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Fusion Protein:ARHGEF10-RALYL

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: ARHGEF10-RALYL
	FusionPDB ID: 6191
	FusionGDB2.0 ID: 6191
		Hgene	Tgene
	Gene symbol	ARHGEF10	RALYL
	Gene ID	9639	138046
	Gene name	Rho guanine nucleotide exchange factor 10	RALY RNA binding protein like
	Synonyms	GEF10\|SNCV	HNRPCL3
	Cytomap	8p23.3	8q21.2
	Type of gene	protein-coding	protein-coding
	Description	rho guanine nucleotide exchange factor 10Rho guanine nucleotide exchange factor (GEF) 10	RNA-binding Raly-like proteinheterogeneous nuclear ribonucleoprotein C-like 3hnRNP core protein C-like 3
	Modification date	20200313	20200313
	UniProtAcc	Q9HCE6 Main function of 5'-partner protein: FUNCTION: Acts as guanine nucleotide exchange factor (GEF) for RHOA, RHOB and RHOC. {ECO:0000269\|PubMed:16112081}.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000262112, ENST00000349830, ENST00000398564, ENST00000518288, ENST00000520359, ENST00000398560, ENST00000521927,	ENST00000517638, ENST00000518566, ENST00000521268, ENST00000521376, ENST00000521695, ENST00000522455, ENST00000523850,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	5 X 5 X 5=125	17 X 15 X 10=2550
	# samples	5	20
	** MAII score	log2(5/125*10)=-1.32192809488736 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(20/2550*10)=-3.6724253419715 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: ARHGEF10 [Title/Abstract] AND RALYL [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: ARHGEF10 [Title/Abstract] AND RALYL [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	ARHGEF10(1857636)-RALYL(85686814), # samples:1
Anticipated loss of major functional domain due to fusion event.	ARHGEF10-RALYL 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. ARHGEF10-RALYL 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. ARHGEF10-RALYL 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. ARHGEF10-RALYL 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	ARHGEF10	GO:0090630	activation of GTPase activity	16896804

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr8:1857636/chr8:85686814)
- 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 ARHGEF10 (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 RALYL (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)
ENST00000349830	ARHGEF10	chr8	1857636	-	ENST00000522455	RALYL	chr8	85686814	+	3873	2328	185	2947	920
ENST00000349830	ARHGEF10	chr8	1857636	-	ENST00000521695	RALYL	chr8	85686814	+	3668	2328	185	2947	920
ENST00000349830	ARHGEF10	chr8	1857636	-	ENST00000521268	RALYL	chr8	85686814	+	3668	2328	185	2947	920
ENST00000349830	ARHGEF10	chr8	1857636	-	ENST00000518566	RALYL	chr8	85686814	+	3840	2328	185	2914	909
ENST00000349830	ARHGEF10	chr8	1857636	-	ENST00000517638	RALYL	chr8	85686814	+	3881	2328	185	2947	920
ENST00000349830	ARHGEF10	chr8	1857636	-	ENST00000523850	RALYL	chr8	85686814	+	3878	2328	185	2947	920
ENST00000349830	ARHGEF10	chr8	1857636	-	ENST00000521376	RALYL	chr8	85686814	+	3660	2328	185	2731	848
ENST00000520359	ARHGEF10	chr8	1857636	-	ENST00000522455	RALYL	chr8	85686814	+	3747	2202	173	2821	882
ENST00000520359	ARHGEF10	chr8	1857636	-	ENST00000521695	RALYL	chr8	85686814	+	3542	2202	173	2821	882
ENST00000520359	ARHGEF10	chr8	1857636	-	ENST00000521268	RALYL	chr8	85686814	+	3542	2202	173	2821	882
ENST00000520359	ARHGEF10	chr8	1857636	-	ENST00000518566	RALYL	chr8	85686814	+	3714	2202	173	2788	871
ENST00000520359	ARHGEF10	chr8	1857636	-	ENST00000517638	RALYL	chr8	85686814	+	3755	2202	173	2821	882
ENST00000520359	ARHGEF10	chr8	1857636	-	ENST00000523850	RALYL	chr8	85686814	+	3752	2202	173	2821	882
ENST00000520359	ARHGEF10	chr8	1857636	-	ENST00000521376	RALYL	chr8	85686814	+	3534	2202	173	2605	810
ENST00000518288	ARHGEF10	chr8	1857636	-	ENST00000522455	RALYL	chr8	85686814	+	3923	2378	73	2997	974
ENST00000518288	ARHGEF10	chr8	1857636	-	ENST00000521695	RALYL	chr8	85686814	+	3718	2378	73	2997	974
ENST00000518288	ARHGEF10	chr8	1857636	-	ENST00000521268	RALYL	chr8	85686814	+	3718	2378	73	2997	974
ENST00000518288	ARHGEF10	chr8	1857636	-	ENST00000518566	RALYL	chr8	85686814	+	3890	2378	73	2964	963
ENST00000518288	ARHGEF10	chr8	1857636	-	ENST00000517638	RALYL	chr8	85686814	+	3931	2378	73	2997	974
ENST00000518288	ARHGEF10	chr8	1857636	-	ENST00000523850	RALYL	chr8	85686814	+	3928	2378	73	2997	974
ENST00000518288	ARHGEF10	chr8	1857636	-	ENST00000521376	RALYL	chr8	85686814	+	3710	2378	73	2781	902
ENST00000398564	ARHGEF10	chr8	1857636	-	ENST00000522455	RALYL	chr8	85686814	+	3763	2218	0	2837	945
ENST00000398564	ARHGEF10	chr8	1857636	-	ENST00000521695	RALYL	chr8	85686814	+	3558	2218	0	2837	945
ENST00000398564	ARHGEF10	chr8	1857636	-	ENST00000521268	RALYL	chr8	85686814	+	3558	2218	0	2837	945
ENST00000398564	ARHGEF10	chr8	1857636	-	ENST00000518566	RALYL	chr8	85686814	+	3730	2218	0	2804	934
ENST00000398564	ARHGEF10	chr8	1857636	-	ENST00000517638	RALYL	chr8	85686814	+	3771	2218	0	2837	945
ENST00000398564	ARHGEF10	chr8	1857636	-	ENST00000523850	RALYL	chr8	85686814	+	3768	2218	0	2837	945
ENST00000398564	ARHGEF10	chr8	1857636	-	ENST00000521376	RALYL	chr8	85686814	+	3550	2218	0	2621	873
ENST00000262112	ARHGEF10	chr8	1857636	-	ENST00000522455	RALYL	chr8	85686814	+	3763	2218	0	2837	945
ENST00000262112	ARHGEF10	chr8	1857636	-	ENST00000521695	RALYL	chr8	85686814	+	3558	2218	0	2837	945
ENST00000262112	ARHGEF10	chr8	1857636	-	ENST00000521268	RALYL	chr8	85686814	+	3558	2218	0	2837	945
ENST00000262112	ARHGEF10	chr8	1857636	-	ENST00000518566	RALYL	chr8	85686814	+	3730	2218	0	2804	934
ENST00000262112	ARHGEF10	chr8	1857636	-	ENST00000517638	RALYL	chr8	85686814	+	3771	2218	0	2837	945
ENST00000262112	ARHGEF10	chr8	1857636	-	ENST00000523850	RALYL	chr8	85686814	+	3768	2218	0	2837	945
ENST00000262112	ARHGEF10	chr8	1857636	-	ENST00000521376	RALYL	chr8	85686814	+	3550	2218	0	2621	873

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
ENST00000349830	ENST00000522455	ARHGEF10	chr8	1857636	-	RALYL	chr8	85686814	+	0.00071636	0.9992836
ENST00000349830	ENST00000521695	ARHGEF10	chr8	1857636	-	RALYL	chr8	85686814	+	0.000893554	0.99910647
ENST00000349830	ENST00000521268	ARHGEF10	chr8	1857636	-	RALYL	chr8	85686814	+	0.000893554	0.99910647
ENST00000349830	ENST00000518566	ARHGEF10	chr8	1857636	-	RALYL	chr8	85686814	+	0.000844281	0.99915576
ENST00000349830	ENST00000517638	ARHGEF10	chr8	1857636	-	RALYL	chr8	85686814	+	0.000688181	0.9993118
ENST00000349830	ENST00000523850	ARHGEF10	chr8	1857636	-	RALYL	chr8	85686814	+	0.000690503	0.99930954
ENST00000349830	ENST00000521376	ARHGEF10	chr8	1857636	-	RALYL	chr8	85686814	+	0.000984765	0.9990152
ENST00000520359	ENST00000522455	ARHGEF10	chr8	1857636	-	RALYL	chr8	85686814	+	0.001429316	0.9985707
ENST00000520359	ENST00000521695	ARHGEF10	chr8	1857636	-	RALYL	chr8	85686814	+	0.001736051	0.998264
ENST00000520359	ENST00000521268	ARHGEF10	chr8	1857636	-	RALYL	chr8	85686814	+	0.001736051	0.998264
ENST00000520359	ENST00000518566	ARHGEF10	chr8	1857636	-	RALYL	chr8	85686814	+	0.001367225	0.9986327
ENST00000520359	ENST00000517638	ARHGEF10	chr8	1857636	-	RALYL	chr8	85686814	+	0.001382292	0.99861765
ENST00000520359	ENST00000523850	ARHGEF10	chr8	1857636	-	RALYL	chr8	85686814	+	0.001385341	0.99861467
ENST00000520359	ENST00000521376	ARHGEF10	chr8	1857636	-	RALYL	chr8	85686814	+	0.001671562	0.9983284
ENST00000518288	ENST00000522455	ARHGEF10	chr8	1857636	-	RALYL	chr8	85686814	+	0.000463111	0.9995369
ENST00000518288	ENST00000521695	ARHGEF10	chr8	1857636	-	RALYL	chr8	85686814	+	0.000589559	0.9994105
ENST00000518288	ENST00000521268	ARHGEF10	chr8	1857636	-	RALYL	chr8	85686814	+	0.000589559	0.9994105
ENST00000518288	ENST00000518566	ARHGEF10	chr8	1857636	-	RALYL	chr8	85686814	+	0.000509642	0.9994904
ENST00000518288	ENST00000517638	ARHGEF10	chr8	1857636	-	RALYL	chr8	85686814	+	0.000447517	0.9995524
ENST00000518288	ENST00000523850	ARHGEF10	chr8	1857636	-	RALYL	chr8	85686814	+	0.000448645	0.99955136
ENST00000518288	ENST00000521376	ARHGEF10	chr8	1857636	-	RALYL	chr8	85686814	+	0.000678638	0.99932134
ENST00000398564	ENST00000522455	ARHGEF10	chr8	1857636	-	RALYL	chr8	85686814	+	0.000400312	0.99959975
ENST00000398564	ENST00000521695	ARHGEF10	chr8	1857636	-	RALYL	chr8	85686814	+	0.000498963	0.999501
ENST00000398564	ENST00000521268	ARHGEF10	chr8	1857636	-	RALYL	chr8	85686814	+	0.000498963	0.999501
ENST00000398564	ENST00000518566	ARHGEF10	chr8	1857636	-	RALYL	chr8	85686814	+	0.000460496	0.9995395
ENST00000398564	ENST00000517638	ARHGEF10	chr8	1857636	-	RALYL	chr8	85686814	+	0.00038779	0.9996123
ENST00000398564	ENST00000523850	ARHGEF10	chr8	1857636	-	RALYL	chr8	85686814	+	0.000388508	0.99961156
ENST00000398564	ENST00000521376	ARHGEF10	chr8	1857636	-	RALYL	chr8	85686814	+	0.000593821	0.9994062
ENST00000262112	ENST00000522455	ARHGEF10	chr8	1857636	-	RALYL	chr8	85686814	+	0.000400312	0.99959975
ENST00000262112	ENST00000521695	ARHGEF10	chr8	1857636	-	RALYL	chr8	85686814	+	0.000498963	0.999501
ENST00000262112	ENST00000521268	ARHGEF10	chr8	1857636	-	RALYL	chr8	85686814	+	0.000498963	0.999501
ENST00000262112	ENST00000518566	ARHGEF10	chr8	1857636	-	RALYL	chr8	85686814	+	0.000460496	0.9995395
ENST00000262112	ENST00000517638	ARHGEF10	chr8	1857636	-	RALYL	chr8	85686814	+	0.00038779	0.9996123
ENST00000262112	ENST00000523850	ARHGEF10	chr8	1857636	-	RALYL	chr8	85686814	+	0.000388508	0.99961156
ENST00000262112	ENST00000521376	ARHGEF10	chr8	1857636	-	RALYL	chr8	85686814	+	0.000593821	0.9994062

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 ARHGEF10-RALYL

+/-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
ARHGEF10	chr8	1857636	RALYL	chr8	85686814	2202	677	PESLAVVANAKPNINMAGEPKPYRPK
ARHGEF10	chr8	1857636	RALYL	chr8	85686814	2218	740	PESLAVVANAKPNINMAGEPKPYRPK
ARHGEF10	chr8	1857636	RALYL	chr8	85686814	2328	715	PESLAVVANAKPNINMAGEPKPYRPK
ARHGEF10	chr8	1857636	RALYL	chr8	85686814	2378	769	PESLAVVANAKPNINMAGEPKPYRPK

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Potential FusionNeoAntigen Information of ARHGEF10-RALYL 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.

ARHGEF10-RALYL_1857636_85686814.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)
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	HLA-C16:01	NAKPNINM	0.99	0.9707	8	16
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	HLA-B78:02	NAKPNINMA	0.7939	0.5153	8	17

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Potential FusionNeoAntigen Information of ARHGEF10-RALYL in HLA II

ARHGEF10-RALYL_1857636_85686814.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)
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-0303	SLAVVANAKPNINMA	2	17
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-0303	ESLAVVANAKPNINM	1	16
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-0303	PESLAVVANAKPNIN	0	15
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-0324	SLAVVANAKPNINMA	2	17
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-0324	ESLAVVANAKPNINM	1	16
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-0324	PESLAVVANAKPNIN	0	15
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-0338	SLAVVANAKPNINMA	2	17
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-0403	PESLAVVANAKPNIN	0	15
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-0413	PESLAVVANAKPNIN	0	15
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-0427	PESLAVVANAKPNIN	0	15
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-0439	PESLAVVANAKPNIN	0	15
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-0440	PESLAVVANAKPNIN	0	15
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-0441	PESLAVVANAKPNIN	0	15
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-0442	PESLAVVANAKPNIN	0	15
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-0444	PESLAVVANAKPNIN	0	15
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-0446	PESLAVVANAKPNIN	0	15
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-0449	PESLAVVANAKPNIN	0	15
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-0450	PESLAVVANAKPNIN	0	15
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-0451	PESLAVVANAKPNIN	0	15
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-0452	PESLAVVANAKPNIN	0	15
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-0453	PESLAVVANAKPNIN	0	15
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-0455	PESLAVVANAKPNIN	0	15
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-0456	PESLAVVANAKPNIN	0	15
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-0458	PESLAVVANAKPNIN	0	15
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-0459	PESLAVVANAKPNIN	0	15
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-0460	PESLAVVANAKPNIN	0	15
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-0465	PESLAVVANAKPNIN	0	15
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-0468	PESLAVVANAKPNIN	0	15
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-0470	PESLAVVANAKPNIN	0	15
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-0471	PESLAVVANAKPNIN	0	15
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-0478	PESLAVVANAKPNIN	0	15
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-0479	PESLAVVANAKPNIN	0	15
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-0485	PESLAVVANAKPNIN	0	15
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-0488	PESLAVVANAKPNIN	0	15
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1117	SLAVVANAKPNINMA	2	17
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1117	ESLAVVANAKPNINM	1	16
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1152	SLAVVANAKPNINMA	2	17
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1152	ESLAVVANAKPNINM	1	16
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1331	SLAVVANAKPNINMA	2	17
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1336	SLAVVANAKPNINMA	2	17
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1396	SLAVVANAKPNINMA	2	17
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1396	ESLAVVANAKPNINM	1	16
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1401	SLAVVANAKPNINMA	2	17
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1401	ESLAVVANAKPNINM	1	16
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1405	SLAVVANAKPNINMA	2	17
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1405	ESLAVVANAKPNINM	1	16
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1408	SLAVVANAKPNINMA	2	17
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1408	ESLAVVANAKPNINM	1	16
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1410	PESLAVVANAKPNIN	0	15
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1418	SLAVVANAKPNINMA	2	17
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1418	ESLAVVANAKPNINM	1	16
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1418	PESLAVVANAKPNIN	0	15
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1419	SLAVVANAKPNINMA	2	17
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1423	SLAVVANAKPNINMA	2	17
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1423	ESLAVVANAKPNINM	1	16
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1426	SLAVVANAKPNINMA	2	17
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1426	ESLAVVANAKPNINM	1	16
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1429	SLAVVANAKPNINMA	2	17
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1434	SLAVVANAKPNINMA	2	17
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1438	SLAVVANAKPNINMA	2	17
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1438	ESLAVVANAKPNINM	1	16
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1438	PESLAVVANAKPNIN	0	15
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1438	LAVVANAKPNINMAG	3	18
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1443	SLAVVANAKPNINMA	2	17
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1443	ESLAVVANAKPNINM	1	16
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1445	SLAVVANAKPNINMA	2	17
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1447	SLAVVANAKPNINMA	2	17
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1450	SLAVVANAKPNINMA	2	17
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1450	ESLAVVANAKPNINM	1	16
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1450	PESLAVVANAKPNIN	0	15
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1451	SLAVVANAKPNINMA	2	17
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1454	SLAVVANAKPNINMA	2	17
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1454	ESLAVVANAKPNINM	1	16
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1456	SLAVVANAKPNINMA	2	17
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1456	ESLAVVANAKPNINM	1	16
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1458	SLAVVANAKPNINMA	2	17
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1458	ESLAVVANAKPNINM	1	16
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1459	SLAVVANAKPNINMA	2	17
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1459	ESLAVVANAKPNINM	1	16
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1460	SLAVVANAKPNINMA	2	17
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1460	ESLAVVANAKPNINM	1	16
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1470	SLAVVANAKPNINMA	2	17
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1470	ESLAVVANAKPNINM	1	16
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1470	PESLAVVANAKPNIN	0	15
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1481	SLAVVANAKPNINMA	2	17
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1482	SLAVVANAKPNINMA	2	17
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1482	ESLAVVANAKPNINM	1	16
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1486	SLAVVANAKPNINMA	2	17
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1486	ESLAVVANAKPNINM	1	16
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1487	SLAVVANAKPNINMA	2	17
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1487	ESLAVVANAKPNINM	1	16
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1488	SLAVVANAKPNINMA	2	17
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1488	ESLAVVANAKPNINM	1	16
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1490	SLAVVANAKPNINMA	2	17
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1490	ESLAVVANAKPNINM	1	16
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1491	SLAVVANAKPNINMA	2	17
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1491	ESLAVVANAKPNINM	1	16
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1493	SLAVVANAKPNINMA	2	17
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1493	ESLAVVANAKPNINM	1	16
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1496	SLAVVANAKPNINMA	2	17
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1496	ESLAVVANAKPNINM	1	16
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1497	SLAVVANAKPNINMA	2	17
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1497	ESLAVVANAKPNINM	1	16
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1499	SLAVVANAKPNINMA	2	17
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1499	ESLAVVANAKPNINM	1	16
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2218	DRB1-1499	PESLAVVANAKPNIN	0	15

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Fusion breakpoint peptide structures of ARHGEF10-RALYL

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
9800	VANAKPNINMAGEP	ARHGEF10	RALYL	chr8	1857636	chr8	85686814	2218

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of ARHGEF10-RALYL

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	9800	VANAKPNINMAGEP	-7.9962	-8.1096
HLA-B14:02	3BVN	9800	VANAKPNINMAGEP	-5.70842	-6.74372
HLA-B52:01	3W39	9800	VANAKPNINMAGEP	-6.83737	-6.95077
HLA-B52:01	3W39	9800	VANAKPNINMAGEP	-4.4836	-5.5189
HLA-A11:01	4UQ2	9800	VANAKPNINMAGEP	-10.0067	-10.1201
HLA-A11:01	4UQ2	9800	VANAKPNINMAGEP	-9.03915	-10.0745
HLA-A24:02	5HGA	9800	VANAKPNINMAGEP	-6.56204	-6.67544
HLA-A24:02	5HGA	9800	VANAKPNINMAGEP	-5.42271	-6.45801
HLA-B44:05	3DX8	9800	VANAKPNINMAGEP	-7.85648	-8.89178
HLA-B44:05	3DX8	9800	VANAKPNINMAGEP	-5.3978	-5.5112
HLA-A02:01	6TDR	9800	VANAKPNINMAGEP	-3.37154	-4.40684

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Vaccine Design for the FusionNeoAntigens of ARHGEF10-RALYL

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
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	8	16	NAKPNINM	CTAACGCGAAACCAAATATCAACA
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	8	17	NAKPNINMA	CTAACGCGAAACCAAATATCAACATGG

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
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	0	15	PESLAVVANAKPNIN	CGCCGGAGAGCCTGGCCGTGGTTGCTAACGCGAAACCAAATATCA
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	1	16	ESLAVVANAKPNINM	CGGAGAGCCTGGCCGTGGTTGCTAACGCGAAACCAAATATCAACA
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	2	17	SLAVVANAKPNINMA	AGAGCCTGGCCGTGGTTGCTAACGCGAAACCAAATATCAACATGG
ARHGEF10-RALYL	chr8	1857636	chr8	85686814	3	18	LAVVANAKPNINMAG	GCCTGGCCGTGGTTGCTAACGCGAAACCAAATATCAACATGGCAG

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Information of the samples that have these potential fusion neoantigens of ARHGEF10-RALYL

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
UCS	ARHGEF10-RALYL	chr8	1857636	ENST00000262112	chr8	85686814	ENST00000517638	TCGA-N5-A59E-01A

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Potential target of CAR-T therapy development for ARHGEF10-RALYL

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 ARHGEF10-RALYL

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 ARHGEF10-RALYL

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)