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Fusion Protein:VOPP1-HS3ST2

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: VOPP1-HS3ST2
	FusionPDB ID: 98233
	FusionGDB2.0 ID: 98233
		Hgene	Tgene
	Gene symbol	VOPP1	HS3ST2
	Gene ID	81552	9956
	Gene name	VOPP1 WW domain binding protein	heparan sulfate-glucosamine 3-sulfotransferase 2
	Synonyms	ECOP\|GASP\|WBP1L2	30ST2\|3OST2
	Cytomap	7p11.2	16p12.2
	Type of gene	protein-coding	protein-coding
	Description	vesicular, overexpressed in cancer, prosurvival protein 1EGFR-coamplified and overexpressed proteinGlioblastoma-amplified secreted proteinVOPP1, WBP1/VOPP1 family memberhypothetical protein DKFZp564K0822putative NF-kappa-B-activating protein 055N	heparan sulfate glucosamine 3-O-sulfotransferase 23-OST-2h3-OST-2heparan sulfate (glucosamine) 3-O-sulfotransferase 2heparan sulfate 3-O-sulfotransferase 2heparan sulfate D-glucosaminyl 3-O-sulfotransferase 2heparin-glucosamine 3-O-sulfotransferase
	Modification date	20200313	20200313
	UniProtAcc	.	Q9Y278 Main function of 5'-partner protein: FUNCTION: Sulfotransferase that utilizes 3'-phospho-5'-adenylyl sulfate (PAPS) to catalyze the transfer of a sulfo group to an N-unsubstituted glucosamine linked to a 2-O-sulfo iduronic acid unit on heparan sulfate. Catalyzes the O-sulfation of glucosamine in GlcA2S-GlcNS. Unlike 3-OST-1, does not convert non-anticoagulant heparan sulfate to anticoagulant heparan sulfate.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000285279, ENST00000418904, ENST00000427700, ENST00000428097, ENST00000428648, ENST00000433959, ENST00000453256, ENST00000454227, ENST00000545390, ENST00000471168,	ENST00000261374,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	7 X 5 X 5=175	1 X 3 X 1=3
	# samples	8	1
	** MAII score	log2(8/175*10)=-1.12928301694497 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(1/3*10)=1.73696559416621
Fusion gene context	PubMed: VOPP1 [Title/Abstract] AND HS3ST2 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: VOPP1 [Title/Abstract] AND HS3ST2 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	VOPP1(55559974)-HS3ST2(22926264), # samples:1 VOPP1(55559975)-HS3ST2(22926265), # samples:1 VOPP1(55559975)-HS3ST2(22865985), # samples:1
Anticipated loss of major functional domain due to fusion event.	VOPP1-HS3ST2 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. VOPP1-HS3ST2 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. VOPP1-HS3ST2 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. VOPP1-HS3ST2 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. VOPP1-HS3ST2 seems lost the major protein functional domain in Tgene partner, which is a cell metabolism gene due to the frame-shifted 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/chr7:55559974/chr16:22926264)
- 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 VOPP1 (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 HS3ST2 (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)
ENST00000285279	VOPP1	chr7	55559974	-	ENST00000261374	HS3ST2	chr16	22926264	+	1924	529	38	1147	369
ENST00000433959	VOPP1	chr7	55559974	-	ENST00000261374	HS3ST2	chr16	22926264	+	1863	468	214	1086	290
ENST00000545390	VOPP1	chr7	55559974	-	ENST00000261374	HS3ST2	chr16	22926264	+	1714	319	65	937	290
ENST00000428097	VOPP1	chr7	55559974	-	ENST00000261374	HS3ST2	chr16	22926264	+	1957	562	308	1180	290
ENST00000418904	VOPP1	chr7	55559974	-	ENST00000261374	HS3ST2	chr16	22926264	+	1869	474	118	1092	324
ENST00000453256	VOPP1	chr7	55559974	-	ENST00000261374	HS3ST2	chr16	22926264	+	1752	357	115	975	286
ENST00000285279	VOPP1	chr7	55559975	-	ENST00000261374	HS3ST2	chr16	22926265	+	1924	529	38	1147	369
ENST00000433959	VOPP1	chr7	55559975	-	ENST00000261374	HS3ST2	chr16	22926265	+	1863	468	214	1086	290
ENST00000545390	VOPP1	chr7	55559975	-	ENST00000261374	HS3ST2	chr16	22926265	+	1714	319	65	937	290
ENST00000428097	VOPP1	chr7	55559975	-	ENST00000261374	HS3ST2	chr16	22926265	+	1957	562	308	1180	290
ENST00000418904	VOPP1	chr7	55559975	-	ENST00000261374	HS3ST2	chr16	22926265	+	1869	474	118	1092	324
ENST00000453256	VOPP1	chr7	55559975	-	ENST00000261374	HS3ST2	chr16	22926265	+	1752	357	115	975	286

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
ENST00000285279	ENST00000261374	VOPP1	chr7	55559974	-	HS3ST2	chr16	22926264	+	0.013215874	0.9867841
ENST00000433959	ENST00000261374	VOPP1	chr7	55559974	-	HS3ST2	chr16	22926264	+	0.011542955	0.988457
ENST00000545390	ENST00000261374	VOPP1	chr7	55559974	-	HS3ST2	chr16	22926264	+	0.012299159	0.9877008
ENST00000428097	ENST00000261374	VOPP1	chr7	55559974	-	HS3ST2	chr16	22926264	+	0.011525527	0.98847455
ENST00000418904	ENST00000261374	VOPP1	chr7	55559974	-	HS3ST2	chr16	22926264	+	0.013651575	0.9863484
ENST00000453256	ENST00000261374	VOPP1	chr7	55559974	-	HS3ST2	chr16	22926264	+	0.018747464	0.9812525
ENST00000285279	ENST00000261374	VOPP1	chr7	55559975	-	HS3ST2	chr16	22926265	+	0.013215874	0.9867841
ENST00000433959	ENST00000261374	VOPP1	chr7	55559975	-	HS3ST2	chr16	22926265	+	0.011542955	0.988457
ENST00000545390	ENST00000261374	VOPP1	chr7	55559975	-	HS3ST2	chr16	22926265	+	0.012299159	0.9877008
ENST00000428097	ENST00000261374	VOPP1	chr7	55559975	-	HS3ST2	chr16	22926265	+	0.011525527	0.98847455
ENST00000418904	ENST00000261374	VOPP1	chr7	55559975	-	HS3ST2	chr16	22926265	+	0.013651575	0.9863484
ENST00000453256	ENST00000261374	VOPP1	chr7	55559975	-	HS3ST2	chr16	22926265	+	0.018747464	0.9812525

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 VOPP1-HS3ST2

+/-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
VOPP1	chr7	55559974	HS3ST2	chr16	22926264	319	84	QCVLHQAAPKSRPRSLMPRTLESQIT
VOPP1	chr7	55559974	HS3ST2	chr16	22926264	357	80	QCVLHQAAPKSRPRSLMPRTLESQIT
VOPP1	chr7	55559974	HS3ST2	chr16	22926264	468	84	QCVLHQAAPKSRPRSLMPRTLESQIT
VOPP1	chr7	55559974	HS3ST2	chr16	22926264	474	118	QCVLHQAAPKSRPRSLMPRTLESQIT
VOPP1	chr7	55559974	HS3ST2	chr16	22926264	529	163	QCVLHQAAPKSRPRSLMPRTLESQIT
VOPP1	chr7	55559974	HS3ST2	chr16	22926264	562	84	QCVLHQAAPKSRPRSLMPRTLESQIT
VOPP1	chr7	55559975	HS3ST2	chr16	22926265	319	84	QCVLHQAAPKSRPRSLMPRTLESQIT
VOPP1	chr7	55559975	HS3ST2	chr16	22926265	357	80	QCVLHQAAPKSRPRSLMPRTLESQIT
VOPP1	chr7	55559975	HS3ST2	chr16	22926265	468	84	QCVLHQAAPKSRPRSLMPRTLESQIT
VOPP1	chr7	55559975	HS3ST2	chr16	22926265	474	118	QCVLHQAAPKSRPRSLMPRTLESQIT
VOPP1	chr7	55559975	HS3ST2	chr16	22926265	529	163	QCVLHQAAPKSRPRSLMPRTLESQIT
VOPP1	chr7	55559975	HS3ST2	chr16	22926265	562	84	QCVLHQAAPKSRPRSLMPRTLESQIT

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Potential FusionNeoAntigen Information of VOPP1-HS3ST2 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.

VOPP1-HS3ST2_55559974_22926264.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)
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-B07:02	APKSRPRSL	0.9997	0.6109	7	16
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-B07:10	APKSRPRSL	0.9997	0.6556	7	16
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-A30:08	KSRPRSLMP	0.9929	0.7771	9	18
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-B07:02	RPRSLMPRT	0.9925	0.5739	11	20
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-B08:09	APKSRPRSL	0.9906	0.5922	7	16
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-A31:02	QAAPKSRPR	0.9383	0.708	5	14
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-B14:01	APKSRPRSL	0.9121	0.8139	7	16
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-B14:02	APKSRPRSL	0.9121	0.8139	7	16
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-B07:02	RPRSLMPRTL	0.9993	0.5888	11	21
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-B07:10	RPRSLMPRTL	0.9993	0.6293	11	21
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-A30:08	KSRPRSLMPR	0.998	0.7511	9	19
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-A74:03	KSRPRSLMPR	0.9961	0.6445	9	19
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-A74:09	KSRPRSLMPR	0.9961	0.6445	9	19
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-A74:11	KSRPRSLMPR	0.9961	0.6445	9	19
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-B07:02	AAPKSRPRSL	0.9838	0.6695	6	16
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-B08:01	AAPKSRPRSL	0.9759	0.5031	6	16
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-A31:02	KSRPRSLMPR	0.9695	0.6117	9	19
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-B08:09	AAPKSRPRSL	0.9218	0.6041	6	16
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-B07:02	QAAPKSRPRSL	0.9998	0.673	5	16
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-B08:01	QAAPKSRPRSL	0.999	0.7277	5	16
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-B07:02	RPRSLMPRTLE	0.9988	0.6528	11	22
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-B07:02	SRPRSLMPRTL	0.9555	0.604	10	21
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-B07:04	PKSRPRSL	0.9769	0.5439	8	16
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-A31:01	QAAPKSRPR	0.9643	0.6573	5	14
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-B07:12	APKSRPRSL	0.8795	0.774	7	16
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-B14:03	APKSRPRSL	0.8165	0.8441	7	16
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-B07:04	APKSRPRSL	0.8016	0.5214	7	16
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-B07:04	RPRSLMPRT	0.7677	0.5475	11	20
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-B39:10	APKSRPRSL	0.2121	0.9376	7	16
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-C07:29	APKSRPRSL	0.1951	0.9667	7	16
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-C04:14	APKSRPRSL	0.0161	0.9679	7	16
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-A31:01	KSRPRSLMPR	0.9961	0.5647	9	19
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-B07:12	RPRSLMPRTL	0.9887	0.7372	11	21
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-C01:17	AAPKSRPRSL	0.9832	0.9815	6	16
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-B07:12	AAPKSRPRSL	0.9719	0.8101	6	16
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-B07:12	APKSRPRSLM	0.9715	0.6323	7	17
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-B07:04	AAPKSRPRSL	0.9669	0.5764	6	16
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-C01:30	AAPKSRPRSL	0.9484	0.9791	6	16
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-B07:04	RPRSLMPRTL	0.9371	0.5676	11	21
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-B42:02	RPRSLMPRTL	0.902	0.6078	11	21
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-B42:01	RPRSLMPRTL	0.8891	0.6004	11	21
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-B07:04	QAAPKSRPRSL	0.9991	0.6648	5	16
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-B42:01	QAAPKSRPRSL	0.9989	0.7232	5	16
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-B42:02	QAAPKSRPRSL	0.9988	0.7278	5	16
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-B07:04	RPRSLMPRTLE	0.9972	0.6199	11	22
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-B07:04	SRPRSLMPRTL	0.9772	0.5728	10	21
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-B08:12	PKSRPRSL	0.9287	0.5933	8	16
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-B07:13	APKSRPRSL	0.9997	0.929	7	16
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-B07:22	APKSRPRSL	0.9997	0.6109	7	16
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-B07:09	APKSRPRSL	0.9996	0.6112	7	16
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-A30:01	KSRPRSLMP	0.9941	0.898	9	18
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-B07:22	RPRSLMPRT	0.9925	0.5739	11	20
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-B07:09	RPRSLMPRT	0.9916	0.6076	11	20
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-B08:12	APKSRPRSL	0.7286	0.6658	7	16
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-C07:22	PRSLMPRTL	0.5026	0.8063	12	21
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-C03:67	APKSRPRSL	0.4752	0.9657	7	16
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-C07:04	APKSRPRSL	0.4003	0.9694	7	16
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-B67:01	APKSRPRSL	0.2462	0.7592	7	16
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-B07:22	RPRSLMPRTL	0.9993	0.5888	11	21
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-B07:09	RPRSLMPRTL	0.9992	0.6211	11	21
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-A30:01	KSRPRSLMPR	0.9981	0.8685	9	19
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-A74:01	KSRPRSLMPR	0.9961	0.6445	9	19
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-B07:22	AAPKSRPRSL	0.9838	0.6695	6	16
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-C01:02	AAPKSRPRSL	0.982	0.9807	6	16
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-B07:09	AAPKSRPRSL	0.9817	0.6702	6	16
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-B08:18	AAPKSRPRSL	0.9759	0.5031	6	16
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-C01:03	AAPKSRPRSL	0.9753	0.9772	6	16
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-B08:12	AAPKSRPRSL	0.9289	0.7068	6	16
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-B27:06	RPRSLMPRTL	0.8218	0.7005	11	21
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-B67:01	RPRSLMPRTL	0.3505	0.8485	11	21
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-B07:22	QAAPKSRPRSL	0.9998	0.673	5	16
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-B08:18	QAAPKSRPRSL	0.999	0.7277	5	16
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-B07:22	RPRSLMPRTLE	0.9988	0.6528	11	22
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-B08:12	QAAPKSRPRSL	0.9942	0.8669	5	16
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-B07:26	QAAPKSRPRSL	0.9909	0.5437	5	16
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	529	HLA-B07:22	SRPRSLMPRTL	0.9555	0.604	10	21

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Potential FusionNeoAntigen Information of VOPP1-HS3ST2 in HLA II

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)

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Fusion breakpoint peptide structures of VOPP1-HS3ST2

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
60	AAPKSRPRSLMPRT	VOPP1	HS3ST2	chr7	55559974	chr16	22926264	529

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of VOPP1-HS3ST2

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	60	AAPKSRPRSLMPRT	-6.74962	-6.86302
HLA-B14:02	3BVN	60	AAPKSRPRSLMPRT	-2.31208	-3.34738
HLA-B52:01	3W39	60	AAPKSRPRSLMPRT	-6.19679	-6.31019
HLA-B52:01	3W39	60	AAPKSRPRSLMPRT	-4.58773	-5.62303
HLA-A11:01	4UQ2	60	AAPKSRPRSLMPRT	-11.392	-12.4273
HLA-A24:02	5HGA	60	AAPKSRPRSLMPRT	-6.28541	-6.39881
HLA-A24:02	5HGA	60	AAPKSRPRSLMPRT	-5.27154	-6.30684
HLA-B44:05	3DX8	60	AAPKSRPRSLMPRT	-6.58553	-6.69893
HLA-B44:05	3DX8	60	AAPKSRPRSLMPRT	-5.61722	-6.65252

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Vaccine Design for the FusionNeoAntigens of VOPP1-HS3ST2

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
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	10	21	SRPRSLMPRTL	CCGGCCCAGGAGCCTGATGCCCAGGACCCTCGA
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	11	20	RPRSLMPRT	GCCCAGGAGCCTGATGCCCAGGACCCT
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	11	21	RPRSLMPRTL	GCCCAGGAGCCTGATGCCCAGGACCCTCGA
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	11	22	RPRSLMPRTLE	GCCCAGGAGCCTGATGCCCAGGACCCTCGAGAG
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	12	21	PRSLMPRTL	CAGGAGCCTGATGCCCAGGACCCTCGA
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	5	14	QAAPKSRPR	GGCAGCCCCCAAATCCCGGCCCAGGAG
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	5	16	QAAPKSRPRSL	GGCAGCCCCCAAATCCCGGCCCAGGAGCCTGAT
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	6	16	AAPKSRPRSL	AGCCCCCAAATCCCGGCCCAGGAGCCTGAT
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	7	16	APKSRPRSL	CCCCAAATCCCGGCCCAGGAGCCTGAT
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	7	17	APKSRPRSLM	CCCCAAATCCCGGCCCAGGAGCCTGATGCC
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	8	16	PKSRPRSL	CAAATCCCGGCCCAGGAGCCTGAT
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	9	18	KSRPRSLMP	ATCCCGGCCCAGGAGCCTGATGCCCAG
VOPP1-HS3ST2	chr7	55559974	chr16	22926264	9	19	KSRPRSLMPR	ATCCCGGCCCAGGAGCCTGATGCCCAGGAC

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

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Information of the samples that have these potential fusion neoantigens of VOPP1-HS3ST2

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
LUSC	VOPP1-HS3ST2	chr7	55559974	ENST00000285279	chr16	22926264	ENST00000261374	TCGA-85-7843

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Potential target of CAR-T therapy development for VOPP1-HS3ST2

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

VOPP1

chr7:55559974

chr16:22926264

ENST00000285279

61_81

109

173.0

Transmembrane

Helical

Hgene

VOPP1

chr7:55559974

chr16:22926264

ENST00000433959

61_81

100

164.0

Transmembrane

Helical

Hgene

VOPP1

chr7:55559974

chr16:22926264

ENST00000545390

61_81

106

170.0

Transmembrane

Helical

Hgene

VOPP1

chr7:55559975

chr16:22926265

ENST00000285279

61_81

109

173.0

Transmembrane

Helical

Hgene

VOPP1

chr7:55559975

chr16:22926265

ENST00000433959

61_81

100

164.0

Transmembrane

Helical

Hgene

VOPP1

chr7:55559975

chr16:22926265

ENST00000545390

61_81

106

170.0

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 VOPP1-HS3ST2

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 VOPP1-HS3ST2

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)