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Fusion Protein:SPTBN1-RTN4

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: SPTBN1-RTN4
	FusionPDB ID: 86137
	FusionGDB2.0 ID: 86137
		Hgene	Tgene
	Gene symbol	SPTBN1	RTN4
	Gene ID	6711	57142
	Gene name	spectrin beta, non-erythrocytic 1	reticulon 4
	Synonyms	ELF\|HEL102\|SPTB2\|betaSpII	ASY\|NI220/250\|NOGO\|NSP\|NSP-CL\|Nbla00271\|Nbla10545\|RTN-X\|RTN4-A\|RTN4-B1\|RTN4-B2\|RTN4-C
	Cytomap	2p16.2	2p16.1
	Type of gene	protein-coding	protein-coding
	Description	spectrin beta chain, non-erythrocytic 1beta-G spectrinbeta-II spectrinbeta-fodrinbeta-spectrin 2beta-spectrin IIbeta-spectrin non-erythrocytic 1embryonic liver beta-fodrinepididymis luminal protein 102fodrin beta chainspectrin beta chain, brain	reticulon-4Human NogoAMy043 proteinfoocenneurite growth inhibitor 220neurite outgrowth inhibitorneuroendocrine-specific protein C homologreticulon 5
	Modification date	20200329	20200327
	UniProtAcc	.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000356805, ENST00000333896,	ENST00000354474, ENST00000402434, ENST00000486085, ENST00000317610, ENST00000337526, ENST00000357376, ENST00000357732, ENST00000394609, ENST00000394611, ENST00000404909, ENST00000405240,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	24 X 20 X 9=4320	27 X 28 X 9=6804
	# samples	26	35
	** MAII score	log2(26/4320*10)=-4.05444778402238 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(35/6804*10)=-4.28095631383106 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: SPTBN1 [Title/Abstract] AND RTN4 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: SPTBN1 [Title/Abstract] AND RTN4 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	SPTBN1(54753703)-RTN4(55214834), # samples:1
Anticipated loss of major functional domain due to fusion event.	SPTBN1-RTN4 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. SPTBN1-RTN4 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. SPTBN1-RTN4 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. SPTBN1-RTN4 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
Tgene	RTN4	GO:0030517	negative regulation of axon extension	10667797
Tgene	RTN4	GO:0071787	endoplasmic reticulum tubular network formation	24262037\|25612671
Tgene	RTN4	GO:1905552	positive regulation of protein localization to endoplasmic reticulum	27353365

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr2:54753703/chr2:55214834)
- 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 SPTBN1 (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 RTN4 (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)
ENST00000356805	SPTBN1	chr2	54753703	+	ENST00000394609	RTN4	chr2	55214834	-	1962	429	266	994	242
ENST00000356805	SPTBN1	chr2	54753703	+	ENST00000405240	RTN4	chr2	55214834	-	1962	429	266	994	242
ENST00000356805	SPTBN1	chr2	54753703	+	ENST00000357376	RTN4	chr2	55214834	-	1962	429	266	994	242
ENST00000356805	SPTBN1	chr2	54753703	+	ENST00000317610	RTN4	chr2	55214834	-	1962	429	266	994	242
ENST00000356805	SPTBN1	chr2	54753703	+	ENST00000357732	RTN4	chr2	55214834	-	1962	429	266	994	242
ENST00000356805	SPTBN1	chr2	54753703	+	ENST00000337526	RTN4	chr2	55214834	-	1962	429	266	994	242
ENST00000356805	SPTBN1	chr2	54753703	+	ENST00000394611	RTN4	chr2	55214834	-	1962	429	266	994	242
ENST00000356805	SPTBN1	chr2	54753703	+	ENST00000404909	RTN4	chr2	55214834	-	1962	429	266	994	242

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
ENST00000356805	ENST00000394609	SPTBN1	chr2	54753703	+	RTN4	chr2	55214834	-	0.000837854	0.9991622
ENST00000356805	ENST00000405240	SPTBN1	chr2	54753703	+	RTN4	chr2	55214834	-	0.000837854	0.9991622
ENST00000356805	ENST00000357376	SPTBN1	chr2	54753703	+	RTN4	chr2	55214834	-	0.000837854	0.9991622
ENST00000356805	ENST00000317610	SPTBN1	chr2	54753703	+	RTN4	chr2	55214834	-	0.000837854	0.9991622
ENST00000356805	ENST00000357732	SPTBN1	chr2	54753703	+	RTN4	chr2	55214834	-	0.000837854	0.9991622
ENST00000356805	ENST00000337526	SPTBN1	chr2	54753703	+	RTN4	chr2	55214834	-	0.000837854	0.9991622
ENST00000356805	ENST00000394611	SPTBN1	chr2	54753703	+	RTN4	chr2	55214834	-	0.000837854	0.9991622
ENST00000356805	ENST00000404909	SPTBN1	chr2	54753703	+	RTN4	chr2	55214834	-	0.000837854	0.9991622

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 SPTBN1-RTN4

+/-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
SPTBN1	chr2	54753703	RTN4	chr2	55214834	429	54	ARLFERSRIKALAVVDLLYWRDIKKT

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Potential FusionNeoAntigen Information of SPTBN1-RTN4 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.

SPTBN1-RTN4_54753703_55214834.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)
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-B39:06	SRIKALAV	0.9995	0.6027	6	14
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-B14:02	SRIKALAV	0.9991	0.5988	6	14
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-B14:01	SRIKALAV	0.9991	0.5988	6	14
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-B58:01	LAVVDLLYW	0.9988	0.9792	11	20
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-B39:06	SRIKALAVV	0.9986	0.6411	6	15
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-B57:01	LAVVDLLYW	0.9986	0.9882	11	20
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-A30:08	RSRIKALAV	0.9983	0.825	5	14
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-B14:01	SRIKALAVV	0.9974	0.7375	6	15
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-B14:02	SRIKALAVV	0.9974	0.7375	6	15
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-B58:02	LAVVDLLYW	0.9969	0.9745	11	20
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-B15:17	LAVVDLLYW	0.9943	0.9882	11	20
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-B15:16	LAVVDLLYW	0.9926	0.9224	11	20
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-A31:06	AVVDLLYWR	0.9898	0.5271	12	21
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-B15:01	ALAVVDLLY	0.9868	0.6437	10	19
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-B53:01	LAVVDLLYW	0.98	0.626	11	20
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-B57:03	LAVVDLLYW	0.9775	0.996	11	20
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-A74:09	AVVDLLYWR	0.9763	0.6836	12	21
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-A74:11	AVVDLLYWR	0.9763	0.6836	12	21
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-A74:03	AVVDLLYWR	0.9763	0.6836	12	21
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-B57:03	KALAVVDLL	0.9743	0.9442	9	18
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-B15:25	ALAVVDLLY	0.9681	0.8136	10	19
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-A31:02	AVVDLLYWR	0.9032	0.6227	12	21
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-B57:01	ALAVVDLLYW	0.9962	0.9849	10	20
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-B15:17	KALAVVDLLY	0.9945	0.7795	9	19
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-B58:01	KALAVVDLLY	0.993	0.7327	9	19
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-B58:01	ALAVVDLLYW	0.9903	0.9757	10	20
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-B57:01	KALAVVDLLYW	0.9994	0.9835	9	20
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-B58:01	KALAVVDLLYW	0.9993	0.974	9	20
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-B58:02	KALAVVDLLYW	0.9991	0.9631	9	20
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-B57:03	KALAVVDLLYW	0.9945	0.991	9	20
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-B39:12	SRIKALAV	0.9984	0.6995	6	14
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-B27:14	SRIKALAVV	0.9998	0.5957	6	15
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-B73:01	SRIKALAVV	0.9974	0.7846	6	15
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-B39:12	SRIKALAVV	0.9947	0.6483	6	15
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-C15:06	RSRIKALAV	0.9928	0.8615	5	14
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-C07:05	SRIKALAVV	0.9926	0.907	6	15
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-A31:01	AVVDLLYWR	0.9806	0.5905	12	21
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-B15:05	ALAVVDLLY	0.8582	0.6337	10	19
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-B15:31	ALAVVDLLY	0.7837	0.6561	10	19
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-C12:16	SRIKALAVV	0.0299	0.9295	6	15
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-B27:10	SRIKALAVV	0.9998	0.6572	6	15
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-B27:09	SRIKALAVV	0.9998	0.6619	6	15
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-B57:10	LAVVDLLYW	0.9986	0.9882	11	20
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-A30:01	RSRIKALAV	0.9984	0.9348	5	14
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-B57:04	LAVVDLLYW	0.998	0.9252	11	20
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-C15:02	RSRIKALAV	0.996	0.8613	5	14
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-B39:31	SRIKALAVV	0.9954	0.637	6	15
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-B58:06	LAVVDLLYW	0.9922	0.9725	11	20
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-B15:50	ALAVVDLLY	0.9895	0.8044	10	19
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-B57:02	LAVVDLLYW	0.9888	0.9828	11	20
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-C07:01	SRIKALAVV	0.9882	0.5567	6	15
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-B15:27	ALAVVDLLY	0.9878	0.7172	10	19
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-B15:34	ALAVVDLLY	0.9868	0.6437	10	19
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-B15:33	ALAVVDLLY	0.9868	0.6437	10	19
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-B15:125	ALAVVDLLY	0.9868	0.6437	10	19
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-B15:12	ALAVVDLLY	0.9858	0.6794	10	19
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-B15:135	ALAVVDLLY	0.9847	0.6505	10	19
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-B15:13	LAVVDLLYW	0.9799	0.9778	11	20
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-A74:01	AVVDLLYWR	0.9763	0.6836	12	21
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-B15:39	ALAVVDLLY	0.9666	0.6274	10	19
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-B53:02	LAVVDLLYW	0.9593	0.6331	11	20
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-C06:08	SRIKALAVV	0.9378	0.9772	6	15
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-B15:35	ALAVVDLLY	0.9377	0.5552	10	19
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-B15:20	ALAVVDLLY	0.8737	0.7696	10	19
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-B35:28	ALAVVDLLY	0.8155	0.7722	10	19
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-C07:22	SRIKALAVV	0.7726	0.5398	6	15
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-C17:01	KALAVVDLL	0.7281	0.8426	9	18
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-B35:13	KALAVVDLL	0.6378	0.8142	9	18
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-C06:02	SRIKALAVV	0.1972	0.9851	6	15
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-C06:17	SRIKALAVV	0.1972	0.9851	6	15
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-B57:04	ALAVVDLLYW	0.997	0.9372	10	20
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-B57:10	ALAVVDLLYW	0.9962	0.9849	10	20
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-B57:10	KALAVVDLLYW	0.9994	0.9835	9	20
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-B58:06	KALAVVDLLYW	0.9993	0.9563	9	20
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-B57:04	KALAVVDLLYW	0.9987	0.9332	9	20
SPTBN1-RTN4	chr2	54753703	chr2	55214834	429	HLA-B57:02	KALAVVDLLYW	0.9842	0.9846	9	20

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Potential FusionNeoAntigen Information of SPTBN1-RTN4 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 SPTBN1-RTN4

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
8955	SRIKALAVVDLLYW	SPTBN1	RTN4	chr2	54753703	chr2	55214834	429

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of SPTBN1-RTN4

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	8955	SRIKALAVVDLLYW	-7.47338	-7.58678
HLA-B14:02	3BVN	8955	SRIKALAVVDLLYW	-4.02131	-5.05661
HLA-B52:01	3W39	8955	SRIKALAVVDLLYW	-6.09305	-6.20645
HLA-B52:01	3W39	8955	SRIKALAVVDLLYW	-5.89116	-6.92646
HLA-B18:01	4JQV	8955	SRIKALAVVDLLYW	-2.29971	-3.33501
HLA-A11:01	4UQ2	8955	SRIKALAVVDLLYW	-9.02997	-9.14337
HLA-A24:02	5HGA	8955	SRIKALAVVDLLYW	-7.5857	-7.6991
HLA-A24:02	5HGA	8955	SRIKALAVVDLLYW	-7.19093	-8.22623
HLA-B27:05	6PYJ	8955	SRIKALAVVDLLYW	-6.48577	-7.52107
HLA-B27:05	6PYJ	8955	SRIKALAVVDLLYW	-3.80826	-3.92166
HLA-B44:05	3DX8	8955	SRIKALAVVDLLYW	-4.50666	-4.62006
HLA-B44:05	3DX8	8955	SRIKALAVVDLLYW	-3.72245	-4.75775

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Vaccine Design for the FusionNeoAntigens of SPTBN1-RTN4

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
SPTBN1-RTN4	chr2	54753703	chr2	55214834	10	19	ALAVVDLLY	CTCTGGCAGTTGTTGACCTCCTGTACT
SPTBN1-RTN4	chr2	54753703	chr2	55214834	10	20	ALAVVDLLYW	CTCTGGCAGTTGTTGACCTCCTGTACTGGA
SPTBN1-RTN4	chr2	54753703	chr2	55214834	11	20	LAVVDLLYW	TGGCAGTTGTTGACCTCCTGTACTGGA
SPTBN1-RTN4	chr2	54753703	chr2	55214834	12	21	AVVDLLYWR	CAGTTGTTGACCTCCTGTACTGGAGAG
SPTBN1-RTN4	chr2	54753703	chr2	55214834	5	14	RSRIKALAV	GGTCCCGCATCAAGGCTCTGGCAGTTG
SPTBN1-RTN4	chr2	54753703	chr2	55214834	6	14	SRIKALAV	CCCGCATCAAGGCTCTGGCAGTTG
SPTBN1-RTN4	chr2	54753703	chr2	55214834	6	15	SRIKALAVV	CCCGCATCAAGGCTCTGGCAGTTGTTG
SPTBN1-RTN4	chr2	54753703	chr2	55214834	9	18	KALAVVDLL	AGGCTCTGGCAGTTGTTGACCTCCTGT
SPTBN1-RTN4	chr2	54753703	chr2	55214834	9	19	KALAVVDLLY	AGGCTCTGGCAGTTGTTGACCTCCTGTACT
SPTBN1-RTN4	chr2	54753703	chr2	55214834	9	20	KALAVVDLLYW	AGGCTCTGGCAGTTGTTGACCTCCTGTACTGGA

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 SPTBN1-RTN4

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
MESO	SPTBN1-RTN4	chr2	54753703	ENST00000356805	chr2	55214834	ENST00000317610	TCGA-MQ-A4LP

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Potential target of CAR-T therapy development for SPTBN1-RTN4

Predicted 3D structure. We used RoseTTAFold.

475_SPTBN1-RTN4_24561_pred.pdb

Retention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, to provide the retention of the transmembrane domain, we only show the protein feature retention information of those transmembrane features

* Minus value of BPloci means that the break point is located before the CDS.

- In-frame and retained 'Transmembrane'.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

Tgene

RTN4

chr2:54753703

chr2:55214834

ENST00000317610

1019_1039

374.0

Transmembrane

Helical

Tgene

RTN4

chr2:54753703

chr2:55214834

ENST00000317610

1134_1154

374.0

Transmembrane

Helical

Tgene

RTN4

chr2:54753703

chr2:55214834

ENST00000337526

1019_1039

1193.0

Transmembrane

Helical

Tgene

RTN4

chr2:54753703

chr2:55214834

ENST00000337526

1134_1154

1193.0

Transmembrane

Helical

Tgene

RTN4

chr2:54753703

chr2:55214834

ENST00000357376

1019_1039

987.0

Transmembrane

Helical

Tgene

RTN4

chr2:54753703

chr2:55214834

ENST00000357376

1134_1154

987.0

Transmembrane

Helical

Tgene

RTN4

chr2:54753703

chr2:55214834

ENST00000357732

1019_1039

393.0

Transmembrane

Helical

Tgene

RTN4

chr2:54753703

chr2:55214834

ENST00000357732

1134_1154

393.0

Transmembrane

Helical

Tgene

RTN4

chr2:54753703

chr2:55214834

ENST00000394609

1019_1039

200.0

Transmembrane

Helical

Tgene

RTN4

chr2:54753703

chr2:55214834

ENST00000394609

1134_1154

200.0

Transmembrane

Helical

Tgene

RTN4

chr2:54753703

chr2:55214834

ENST00000394611

1019_1039

987.0

Transmembrane

Helical

Tgene

RTN4

chr2:54753703

chr2:55214834

ENST00000394611

1134_1154

987.0

Transmembrane

Helical

Tgene

RTN4

chr2:54753703

chr2:55214834

ENST00000404909

1019_1039

987.0

Transmembrane

Helical

Tgene

RTN4

chr2:54753703

chr2:55214834

ENST00000404909

1134_1154

987.0

Transmembrane

Helical

Tgene

RTN4

chr2:54753703

chr2:55214834

ENST00000405240

1019_1039

987.0

Transmembrane

Helical

Tgene

RTN4

chr2:54753703

chr2:55214834

ENST00000405240

1134_1154

987.0

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
SPTBN1	chr2	54753703	ENST00000356805	RTN4	chr2	55214834	ENST00000317610

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Related Drugs to SPTBN1-RTN4

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 SPTBN1-RTN4

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)