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Fusion Protein:GORASP2-GAD1

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: GORASP2-GAD1
	FusionPDB ID: 34020
	FusionGDB2.0 ID: 34020
		Hgene	Tgene
	Gene symbol	GORASP2	GAD1
	Gene ID	26003	2571
	Gene name	golgi reassembly stacking protein 2	glutamate decarboxylase 1
	Synonyms	GOLPH6\|GRASP55\|GRS2\|p59	CPSQ1\|GAD\|SCP
	Cytomap	2q31.1	2q31.1
	Type of gene	protein-coding	protein-coding
	Description	Golgi reassembly-stacking protein 2golgi phosphoprotein 6golgi reassembly stacking protein 2, 55kDa	glutamate decarboxylase 167 kDa glutamic acid decarboxylaseGAD-67glutamate decarboxylase 1 (brain, 67kDa)glutamate decarboxylase 67 kDa isoform
	Modification date	20200327	20200315
	UniProtAcc	Q9H8Y8 Main function of 5'-partner protein: FUNCTION: Plays a role in the assembly and membrane stacking of the Golgi cisternae, and in the process by which Golgi stacks reform after breakdown during mitosis and meiosis (PubMed:10487747, PubMed:21515684, PubMed:22523075). May regulate the intracellular transport and presentation of a defined set of transmembrane proteins, such as transmembrane TGFA (PubMed:11101516). Required for normal acrosome formation during spermiogenesis and normal male fertility, probably by promoting colocalization of JAM2 and JAM3 at contact sites between germ cells and Sertoli cells (By similarity). Mediates ER stress-induced unconventional (ER/Golgi-independent) trafficking of core-glycosylated CFTR to cell membrane (PubMed:21884936, PubMed:27062250, PubMed:28067262). {ECO:0000250\|UniProtKB:Q99JX3, ECO:0000269\|PubMed:10487747, ECO:0000269\|PubMed:11101516, ECO:0000269\|PubMed:21515684, ECO:0000269\|PubMed:21884936, ECO:0000269\|PubMed:22523075, ECO:0000269\|PubMed:27062250, ECO:0000269\|PubMed:28067262}.	Q99259 Main function of 5'-partner protein: FUNCTION: Catalyzes the production of GABA.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000493692, ENST00000234160, ENST00000452526,	ENST00000358196, ENST00000344257, ENST00000375272, ENST00000429023,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	8 X 5 X 5=200	3 X 4 X 3=36
	# samples	9	3
	** MAII score	log2(9/200*10)=-1.15200309344505 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(3/36*10)=-0.263034405833794 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: GORASP2 [Title/Abstract] AND GAD1 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: GORASP2 [Title/Abstract] AND GAD1 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	GORASP2(171804940)-GAD1(171704186), # samples:2
Anticipated loss of major functional domain due to fusion event.	GORASP2-GAD1 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. GORASP2-GAD1 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. GORASP2-GAD1 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. GORASP2-GAD1 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	GORASP2	GO:0034976	response to endoplasmic reticulum stress	21884936\|27062250\|28067262
Hgene	GORASP2	GO:0061951	establishment of protein localization to plasma membrane	28067262

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr2:171804940/chr2:171704186)
- 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 GORASP2 (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 GAD1 (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)

ENST00000234160

GORASP2

chr2

171804940

ENST00000358196

GAD1

chr2

171704186

3011

959

518

1741

407

ENST00000452526

GORASP2

chr2

171804940

ENST00000358196

GAD1

chr2

171704186

2320

268

1050

320

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
ENST00000234160	ENST00000358196	GORASP2	chr2	171804940	+	GAD1	chr2	171704186	+	0.001951823	0.9980482
ENST00000452526	ENST00000358196	GORASP2	chr2	171804940	+	GAD1	chr2	171704186	+	0.000329428	0.9996706

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 GORASP2-GAD1

+/-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
GORASP2	chr2	171804940	GAD1	chr2	171704186	268	60	FFDFIVSINGSRLGYVPFYVNATAGT
GORASP2	chr2	171804940	GAD1	chr2	171704186	959	147	FFDFIVSINGSRLGYVPFYVNATAGT

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Potential FusionNeoAntigen Information of GORASP2-GAD1 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.

GORASP2-GAD1_171804940_171704186.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)
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-B27:02	SRLGYVPFY	0.9996	0.6704	10	19
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-B27:05	SRLGYVPFY	0.9996	0.9158	10	19
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-B27:04	SRLGYVPFY	0.9995	0.7376	10	19
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-B15:01	SINGSRLGY	0.9982	0.7861	6	15
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-B15:25	SINGSRLGY	0.998	0.7668	6	15
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-A02:22	RLGYVPFYV	0.9938	0.5586	11	20
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-A02:11	RLGYVPFYV	0.9937	0.6718	11	20
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-A02:21	RLGYVPFYV	0.9935	0.7506	11	20
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-A02:60	RLGYVPFYV	0.9935	0.6131	11	20
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-A02:67	RLGYVPFYV	0.9934	0.6573	11	20
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-A02:30	RLGYVPFYV	0.9934	0.6573	11	20
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-A02:24	RLGYVPFYV	0.9934	0.6573	11	20
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-A02:16	RLGYVPFYV	0.993	0.5948	11	20
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-B15:02	SINGSRLGY	0.9922	0.7764	6	15
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-A02:13	RLGYVPFYV	0.9914	0.7272	11	20
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-A02:27	RLGYVPFYV	0.9906	0.5994	11	20
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-A02:04	RLGYVPFYV	0.9858	0.6469	11	20
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-A02:38	RLGYVPFYV	0.9845	0.7279	11	20
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-A02:17	RLGYVPFYV	0.9787	0.6029	11	20
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-A02:19	RLGYVPFYV	0.9749	0.5057	11	20
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-A02:29	RLGYVPFYV	0.9675	0.6615	11	20
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-A02:20	RLGYVPFYV	0.9611	0.6585	11	20
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-A02:35	RLGYVPFYV	0.9529	0.7002	11	20
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-B47:01	SRLGYVPFY	0.6118	0.6765	10	19
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-B15:03	SRLGYVPFY	0.3451	0.8712	10	19
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-B15:18	SRLGYVPFY	0.3355	0.8291	10	19
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-B13:02	RLGYVPFYV	0.1299	0.7607	11	20
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-B27:02	SRLGYVPFYV	0.9998	0.7576	10	20
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-B15:17	VSINGSRLGY	0.9986	0.6447	5	15
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-B27:05	GSRLGYVPFY	0.9852	0.9328	9	19
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-B27:04	GSRLGYVPFY	0.9768	0.8017	9	19
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-B27:02	GSRLGYVPFY	0.9765	0.7828	9	19
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-B27:14	SRLGYVPFY	0.9981	0.7953	10	19
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-C07:95	SRLGYVPFY	0.9964	0.7507	10	19
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-B27:03	SRLGYVPFY	0.9961	0.9263	10	19
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-A02:07	RLGYVPFYV	0.9936	0.7147	11	20
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-A02:01	RLGYVPFYV	0.9934	0.6573	11	20
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-C07:05	SRLGYVPFY	0.9912	0.9532	10	19
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-B15:21	SINGSRLGY	0.9912	0.7311	6	15
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-C07:27	SRLGYVPFY	0.991	0.9679	10	19
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-C07:46	SRLGYVPFY	0.9561	0.9228	10	19
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-C07:19	SRLGYVPFY	0.955	0.8175	10	19
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-C07:67	SRLGYVPFY	0.8921	0.9646	10	19
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-C07:80	SRLGYVPFY	0.8921	0.9646	10	19
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-B15:31	SINGSRLGY	0.8852	0.6519	6	15
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-B15:04	SINGSRLGY	0.8787	0.8001	6	15
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-C07:10	SRLGYVPFY	0.8685	0.9673	10	19
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-C15:04	SINGSRLGY	0.5455	0.8103	6	15
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-C12:16	SRLGYVPFY	0.0318	0.9429	10	19
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-B27:14	SRLGYVPFYV	0.9998	0.8291	10	20
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-C15:04	VSINGSRLGY	0.9914	0.8503	5	15
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-B27:03	SRLGYVPFYV	0.9867	0.9425	10	20
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-B27:14	GSRLGYVPFY	0.9735	0.8474	9	19
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-B27:03	GSRLGYVPFY	0.8102	0.9382	9	19
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-B27:08	SRLGYVPFY	0.9996	0.8239	10	19
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-B27:10	SRLGYVPFY	0.9994	0.8611	10	19
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-B15:50	SINGSRLGY	0.9984	0.8236	6	15
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-B15:125	SINGSRLGY	0.9982	0.7861	6	15
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-B15:33	SINGSRLGY	0.9982	0.7861	6	15
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-B15:27	SINGSRLGY	0.9982	0.7879	6	15
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-B15:34	SINGSRLGY	0.9982	0.7861	6	15
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-B15:135	SINGSRLGY	0.9981	0.793	6	15
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-B15:39	SINGSRLGY	0.9978	0.6058	6	15
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-C07:01	SRLGYVPFY	0.9974	0.7373	10	19
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-B27:06	SRLGYVPFY	0.9964	0.7209	10	19
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-B15:12	SINGSRLGY	0.9961	0.7344	6	15
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-A02:03	RLGYVPFYV	0.9959	0.7081	11	20
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-B15:11	SINGSRLGY	0.9957	0.6847	6	15
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-B15:08	SINGSRLGY	0.9945	0.6842	6	15
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-B15:35	SINGSRLGY	0.9942	0.7523	6	15
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-A02:14	RLGYVPFYV	0.9935	0.6747	11	20
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-A02:06	RLGYVPFYV	0.9935	0.7506	11	20
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-B27:09	SRLGYVPFY	0.9791	0.8741	10	19
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-C07:17	SRLGYVPFY	0.9791	0.9642	10	19
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-C07:02	SRLGYVPFY	0.8921	0.9646	10	19
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-C07:22	SRLGYVPFY	0.8127	0.6931	10	19
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-C06:08	SRLGYVPFY	0.5749	0.9885	10	19
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-C15:09	SINGSRLGY	0.5455	0.8103	6	15
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-C06:06	SRLGYVPFY	0.0641	0.9831	10	19
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-B15:68	SRLGYVPFY	0.0107	0.731	10	19
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-C06:02	SRLGYVPFY	0.0056	0.9923	10	19
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-C06:17	SRLGYVPFY	0.0056	0.9923	10	19
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-B27:08	SRLGYVPFYV	0.9997	0.876	10	20
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-B27:09	SRLGYVPFYV	0.9996	0.9161	10	20
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-B58:06	VSINGSRLGY	0.9973	0.533	5	15
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-C15:09	VSINGSRLGY	0.9914	0.8503	5	15
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-B27:10	GSRLGYVPFY	0.9803	0.8993	9	19
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	HLA-B27:08	GSRLGYVPFY	0.9783	0.8681	9	19

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Potential FusionNeoAntigen Information of GORASP2-GAD1 in HLA II

GORASP2-GAD1_171804940_171704186.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)
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	DRB1-0102	FDFIVSINGSRLGYV	1	16
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	DRB1-0102	FFDFIVSINGSRLGY	0	15
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	DRB1-0431	RLGYVPFYVNATAGT	11	26
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	DRB1-0475	RLGYVPFYVNATAGT	11	26
GORASP2-GAD1	chr2	171804940	chr2	171704186	959	DRB1-1515	RLGYVPFYVNATAGT	11	26

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Fusion breakpoint peptide structures of GORASP2-GAD1

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
8660	SINGSRLGYVPFYV	GORASP2	GAD1	chr2	171804940	chr2	171704186	959

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of GORASP2-GAD1

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	8660	SINGSRLGYVPFYV	-7.15543	-7.26883
HLA-B14:02	3BVN	8660	SINGSRLGYVPFYV	-4.77435	-5.80965
HLA-B52:01	3W39	8660	SINGSRLGYVPFYV	-6.80875	-6.92215
HLA-B52:01	3W39	8660	SINGSRLGYVPFYV	-4.20386	-5.23916
HLA-A11:01	4UQ2	8660	SINGSRLGYVPFYV	-7.5194	-8.5547
HLA-A11:01	4UQ2	8660	SINGSRLGYVPFYV	-6.9601	-7.0735
HLA-A24:02	5HGA	8660	SINGSRLGYVPFYV	-7.52403	-7.63743
HLA-A24:02	5HGA	8660	SINGSRLGYVPFYV	-5.82433	-6.85963
HLA-B27:05	6PYJ	8660	SINGSRLGYVPFYV	-3.28285	-4.31815
HLA-B44:05	3DX8	8660	SINGSRLGYVPFYV	-5.91172	-6.94702
HLA-B44:05	3DX8	8660	SINGSRLGYVPFYV	-4.24346	-4.35686

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Vaccine Design for the FusionNeoAntigens of GORASP2-GAD1

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
GORASP2-GAD1	chr2	171804940	chr2	171704186	10	19	SRLGYVPFY	TCAAGATTAGGATATGTTCCCTTTTAT
GORASP2-GAD1	chr2	171804940	chr2	171704186	10	20	SRLGYVPFYV	TCAAGATTAGGATATGTTCCCTTTTATGTC
GORASP2-GAD1	chr2	171804940	chr2	171704186	11	20	RLGYVPFYV	AGATTAGGATATGTTCCCTTTTATGTC
GORASP2-GAD1	chr2	171804940	chr2	171704186	5	15	VSINGSRLGY	GTTTCTATTAATGGTTCAAGATTAGGATAT
GORASP2-GAD1	chr2	171804940	chr2	171704186	6	15	SINGSRLGY	TCTATTAATGGTTCAAGATTAGGATAT
GORASP2-GAD1	chr2	171804940	chr2	171704186	9	19	GSRLGYVPFY	GGTTCAAGATTAGGATATGTTCCCTTTTAT

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
GORASP2-GAD1	chr2	171804940	chr2	171704186	0	15	FFDFIVSINGSRLGY	TTCTTTGATTTTATTGTTTCTATTAATGGTTCAAGATTAGGATAT
GORASP2-GAD1	chr2	171804940	chr2	171704186	1	16	FDFIVSINGSRLGYV	TTTGATTTTATTGTTTCTATTAATGGTTCAAGATTAGGATATGTT
GORASP2-GAD1	chr2	171804940	chr2	171704186	11	26	RLGYVPFYVNATAGT	AGATTAGGATATGTTCCCTTTTATGTCAATGCAACTGCTGGCACG

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Information of the samples that have these potential fusion neoantigens of GORASP2-GAD1

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
OV	GORASP2-GAD1	chr2	171804940	ENST00000234160	chr2	171704186	ENST00000358196	TCGA-61-2009-01A

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Potential target of CAR-T therapy development for GORASP2-GAD1

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 GORASP2-GAD1

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 GORASP2-GAD1

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)