fusion Protein:AGPAT5-FDFT1

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: AGPAT5-FDFT1
	FusionPDB ID: 2963
	FusionGDB2.0 ID: 2963
		Hgene	Tgene
	Gene symbol	AGPAT5	FDFT1
	Gene ID	55326	2222
	Gene name	1-acylglycerol-3-phosphate O-acyltransferase 5	farnesyl-diphosphate farnesyltransferase 1
	Synonyms	1AGPAT5\|LPAATE	DGPT\|ERG9\|SQS\|SQSD\|SS
	Cytomap	8p23.1	8p23.1
	Type of gene	protein-coding	protein-coding
	Description	1-acyl-sn-glycerol-3-phosphate acyltransferase epsilon1-AGP acyltransferase 51-AGPAT 51-acylglycerol-3-phosphate O-acyltransferase 5 (lysophosphatidic acid acyltransferase, epsilon)lysophosphatidic acid acyltransferase epsilontesticular tissue protei	squalene synthaseFPP:FPP farnesyltransferasepresqualene-di-diphosphate synthasesqualene synthetase
	Modification date	20200313	20200320
	UniProtAcc	Q9NUQ2 Main function of 5'-partner protein: FUNCTION: Converts 1-acyl-sn-glycerol-3-phosphate (lysophosphatidic acid or LPA) into 1,2-diacyl-sn-glycerol-3-phosphate (phosphatidic acid or PA) by incorporating an acyl moiety at the sn-2 position of the glycerol backbone (PubMed:21173190). Acts on LPA containing saturated or unsaturated fatty acids C15:0-C20:4 at the sn-1 position using C18:1-CoA as the acyl donor (PubMed:21173190). Also acts on lysophosphatidylethanolamine using oleoyl-CoA, but not arachidonoyl-CoA, and lysophosphatidylinositol using arachidonoyl-CoA, but not oleoyl-CoA (PubMed:21173190). Activity toward lysophosphatidylglycerol not detectable (PubMed:21173190). {ECO:0000269\|PubMed:21173190}.	P37268 Main function of 5'-partner protein: FUNCTION: Catalyzes the condensation of 2 farnesyl pyrophosphate (FPP) moieties to form squalene. Proceeds in two distinct steps. In the first half-reaction, two molecules of FPP react to form the stable presqualene diphosphate intermediate (PSQPP), with concomitant release of a proton and a molecule of inorganic diphosphate. In the second half-reaction, PSQPP undergoes heterolysis, isomerization, and reduction with NADPH or NADH to form squalene. It is the first committed enzyme of the sterol biosynthesis pathway. {ECO:0000269\|PubMed:10896663, ECO:0000269\|PubMed:24531458}.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000285518, ENST00000530716,	ENST00000443614, ENST00000446331, ENST00000525777, ENST00000525900, ENST00000528643, ENST00000528812, ENST00000530664, ENST00000220584, ENST00000538689,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	9 X 7 X 6=378	12 X 9 X 5=540
	# samples	9	11
	** MAII score	log2(9/378*10)=-2.0703893278914 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(11/540*10)=-2.29545588352617 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: AGPAT5 [Title/Abstract] AND FDFT1 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: AGPAT5 [Title/Abstract] AND FDFT1 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	AGPAT5(6590171)-FDFT1(11689027), # samples:1
Anticipated loss of major functional domain due to fusion event.	AGPAT5-FDFT1 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. AGPAT5-FDFT1 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

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr8:6590171/chr8:11689027)
- 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 AGPAT5 (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 FDFT1 (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)

ENST00000285518

AGPAT5

chr8

6590171

ENST00000538689

FDFT1

chr8

11689027

1540

807

231

1181

316

ENST00000285518

AGPAT5

chr8

6590171

ENST00000220584

FDFT1

chr8

11689027

1882

807

231

1181

316

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
ENST00000285518	ENST00000538689	AGPAT5	chr8	6590171	+	FDFT1	chr8	11689027	+	0.002313243	0.99768674
ENST00000285518	ENST00000220584	AGPAT5	chr8	6590171	+	FDFT1	chr8	11689027	+	0.001298608	0.99870133

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 AGPAT5-FDFT1

+/-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
AGPAT5	chr8	6590171	FDFT1	chr8	11689027	807	192	RNKLQSYVDAGTPVMAIATLAACYNN

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Potential FusionNeoAntigen Information of AGPAT5-FDFT1 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.

AGPAT5-FDFT1_6590171_11689027.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)
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B51:01	DAGTPVMAI	0.996	0.8092	8	17
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B35:03	TPVMAIATL	0.9875	0.8586	11	20
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B35:01	TPVMAIATL	0.9807	0.9014	11	20
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B35:08	YVDAGTPVM	0.9794	0.7572	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B35:08	TPVMAIATL	0.9742	0.8904	11	20
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B35:01	YVDAGTPVM	0.9698	0.8263	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B35:03	YVDAGTPVM	0.9669	0.8211	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B35:04	TPVMAIATL	0.96	0.9466	11	20
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B35:02	TPVMAIATL	0.96	0.9466	11	20
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B35:05	TPVMAIATL	0.9441	0.6285	11	20
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B15:02	YVDAGTPVM	0.9389	0.911	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B51:02	DAGTPVMAI	0.9212	0.7528	8	17
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-A02:17	YVDAGTPVM	0.918	0.7282	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B35:04	YVDAGTPVM	0.911	0.9607	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B35:02	YVDAGTPVM	0.911	0.9607	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B15:18	YVDAGTPVM	0.9105	0.8113	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B35:05	YVDAGTPVM	0.9093	0.6741	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B15:10	YVDAGTPVM	0.8981	0.6393	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B39:01	YVDAGTPVM	0.8949	0.8901	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-A02:13	YVDAGTPVM	0.6325	0.5228	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B15:37	YVDAGTPVM	0.586	0.6522	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B81:01	TPVMAIATL	0.481	0.511	11	20
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B46:01	YVDAGTPVM	0.2055	0.6922	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B81:01	GTPVMAIATL	0.7862	0.6903	10	20
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B81:01	AGTPVMAIATL	0.9756	0.8172	9	20
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C05:09	YVDAGTPV	1	0.9545	6	14
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C08:15	VDAGTPVM	1	0.9907	7	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C08:15	YVDAGTPV	0.9999	0.9825	6	14
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C08:04	YVDAGTPV	0.9955	0.9921	6	14
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C08:13	YVDAGTPV	0.9955	0.9921	6	14
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C04:07	YVDAGTPVM	0.9999	0.933	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C05:09	YVDAGTPVM	0.9999	0.9778	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C04:10	YVDAGTPVM	0.9999	0.9216	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C08:15	YVDAGTPVM	0.9999	0.9872	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C01:17	YVDAGTPVM	0.9998	0.9597	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C01:30	YVDAGTPVM	0.9993	0.9687	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C03:19	YVDAGTPVM	0.9985	0.9928	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C03:07	YVDAGTPVM	0.9981	0.9692	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C03:08	YVDAGTPVM	0.9973	0.8676	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C04:06	YVDAGTPVM	0.9967	0.9635	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C15:06	YVDAGTPVM	0.9964	0.8557	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B51:07	DAGTPVMAI	0.9959	0.9879	8	17
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B78:01	DAGTPVMAI	0.9955	0.829	8	17
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C15:04	YVDAGTPVM	0.9944	0.8754	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C08:13	YVDAGTPVM	0.9937	0.9907	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C08:04	YVDAGTPVM	0.9937	0.9907	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C03:14	YVDAGTPVM	0.9897	0.9853	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B51:08	DAGTPVMAI	0.9864	0.7677	8	17
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C08:03	YVDAGTPVM	0.9822	0.9899	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C07:13	YVDAGTPVM	0.9798	0.9464	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C04:14	YVDAGTPVM	0.9789	0.9327	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C07:29	YVDAGTPVM	0.9709	0.908	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B15:31	YVDAGTPVM	0.9681	0.8459	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B35:12	TPVMAIATL	0.96	0.9466	11	20
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C02:06	YVDAGTPVM	0.9563	0.9591	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B15:21	YVDAGTPVM	0.9443	0.8852	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B39:09	YVDAGTPVM	0.9427	0.7737	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B07:12	YVDAGTPVM	0.9381	0.5109	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B39:08	YVDAGTPVM	0.9253	0.8237	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B56:04	YVDAGTPVM	0.9185	0.5891	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B07:12	TPVMAIATL	0.9117	0.5181	11	20
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B39:10	YVDAGTPVM	0.9114	0.8834	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B35:12	YVDAGTPVM	0.911	0.9607	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B39:10	TPVMAIATL	0.9085	0.8975	11	20
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B39:09	TPVMAIATL	0.8989	0.7222	11	20
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C12:12	YVDAGTPVM	0.8849	0.9682	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B51:07	TPVMAIATL	0.7473	0.9185	11	20
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B42:02	TPVMAIATL	0.7319	0.7414	11	20
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B39:05	YVDAGTPVM	0.7032	0.8829	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B42:01	TPVMAIATL	0.6734	0.7305	11	20
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C04:14	SYVDAGTPV	0.4833	0.9217	5	14
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C05:09	SYVDAGTPVM	0.9996	0.9451	5	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C04:10	SYVDAGTPVM	0.9995	0.915	5	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C04:07	SYVDAGTPVM	0.9994	0.9083	5	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C08:15	SYVDAGTPVM	0.9992	0.9721	5	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C07:29	SYVDAGTPVM	0.9789	0.8313	5	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C07:10	SYVDAGTPVM	0.9671	0.9316	5	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C07:80	SYVDAGTPVM	0.9654	0.9329	5	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C07:67	SYVDAGTPVM	0.9654	0.9329	5	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C04:14	SYVDAGTPVM	0.9598	0.9271	5	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B15:21	SYVDAGTPVM	0.9327	0.8608	5	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B54:01	TPVMAIATLAA	0.9991	0.6718	11	22
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C04:03	YVDAGTPV	1	0.927	6	14
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C08:02	VDAGTPVM	1	0.9907	7	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C05:01	YVDAGTPV	1	0.9545	6	14
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C08:02	YVDAGTPV	0.9999	0.9825	6	14
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C08:02	YVDAGTPVM	0.9999	0.9872	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C04:01	YVDAGTPVM	0.9999	0.933	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C01:03	YVDAGTPVM	0.9999	0.9573	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C05:01	YVDAGTPVM	0.9999	0.9778	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C18:01	YVDAGTPVM	0.9999	0.9299	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C04:03	YVDAGTPVM	0.9999	0.9478	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C01:02	YVDAGTPVM	0.9998	0.9607	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C03:03	YVDAGTPVM	0.999	0.9899	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C03:04	YVDAGTPVM	0.999	0.9899	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C03:02	YVDAGTPVM	0.9979	0.9785	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C06:06	YVDAGTPVM	0.9977	0.9875	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C03:05	YVDAGTPVM	0.9973	0.9355	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C03:67	YVDAGTPVM	0.9972	0.9852	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B51:06	DAGTPVMAI	0.9968	0.7902	8	17
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B78:02	DAGTPVMAI	0.9966	0.9177	8	17
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B51:14	DAGTPVMAI	0.9966	0.7317	8	17
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C03:17	YVDAGTPVM	0.996	0.9759	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B51:09	DAGTPVMAI	0.9957	0.808	8	17
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B51:13	DAGTPVMAI	0.9956	0.7052	8	17
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C15:09	YVDAGTPVM	0.9944	0.8754	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C15:05	YVDAGTPVM	0.9937	0.8743	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C04:04	YVDAGTPVM	0.9933	0.9616	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C16:01	YVDAGTPVM	0.9912	0.9813	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B51:21	DAGTPVMAI	0.9883	0.8302	8	17
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C15:02	YVDAGTPVM	0.9868	0.8755	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B35:13	TPVMAIATL	0.9858	0.8674	11	20
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B35:23	TPVMAIATL	0.9834	0.9206	11	20
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C08:01	YVDAGTPVM	0.9822	0.9899	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C16:04	YVDAGTPVM	0.9807	0.9795	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B35:77	TPVMAIATL	0.9807	0.9014	11	20
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B51:29	DAGTPVMAI	0.9728	0.7469	8	17
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C03:06	YVDAGTPVM	0.9699	0.991	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B35:77	YVDAGTPVM	0.9698	0.8263	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B35:23	YVDAGTPVM	0.9697	0.8465	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B35:13	YVDAGTPVM	0.9679	0.8237	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B35:20	YVDAGTPVM	0.9617	0.8713	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B35:09	TPVMAIATL	0.96	0.9466	11	20
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C12:03	YVDAGTPVM	0.9535	0.9904	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C07:17	YVDAGTPVM	0.9503	0.9785	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B35:11	YVDAGTPVM	0.9458	0.8657	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B35:17	TPVMAIATL	0.9451	0.8034	11	20
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B35:30	TPVMAIATL	0.9451	0.8034	11	20
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C07:04	YVDAGTPVM	0.9416	0.9278	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C12:02	YVDAGTPVM	0.9408	0.9747	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C02:02	YVDAGTPVM	0.9399	0.971	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C02:10	YVDAGTPVM	0.9399	0.971	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B07:13	YVDAGTPVM	0.9274	0.8046	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B67:01	YVDAGTPVM	0.924	0.8725	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B56:02	YVDAGTPVM	0.9185	0.5891	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B35:30	YVDAGTPVM	0.9172	0.7595	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B35:17	YVDAGTPVM	0.9172	0.7595	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B48:05	YVDAGTPVM	0.9129	0.5094	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B35:09	YVDAGTPVM	0.911	0.9607	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B51:05	DAGTPVMAI	0.9084	0.5559	8	17
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B67:01	TPVMAIATL	0.9056	0.8534	11	20
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C17:01	YVDAGTPVM	0.8998	0.9864	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B39:11	YVDAGTPVM	0.8917	0.7435	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B35:22	YVDAGTPVM	0.8878	0.5341	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B35:24	TPVMAIATL	0.8835	0.8902	11	20
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B35:11	TPVMAIATL	0.8788	0.9444	11	20
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B35:24	YVDAGTPVM	0.8691	0.7783	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-A69:01	YVDAGTPVM	0.7696	0.6542	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B15:09	YVDAGTPVM	0.654	0.8557	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C04:04	SYVDAGTPV	0.6534	0.9107	5	14
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-A69:01	DAGTPVMAI	0.6466	0.6201	8	17
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B08:12	YVDAGTPVM	0.5467	0.5665	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B15:08	YVDAGTPVM	0.5465	0.8765	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B35:43	YVDAGTPVM	0.5386	0.8757	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B15:11	YVDAGTPVM	0.5156	0.896	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C03:67	SYVDAGTPV	0.4703	0.9666	5	14
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B51:06	YVDAGTPVM	0.4688	0.8528	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B15:73	YVDAGTPVM	0.4252	0.9435	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B15:30	YVDAGTPVM	0.4245	0.9756	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C14:03	SYVDAGTPV	0.3377	0.9435	5	14
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C14:02	SYVDAGTPV	0.3377	0.9435	5	14
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B40:21	YVDAGTPVM	0.2532	0.7069	6	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B18:07	TPVMAIATL	0.1108	0.7572	11	20
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B35:43	TPVMAIATL	0.0461	0.843	11	20
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B15:08	TPVMAIATL	0.0271	0.8339	11	20
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-B15:11	TPVMAIATL	0.024	0.8374	11	20
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C05:01	SYVDAGTPVM	0.9996	0.9451	5	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C04:01	SYVDAGTPVM	0.9994	0.9083	5	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C18:01	SYVDAGTPVM	0.9993	0.907	5	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C08:02	SYVDAGTPVM	0.9992	0.9721	5	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C03:67	SYVDAGTPVM	0.9912	0.9725	5	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C04:04	SYVDAGTPVM	0.979	0.9354	5	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C14:02	SYVDAGTPVM	0.9694	0.9474	5	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C14:03	SYVDAGTPVM	0.9694	0.9474	5	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	HLA-C07:02	SYVDAGTPVM	0.9654	0.9329	5	15

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Potential FusionNeoAntigen Information of AGPAT5-FDFT1 in HLA II

AGPAT5-FDFT1_6590171_11689027.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)
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	DRB1-1501	RNKLQSYVDAGTPVM	0	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	DRB1-1504	RNKLQSYVDAGTPVM	0	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	DRB1-1506	RNKLQSYVDAGTPVM	0	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	DRB1-1507	RNKLQSYVDAGTPVM	0	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	DRB1-1509	RNKLQSYVDAGTPVM	0	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	DRB1-1513	RNKLQSYVDAGTPVM	0	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	DRB1-1516	RNKLQSYVDAGTPVM	0	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	DRB1-1518	RNKLQSYVDAGTPVM	0	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	DRB1-1520	RNKLQSYVDAGTPVM	0	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	DRB1-1522	RNKLQSYVDAGTPVM	0	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	DRB1-1524	RNKLQSYVDAGTPVM	0	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	DRB1-1532	RNKLQSYVDAGTPVM	0	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	DRB1-1533	RNKLQSYVDAGTPVM	0	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	DRB1-1536	RNKLQSYVDAGTPVM	0	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	DRB1-1540	RNKLQSYVDAGTPVM	0	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	DRB1-1541	RNKLQSYVDAGTPVM	0	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	DRB1-1542	RNKLQSYVDAGTPVM	0	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	DRB1-1543	RNKLQSYVDAGTPVM	0	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	DRB1-1545	RNKLQSYVDAGTPVM	0	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	DRB1-1546	RNKLQSYVDAGTPVM	0	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	DRB1-1548	RNKLQSYVDAGTPVM	0	15
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	807	DRB1-1549	RNKLQSYVDAGTPVM	0	15

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Fusion breakpoint peptide structures of AGPAT5-FDFT1

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
10840	YVDAGTPVMAIATL	AGPAT5	FDFT1	chr8	6590171	chr8	11689027	807

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of AGPAT5-FDFT1

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	10840	YVDAGTPVMAIATL	-7.9962	-8.1096
HLA-B14:02	3BVN	10840	YVDAGTPVMAIATL	-5.70842	-6.74372
HLA-B52:01	3W39	10840	YVDAGTPVMAIATL	-6.83737	-6.95077
HLA-B52:01	3W39	10840	YVDAGTPVMAIATL	-4.4836	-5.5189
HLA-A11:01	4UQ2	10840	YVDAGTPVMAIATL	-10.0067	-10.1201
HLA-A11:01	4UQ2	10840	YVDAGTPVMAIATL	-9.03915	-10.0745
HLA-A24:02	5HGA	10840	YVDAGTPVMAIATL	-6.56204	-6.67544
HLA-A24:02	5HGA	10840	YVDAGTPVMAIATL	-5.42271	-6.45801
HLA-B44:05	3DX8	10840	YVDAGTPVMAIATL	-7.85648	-8.89178
HLA-B44:05	3DX8	10840	YVDAGTPVMAIATL	-5.3978	-5.5112
HLA-A02:01	6TDR	10840	YVDAGTPVMAIATL	-3.37154	-4.40684

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Vaccine Design for the FusionNeoAntigens of AGPAT5-FDFT1

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
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	10	20	GTPVMAIATL	GGAACTCCAGTGATGGCCATTGCCACTTTG
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	11	20	TPVMAIATL	ACTCCAGTGATGGCCATTGCCACTTTG
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	11	22	TPVMAIATLAA	ACTCCAGTGATGGCCATTGCCACTTTGGCTGCC
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	5	14	SYVDAGTPV	AGCTACGTGGACGCAGGAACTCCAGTG
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	5	15	SYVDAGTPVM	AGCTACGTGGACGCAGGAACTCCAGTGATG
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	6	14	YVDAGTPV	TACGTGGACGCAGGAACTCCAGTG
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	6	15	YVDAGTPVM	TACGTGGACGCAGGAACTCCAGTGATG
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	7	15	VDAGTPVM	GTGGACGCAGGAACTCCAGTGATG
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	8	17	DAGTPVMAI	GACGCAGGAACTCCAGTGATGGCCATT
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	9	20	AGTPVMAIATL	GCAGGAACTCCAGTGATGGCCATTGCCACTTTG

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
AGPAT5-FDFT1	chr8	6590171	chr8	11689027	0	15	RNKLQSYVDAGTPVM	CGAAACAAGTTGCAGAGCTACGTGGACGCAGGAACTCCAGTGATG

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Information of the samples that have these potential fusion neoantigens of AGPAT5-FDFT1

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	AGPAT5-FDFT1	chr8	6590171	ENST00000285518	chr8	11689027	ENST00000220584	TCGA-BR-8372-01A

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Potential target of CAR-T therapy development for AGPAT5-FDFT1

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

AGPAT5

chr8:6590171

chr8:11689027

ENST00000285518

15_35

165

365.0

Transmembrane

Helical

Hgene

AGPAT5

chr8:6590171

chr8:11689027

ENST00000285518

61_81

165

365.0

Transmembrane

Helical

Tgene

FDFT1

chr8:6590171

chr8:11689027

ENST00000220584

384_404

418.0

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 AGPAT5-FDFT1

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 AGPAT5-FDFT1

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)