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Fusion Protein:ACYP2-RTN4

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: ACYP2-RTN4
	FusionPDB ID: 1924
	FusionGDB2.0 ID: 1924
		Hgene	Tgene
	Gene symbol	ACYP2	RTN4
	Gene ID	98	57142
	Gene name	acylphosphatase 2	reticulon 4
	Synonyms	ACYM\|ACYP	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	acylphosphatase-2acylphosphatase 2, muscle typeacylphosphatase, muscle type isozymeacylphosphate phosphohydrolase 2testicular tissue protein Li 11	reticulon-4Human NogoAMy043 proteinfoocenneurite growth inhibitor 220neurite outgrowth inhibitorneuroendocrine-specific protein C homologreticulon 5
	Modification date	20200313	20200327
	UniProtAcc	P14621 Main function of 5'-partner protein: FUNCTION: Its physiological role is not yet clear.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000303536, ENST00000394666, ENST00000406041, ENST00000422521, ENST00000458030, ENST00000606082, ENST00000606865, ENST00000607452,	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	9 X 8 X 6=432	27 X 28 X 9=6804
	# samples	9	35
	** MAII score	log2(9/432*10)=-2.26303440583379 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: ACYP2 [Title/Abstract] AND RTN4 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: ACYP2 [Title/Abstract] AND RTN4 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	ACYP2(54342893)-RTN4(55214834), # samples:1
Anticipated loss of major functional domain due to fusion event.	ACYP2-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. ACYP2-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. ACYP2-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. ACYP2-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/chr2:54342893/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 ACYP2 (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)
ENST00000303536	ACYP2	chr2	54342893	+	ENST00000394609	RTN4	chr2	55214834	-	1786	253	111	818	235
ENST00000303536	ACYP2	chr2	54342893	+	ENST00000405240	RTN4	chr2	55214834	-	1786	253	111	818	235
ENST00000303536	ACYP2	chr2	54342893	+	ENST00000357376	RTN4	chr2	55214834	-	1786	253	111	818	235
ENST00000303536	ACYP2	chr2	54342893	+	ENST00000317610	RTN4	chr2	55214834	-	1786	253	111	818	235
ENST00000303536	ACYP2	chr2	54342893	+	ENST00000357732	RTN4	chr2	55214834	-	1786	253	111	818	235
ENST00000303536	ACYP2	chr2	54342893	+	ENST00000337526	RTN4	chr2	55214834	-	1786	253	111	818	235
ENST00000303536	ACYP2	chr2	54342893	+	ENST00000394611	RTN4	chr2	55214834	-	1786	253	111	818	235
ENST00000303536	ACYP2	chr2	54342893	+	ENST00000404909	RTN4	chr2	55214834	-	1786	253	111	818	235
ENST00000394666	ACYP2	chr2	54342893	+	ENST00000394609	RTN4	chr2	55214834	-	1786	253	111	818	235
ENST00000394666	ACYP2	chr2	54342893	+	ENST00000405240	RTN4	chr2	55214834	-	1786	253	111	818	235
ENST00000394666	ACYP2	chr2	54342893	+	ENST00000357376	RTN4	chr2	55214834	-	1786	253	111	818	235
ENST00000394666	ACYP2	chr2	54342893	+	ENST00000317610	RTN4	chr2	55214834	-	1786	253	111	818	235
ENST00000394666	ACYP2	chr2	54342893	+	ENST00000357732	RTN4	chr2	55214834	-	1786	253	111	818	235
ENST00000394666	ACYP2	chr2	54342893	+	ENST00000337526	RTN4	chr2	55214834	-	1786	253	111	818	235
ENST00000394666	ACYP2	chr2	54342893	+	ENST00000394611	RTN4	chr2	55214834	-	1786	253	111	818	235
ENST00000394666	ACYP2	chr2	54342893	+	ENST00000404909	RTN4	chr2	55214834	-	1786	253	111	818	235
ENST00000406041	ACYP2	chr2	54342893	+	ENST00000394609	RTN4	chr2	55214834	-	1887	354	212	919	235
ENST00000406041	ACYP2	chr2	54342893	+	ENST00000405240	RTN4	chr2	55214834	-	1887	354	212	919	235
ENST00000406041	ACYP2	chr2	54342893	+	ENST00000357376	RTN4	chr2	55214834	-	1887	354	212	919	235
ENST00000406041	ACYP2	chr2	54342893	+	ENST00000317610	RTN4	chr2	55214834	-	1887	354	212	919	235
ENST00000406041	ACYP2	chr2	54342893	+	ENST00000357732	RTN4	chr2	55214834	-	1887	354	212	919	235
ENST00000406041	ACYP2	chr2	54342893	+	ENST00000337526	RTN4	chr2	55214834	-	1887	354	212	919	235
ENST00000406041	ACYP2	chr2	54342893	+	ENST00000394611	RTN4	chr2	55214834	-	1887	354	212	919	235
ENST00000406041	ACYP2	chr2	54342893	+	ENST00000404909	RTN4	chr2	55214834	-	1887	354	212	919	235

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
ENST00000303536	ENST00000394609	ACYP2	chr2	54342893	+	RTN4	chr2	55214834	-	0.000625709	0.99937433
ENST00000303536	ENST00000405240	ACYP2	chr2	54342893	+	RTN4	chr2	55214834	-	0.000625709	0.99937433
ENST00000303536	ENST00000357376	ACYP2	chr2	54342893	+	RTN4	chr2	55214834	-	0.000625709	0.99937433
ENST00000303536	ENST00000317610	ACYP2	chr2	54342893	+	RTN4	chr2	55214834	-	0.000625709	0.99937433
ENST00000303536	ENST00000357732	ACYP2	chr2	54342893	+	RTN4	chr2	55214834	-	0.000625709	0.99937433
ENST00000303536	ENST00000337526	ACYP2	chr2	54342893	+	RTN4	chr2	55214834	-	0.000625709	0.99937433
ENST00000303536	ENST00000394611	ACYP2	chr2	54342893	+	RTN4	chr2	55214834	-	0.000625709	0.99937433
ENST00000303536	ENST00000404909	ACYP2	chr2	54342893	+	RTN4	chr2	55214834	-	0.000625709	0.99937433
ENST00000394666	ENST00000394609	ACYP2	chr2	54342893	+	RTN4	chr2	55214834	-	0.000625709	0.99937433
ENST00000394666	ENST00000405240	ACYP2	chr2	54342893	+	RTN4	chr2	55214834	-	0.000625709	0.99937433
ENST00000394666	ENST00000357376	ACYP2	chr2	54342893	+	RTN4	chr2	55214834	-	0.000625709	0.99937433
ENST00000394666	ENST00000317610	ACYP2	chr2	54342893	+	RTN4	chr2	55214834	-	0.000625709	0.99937433
ENST00000394666	ENST00000357732	ACYP2	chr2	54342893	+	RTN4	chr2	55214834	-	0.000625709	0.99937433
ENST00000394666	ENST00000337526	ACYP2	chr2	54342893	+	RTN4	chr2	55214834	-	0.000625709	0.99937433
ENST00000394666	ENST00000394611	ACYP2	chr2	54342893	+	RTN4	chr2	55214834	-	0.000625709	0.99937433
ENST00000394666	ENST00000404909	ACYP2	chr2	54342893	+	RTN4	chr2	55214834	-	0.000625709	0.99937433
ENST00000406041	ENST00000394609	ACYP2	chr2	54342893	+	RTN4	chr2	55214834	-	0.000668216	0.9993318
ENST00000406041	ENST00000405240	ACYP2	chr2	54342893	+	RTN4	chr2	55214834	-	0.000668216	0.9993318
ENST00000406041	ENST00000357376	ACYP2	chr2	54342893	+	RTN4	chr2	55214834	-	0.000668216	0.9993318
ENST00000406041	ENST00000317610	ACYP2	chr2	54342893	+	RTN4	chr2	55214834	-	0.000668216	0.9993318
ENST00000406041	ENST00000357732	ACYP2	chr2	54342893	+	RTN4	chr2	55214834	-	0.000668216	0.9993318
ENST00000406041	ENST00000337526	ACYP2	chr2	54342893	+	RTN4	chr2	55214834	-	0.000668216	0.9993318
ENST00000406041	ENST00000394611	ACYP2	chr2	54342893	+	RTN4	chr2	55214834	-	0.000668216	0.9993318
ENST00000406041	ENST00000404909	ACYP2	chr2	54342893	+	RTN4	chr2	55214834	-	0.000668216	0.9993318

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 ACYP2-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
ACYP2	chr2	54342893	RTN4	chr2	55214834	253	47	LKSVDYEVFGRVQVVDLLYWRDIKKT
ACYP2	chr2	54342893	RTN4	chr2	55214834	354	47	LKSVDYEVFGRVQVVDLLYWRDIKKT

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Potential FusionNeoAntigen Information of ACYP2-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.

ACYP2-RTN4_54342893_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)
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B58:01	QVVDLLYW	0.9959	0.9727	12	20
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-A66:01	EVFGRVQVV	0.9995	0.7286	6	15
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B27:04	GRVQVVDLL	0.9995	0.6826	9	18
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B27:05	GRVQVVDLL	0.9994	0.7234	9	18
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-A68:06	EVFGRVQVV	0.9986	0.5751	6	15
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-A26:03	EVFGRVQVV	0.9978	0.758	6	15
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B45:01	YEVFGRVQV	0.994	0.7869	5	14
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B50:02	YEVFGRVQV	0.9928	0.5965	5	14
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B15:25	RVQVVDLLY	0.9889	0.8471	10	19
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-A26:02	EVFGRVQVV	0.9878	0.7097	6	15
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B39:01	GRVQVVDLL	0.9831	0.6726	9	18
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B08:09	EVFGRVQVV	0.9822	0.5884	6	15
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-A26:14	EVFGRVQVV	0.9776	0.7707	6	15
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-A26:15	EVFGRVQVV	0.9776	0.7707	6	15
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B14:01	EVFGRVQVV	0.9697	0.9327	6	15
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B14:02	EVFGRVQVV	0.9697	0.9327	6	15
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B15:01	RVQVVDLLY	0.9693	0.574	10	19
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B15:17	RVQVVDLLY	0.9596	0.8095	10	19
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B18:01	YEVFGRVQV	0.9498	0.6998	5	14
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B15:16	RVQVVDLLY	0.9136	0.6788	10	19
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B38:01	GRVQVVDLL	0.9109	0.7695	9	18
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-A34:05	EVFGRVQVV	0.9074	0.658	6	15
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-A34:01	EVFGRVQVV	0.9074	0.658	6	15
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B51:01	EVFGRVQVV	0.903	0.745	6	15
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B58:01	VQVVDLLYW	0.8976	0.9678	11	20
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B38:02	GRVQVVDLL	0.8976	0.7747	9	18
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B52:01	EVFGRVQVV	0.8912	0.9703	6	15
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B57:01	VQVVDLLYW	0.8534	0.9841	11	20
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B41:01	YEVFGRVQV	0.853	0.8291	5	14
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-A32:13	RVQVVDLLY	0.8348	0.6124	10	19
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B50:01	YEVFGRVQV	0.8265	0.839	5	14
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B47:01	YEVFGRVQV	0.7439	0.5753	5	14
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B58:02	VQVVDLLYW	0.7376	0.9627	11	20
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B39:13	YEVFGRVQV	0.5105	0.8978	5	14
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B27:05	GRVQVVDLLY	0.9999	0.6632	9	19
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B27:04	GRVQVVDLLY	0.9999	0.5944	9	19
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B57:01	RVQVVDLLYW	0.9998	0.9851	10	20
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B58:02	RVQVVDLLYW	0.999	0.9668	10	20
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B58:01	RVQVVDLLYW	0.9984	0.9728	10	20
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B57:03	RVQVVDLLYW	0.9928	0.9899	10	20
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-A32:13	RVQVVDLLYW	0.9786	0.9216	10	20
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B40:06	YEVFGRVQV	0.9998	0.5899	5	14
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B27:14	GRVQVVDLL	0.9994	0.6788	9	18
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-C07:05	GRVQVVDLL	0.9914	0.9274	9	18
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B27:03	GRVQVVDLL	0.9861	0.7576	9	18
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B39:12	GRVQVVDLL	0.9841	0.6855	9	18
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-C07:27	GRVQVVDLL	0.9827	0.9102	9	18
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-A26:01	EVFGRVQVV	0.9776	0.7707	6	15
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-C07:13	GRVQVVDLL	0.9754	0.888	9	18
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B78:01	EVFGRVQVV	0.9498	0.8547	6	15
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-C12:04	EVFGRVQVV	0.9266	0.9928	6	15
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-C06:03	EVFGRVQVV	0.9186	0.9934	6	15
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B51:07	EVFGRVQVV	0.9164	0.8994	6	15
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B51:08	EVFGRVQVV	0.9085	0.504	6	15
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B15:05	RVQVVDLLY	0.8739	0.7358	10	19
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-C12:12	EVFGRVQVV	0.813	0.9041	6	15
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-C15:04	RVQVVDLLY	0.7591	0.7833	10	19
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B39:08	YEVFGRVQV	0.6605	0.691	5	14
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B27:14	GRVQVVDLLY	0.9999	0.6105	9	19
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B27:03	GRVQVVDLLY	0.9994	0.7008	9	19
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B40:06	YEVFGRVQVV	0.9991	0.5941	5	15
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B35:28	VQVVDLLY	0.915	0.8238	11	19
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B27:10	GRVQVVDLL	0.9995	0.8312	9	18
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B27:06	GRVQVVDLL	0.9994	0.6609	9	18
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B27:08	GRVQVVDLL	0.9994	0.6057	9	18
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B27:09	GRVQVVDLL	0.999	0.6596	9	18
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-A69:01	EVFGRVQVV	0.9983	0.5555	6	15
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B40:04	YEVFGRVQV	0.998	0.7793	5	14
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-A25:01	EVFGRVQVV	0.9929	0.794	6	15
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B15:39	RVQVVDLLY	0.9895	0.5823	10	19
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B39:31	GRVQVVDLL	0.9821	0.6776	9	18
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B51:21	EVFGRVQVV	0.9702	0.7448	6	15
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B15:135	RVQVVDLLY	0.9694	0.6087	10	19
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B15:33	RVQVVDLLY	0.9693	0.574	10	19
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B15:34	RVQVVDLLY	0.9693	0.574	10	19
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B15:125	RVQVVDLLY	0.9693	0.574	10	19
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B15:27	RVQVVDLLY	0.9691	0.645	10	19
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B15:50	RVQVVDLLY	0.9649	0.6204	10	19
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B18:05	YEVFGRVQV	0.9498	0.6998	5	14
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-A32:01	RVQVVDLLY	0.9464	0.6512	10	19
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B18:08	YEVFGRVQV	0.9459	0.8317	5	14
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B18:06	YEVFGRVQV	0.9438	0.7342	5	14
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B15:24	VQVVDLLYW	0.9413	0.9637	11	20
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B15:35	RVQVVDLLY	0.93	0.608	10	19
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B78:02	EVFGRVQVV	0.9228	0.9104	6	15
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B38:05	GRVQVVDLL	0.9109	0.7695	9	18
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-C06:08	EVFGRVQVV	0.9106	0.9868	6	15
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B18:03	YEVFGRVQV	0.9075	0.6927	5	14
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-C16:04	EVFGRVQVV	0.905	0.9657	6	15
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-C06:08	GRVQVVDLL	0.9036	0.9812	9	18
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-C07:22	GRVQVVDLL	0.8922	0.5236	9	18
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B51:14	EVFGRVQVV	0.8804	0.6214	6	15
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B15:20	RVQVVDLLY	0.8743	0.8378	10	19
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B51:09	EVFGRVQVV	0.8722	0.6151	6	15
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-C06:02	EVFGRVQVV	0.8585	0.9922	6	15
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-C06:17	EVFGRVQVV	0.8585	0.9922	6	15
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B57:10	VQVVDLLYW	0.8534	0.9841	11	20
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B35:28	RVQVVDLLY	0.8517	0.8358	10	19
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B50:04	YEVFGRVQV	0.8265	0.839	5	14
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B50:05	YEVFGRVQV	0.8265	0.839	5	14
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-C15:09	RVQVVDLLY	0.7591	0.7833	10	19
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B18:11	YEVFGRVQV	0.6723	0.6492	5	14
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B15:13	VQVVDLLYW	0.6707	0.9055	11	20
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-C12:03	EVFGRVQVV	0.6579	0.977	6	15
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B39:02	YEVFGRVQV	0.469	0.9029	5	14
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-C06:02	GRVQVVDLL	0.0721	0.9778	9	18
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-C06:17	GRVQVVDLL	0.0721	0.9778	9	18
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B27:08	GRVQVVDLLY	0.9999	0.5086	9	19
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B27:10	GRVQVVDLLY	0.9999	0.7505	9	19
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B57:10	RVQVVDLLYW	0.9998	0.9851	10	20
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B57:04	RVQVVDLLYW	0.9991	0.9019	10	20
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B58:06	RVQVVDLLYW	0.9982	0.958	10	20
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B27:09	GRVQVVDLLY	0.9973	0.581	9	19
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-A32:01	RVQVVDLLYW	0.995	0.9521	10	20
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B57:02	RVQVVDLLYW	0.9841	0.9622	10	20
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	HLA-B15:24	RVQVVDLLYW	0.9225	0.973	10	20

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Potential FusionNeoAntigen Information of ACYP2-RTN4 in HLA II

ACYP2-RTN4_54342893_55214834.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)
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	DRB1-1182	KSVDYEVFGRVQVVD	1	16
ACYP2-RTN4	chr2	54342893	chr2	55214834	253	DRB1-1468	KSVDYEVFGRVQVVD	1	16

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Fusion breakpoint peptide structures of ACYP2-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
2208	EVFGRVQVVDLLYW	ACYP2	RTN4	chr2	54342893	chr2	55214834	253

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of ACYP2-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	2208	EVFGRVQVVDLLYW	-4.27183	-4.27183
HLA-A24:02	5HGA	2208	EVFGRVQVVDLLYW	-5.8734	-5.8734

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Vaccine Design for the FusionNeoAntigens of ACYP2-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
ACYP2-RTN4	chr2	54342893	chr2	55214834	10	19	RVQVVDLLY	GAGTGCAGGTTGTTGACCTCCTGTACT
ACYP2-RTN4	chr2	54342893	chr2	55214834	10	20	RVQVVDLLYW	GAGTGCAGGTTGTTGACCTCCTGTACTGGA
ACYP2-RTN4	chr2	54342893	chr2	55214834	11	19	VQVVDLLY	TGCAGGTTGTTGACCTCCTGTACT
ACYP2-RTN4	chr2	54342893	chr2	55214834	11	20	VQVVDLLYW	TGCAGGTTGTTGACCTCCTGTACTGGA
ACYP2-RTN4	chr2	54342893	chr2	55214834	12	20	QVVDLLYW	AGGTTGTTGACCTCCTGTACTGGA
ACYP2-RTN4	chr2	54342893	chr2	55214834	5	14	YEVFGRVQV	ACGAGGTGTTCGGAAGAGTGCAGGTTG
ACYP2-RTN4	chr2	54342893	chr2	55214834	5	15	YEVFGRVQVV	ACGAGGTGTTCGGAAGAGTGCAGGTTGTTG
ACYP2-RTN4	chr2	54342893	chr2	55214834	6	15	EVFGRVQVV	AGGTGTTCGGAAGAGTGCAGGTTGTTG
ACYP2-RTN4	chr2	54342893	chr2	55214834	9	18	GRVQVVDLL	GAAGAGTGCAGGTTGTTGACCTCCTGT
ACYP2-RTN4	chr2	54342893	chr2	55214834	9	19	GRVQVVDLLY	GAAGAGTGCAGGTTGTTGACCTCCTGTACT

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
ACYP2-RTN4	chr2	54342893	chr2	55214834	1	16	KSVDYEVFGRVQVVD	AATCCGTGGACTACGAGGTGTTCGGAAGAGTGCAGGTTGTTGACC

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Information of the samples that have these potential fusion neoantigens of ACYP2-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
GBM	ACYP2-RTN4	chr2	54342893	ENST00000303536	chr2	55214834	ENST00000317610	TCGA-06-0882-01A

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Potential target of CAR-T therapy development for ACYP2-RTN4

Predicted 3D structure. We used RoseTTAFold.

12_ACYP2-RTN4_91cab_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

chr2:54342893

chr2:55214834

ENST00000317610

1019_1039

374.0

Transmembrane

Helical

Tgene

RTN4

chr2:54342893

chr2:55214834

ENST00000317610

1134_1154

374.0

Transmembrane

Helical

Tgene

RTN4

chr2:54342893

chr2:55214834

ENST00000337526

1019_1039

1193.0

Transmembrane

Helical

Tgene

RTN4

chr2:54342893

chr2:55214834

ENST00000337526

1134_1154

1193.0

Transmembrane

Helical

Tgene

RTN4

chr2:54342893

chr2:55214834

ENST00000357376

1019_1039

987.0

Transmembrane

Helical

Tgene

RTN4

chr2:54342893

chr2:55214834

ENST00000357376

1134_1154

987.0

Transmembrane

Helical

Tgene

RTN4

chr2:54342893

chr2:55214834

ENST00000357732

1019_1039

393.0

Transmembrane

Helical

Tgene

RTN4

chr2:54342893

chr2:55214834

ENST00000357732

1134_1154

393.0

Transmembrane

Helical

Tgene

RTN4

chr2:54342893

chr2:55214834

ENST00000394609

1019_1039

200.0

Transmembrane

Helical

Tgene

RTN4

chr2:54342893

chr2:55214834

ENST00000394609

1134_1154

200.0

Transmembrane

Helical

Tgene

RTN4

chr2:54342893

chr2:55214834

ENST00000394611

1019_1039

987.0

Transmembrane

Helical

Tgene

RTN4

chr2:54342893

chr2:55214834

ENST00000394611

1134_1154

987.0

Transmembrane

Helical

Tgene

RTN4

chr2:54342893

chr2:55214834

ENST00000404909

1019_1039

987.0

Transmembrane

Helical

Tgene

RTN4

chr2:54342893

chr2:55214834

ENST00000404909

1134_1154

987.0

Transmembrane

Helical

Tgene

RTN4

chr2:54342893

chr2:55214834

ENST00000405240

1019_1039

987.0

Transmembrane

Helical

Tgene

RTN4

chr2:54342893

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
ACYP2	chr2	54342893	ENST00000303536	RTN4	chr2	55214834	ENST00000317610

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Related Drugs to ACYP2-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 ACYP2-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)