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Fusion Protein:ROR1-ALG6

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: ROR1-ALG6
	FusionPDB ID: 75353
	FusionGDB2.0 ID: 75353
		Hgene	Tgene
	Gene symbol	ROR1	ALG6
	Gene ID	6095	29929
	Gene name	RAR related orphan receptor A	ALG6 alpha-1,3-glucosyltransferase
	Synonyms	IDDECA\|NR1F1\|ROR1\|ROR2\|ROR3\|RZR-ALPHA\|RZRA	CDG1C
	Cytomap	15q22.2	1p31.3
	Type of gene	protein-coding	protein-coding
	Description	nuclear receptor ROR-alphaROR-alphanuclear receptor RZR-alphanuclear receptor subfamily 1 group F member 1retinoic acid receptor-related orphan receptor alpharetinoid-related orphan receptor alphathyroid hormone nuclear receptor alpha variant 4tran	dolichyl pyrophosphate Man9GlcNAc2 alpha-1,3-glucosyltransferaseMan(9)GlcNAc(2)-PP-Dol alpha-1,3-glucosyltransferaseasparagine-linked glycosylation 6 homolog (S. cerevisiae, alpha-1,3-glucosyltransferase)asparagine-linked glycosylation 6 homolog (yeast
	Modification date	20200322	20200313
	UniProtAcc	.	Q9Y672 Main function of 5'-partner protein: FUNCTION: Adds the first glucose residue to the lipid-linked oligosaccharide precursor for N-linked glycosylation. Transfers glucose from dolichyl phosphate glucose (Dol-P-Glc) onto the lipid-linked oligosaccharide Man(9)GlcNAc(2)-PP-Dol.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000482426, ENST00000371079, ENST00000371080, ENST00000545203,	ENST00000263440, ENST00000371108, ENST00000494765,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	15 X 10 X 7=1050	5 X 6 X 5=150
	# samples	17	6
	** MAII score	log2(17/1050*10)=-2.62678267641578 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(6/150*10)=-1.32192809488736 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: ROR1 [Title/Abstract] AND ALG6 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: ROR1 [Title/Abstract] AND ALG6 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	ROR1(64516388)-ALG6(63867924), # samples:1 ROR1(64516388)-ALG6(63902494), # samples:1
Anticipated loss of major functional domain due to fusion event.	ROR1-ALG6 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. ROR1-ALG6 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. ROR1-ALG6 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. ROR1-ALG6 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. ROR1-ALG6 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF. ROR1-ALG6 seems lost the major protein functional domain in Hgene partner, which is a kinase due to the frame-shifted ORF. ROR1-ALG6 seems lost the major protein functional domain in Tgene partner, which is a cell metabolism gene due to the frame-shifted ORF. ROR1-ALG6 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.

* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner	Gene	GO ID	GO term	PubMed ID
Hgene	ROR1	GO:0006355	regulation of transcription, DNA-templated	9328355
Hgene	ROR1	GO:0030522	intracellular receptor signaling pathway	19965867
Hgene	ROR1	GO:0036315	cellular response to sterol	19965867
Hgene	ROR1	GO:0045893	positive regulation of transcription, DNA-templated	7926749
Hgene	ROR1	GO:0045944	positive regulation of transcription by RNA polymerase II	17545671\|19955433
Tgene	ALG6	GO:0006487	protein N-linked glycosylation	10924277

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr1:64516388/chr1:63867924)
- 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 ROR1 (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 ALG6 (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)
ENST00000371080	ROR1	chr1	64516388	+	ENST00000371108	ALG6	chr1	63867924	+	3777	878	357	2234	625
ENST00000371080	ROR1	chr1	64516388	+	ENST00000263440	ALG6	chr1	63867924	+	2398	878	357	2240	627
ENST00000371079	ROR1	chr1	64516388	+	ENST00000371108	ALG6	chr1	63867924	+	3756	857	336	2213	625
ENST00000371079	ROR1	chr1	64516388	+	ENST00000263440	ALG6	chr1	63867924	+	2377	857	336	2219	627
ENST00000371080	ROR1	chr1	64516388	+	ENST00000263440	ALG6	chr1	63902494	+	1233	878	357	911	184
ENST00000371079	ROR1	chr1	64516388	+	ENST00000263440	ALG6	chr1	63902494	+	1212	857	336	890	184

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
ENST00000371080	ENST00000371108	ROR1	chr1	64516388	+	ALG6	chr1	63867924	+	0.001114187	0.9988858
ENST00000371080	ENST00000263440	ROR1	chr1	64516388	+	ALG6	chr1	63867924	+	0.003534239	0.9964658
ENST00000371079	ENST00000371108	ROR1	chr1	64516388	+	ALG6	chr1	63867924	+	0.001077978	0.9989221
ENST00000371079	ENST00000263440	ROR1	chr1	64516388	+	ALG6	chr1	63867924	+	0.00328953	0.9967104
ENST00000371080	ENST00000263440	ROR1	chr1	64516388	+	ALG6	chr1	63902494	+	0.07864132	0.9213587
ENST00000371079	ENST00000263440	ROR1	chr1	64516388	+	ALG6	chr1	63902494	+	0.05859809	0.94140184

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 ROR1-ALG6

+/-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
ROR1	chr1	64516388	ALG6	chr1	63867924	857	174	KFGPPPTASPGYSYFNSSDNNLQYWG
ROR1	chr1	64516388	ALG6	chr1	63867924	878	174	KFGPPPTASPGYSYFNSSDNNLQYWG

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Potential FusionNeoAntigen Information of ROR1-ALG6 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.

ROR1-ALG6_64516388_63867924.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)
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-B15:02	TASPGYSY	0.997	0.9548	6	14
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-B35:08	TASPGYSY	0.9928	0.9406	6	14
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-B35:01	TASPGYSY	0.992	0.9407	6	14
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-B35:05	TASPGYSY	0.9735	0.761	6	14
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-B35:08	TASPGYSYF	0.9975	0.9455	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-B15:02	TASPGYSYF	0.9955	0.9541	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-B35:01	TASPGYSYF	0.9928	0.9438	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-B15:17	TASPGYSYF	0.9928	0.9205	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-B15:16	TASPGYSYF	0.9883	0.8134	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-B35:05	TASPGYSYF	0.9877	0.7605	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-B46:01	TASPGYSYF	0.9806	0.5604	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-B58:01	TASPGYSYF	0.9709	0.9642	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-B57:03	TASPGYSYF	0.9517	0.9686	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-B58:02	TASPGYSYF	0.9462	0.974	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-B35:04	TASPGYSYF	0.684	0.9741	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-B35:02	TASPGYSYF	0.684	0.9741	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-A24:14	TASPGYSYF	0.6697	0.5503	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-B15:31	TASPGYSY	0.9925	0.9404	6	14
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C03:14	TASPGYSY	0.9032	0.9896	6	14
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C12:12	TASPGYSY	0.8604	0.8712	6	14
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-B15:21	TASPGYSYF	0.9957	0.9483	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-B15:31	TASPGYSYF	0.9935	0.9372	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C03:08	TASPGYSYF	0.9932	0.9071	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C12:16	TASPGYSYF	0.9919	0.9326	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C03:19	TASPGYSYF	0.9845	0.9818	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C15:04	TASPGYSYF	0.9827	0.9461	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C03:07	TASPGYSYF	0.9749	0.9854	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C15:06	TASPGYSYF	0.9557	0.9106	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C12:12	TASPGYSYF	0.9371	0.8852	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C04:06	TASPGYSYF	0.9168	0.9507	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C04:10	TASPGYSYF	0.8876	0.7805	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C04:07	TASPGYSYF	0.8779	0.8179	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C07:10	TASPGYSYF	0.8721	0.9718	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C03:14	TASPGYSYF	0.8638	0.9888	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C07:29	TASPGYSYF	0.8469	0.9346	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C05:09	TASPGYSYF	0.8432	0.9177	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C07:95	TASPGYSYF	0.839	0.7827	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C07:80	TASPGYSYF	0.8228	0.9629	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C07:67	TASPGYSYF	0.8228	0.9629	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C04:14	TASPGYSYF	0.8141	0.808	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C07:19	TASPGYSYF	0.8141	0.8306	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C12:04	TASPGYSYF	0.812	0.9964	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C07:05	TASPGYSYF	0.8084	0.9783	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C06:03	TASPGYSYF	0.799	0.9959	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C07:27	TASPGYSYF	0.7952	0.972	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C08:13	TASPGYSYF	0.7582	0.9566	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C08:04	TASPGYSYF	0.7582	0.9566	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C01:17	TASPGYSYF	0.6993	0.9176	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-B35:12	TASPGYSYF	0.684	0.9741	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C01:30	TASPGYSYF	0.611	0.9285	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C08:15	TASPGYSYF	0.5478	0.9289	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C02:06	TASPGYSYF	0.4673	0.9692	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C08:03	TASPGYSYF	0.4565	0.9436	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-B35:11	TASPGYSY	0.9966	0.9449	6	14
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-B15:11	TASPGYSY	0.9959	0.9164	6	14
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-B15:08	TASPGYSY	0.9956	0.9297	6	14
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C03:02	TASPGYSY	0.9949	0.9726	6	14
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-B35:30	TASPGYSY	0.9942	0.8939	6	14
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-B35:17	TASPGYSY	0.9942	0.8939	6	14
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-B35:43	TASPGYSY	0.9939	0.931	6	14
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-B35:23	TASPGYSY	0.9933	0.9483	6	14
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-B35:20	TASPGYSY	0.9928	0.9572	6	14
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-B35:77	TASPGYSY	0.992	0.9407	6	14
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-B35:24	TASPGYSY	0.9765	0.9181	6	14
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C12:02	TASPGYSY	0.9725	0.943	6	14
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C12:03	TASPGYSY	0.9219	0.9749	6	14
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C16:02	TASPGYSY	0.9037	0.9958	6	14
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C16:04	TASPGYSY	0.872	0.9703	6	14
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C16:01	TASPGYSY	0.814	0.9573	6	14
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-B18:07	TASPGYSY	0.7106	0.8904	6	14
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C03:02	TASPGYSYF	0.9974	0.9729	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C03:67	TASPGYSYF	0.9961	0.977	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C03:04	TASPGYSYF	0.9949	0.9834	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C03:03	TASPGYSYF	0.9949	0.9834	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-B35:11	TASPGYSYF	0.9944	0.9456	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-B35:28	TASPGYSYF	0.9939	0.9475	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-B35:77	TASPGYSYF	0.9928	0.9438	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-B35:23	TASPGYSYF	0.9923	0.9487	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-B35:20	TASPGYSYF	0.9921	0.9584	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-B57:04	TASPGYSYF	0.9919	0.8208	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-B15:13	TASPGYSYF	0.9904	0.6847	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-B35:17	TASPGYSYF	0.99	0.8986	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-B35:30	TASPGYSYF	0.99	0.8986	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-B57:02	TASPGYSYF	0.9877	0.8966	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C03:17	TASPGYSYF	0.9847	0.9742	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C03:05	TASPGYSYF	0.984	0.9224	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-B15:11	TASPGYSYF	0.9831	0.9063	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C15:09	TASPGYSYF	0.9827	0.9461	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-B15:08	TASPGYSYF	0.9827	0.9217	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-B35:43	TASPGYSYF	0.9794	0.9228	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-B15:24	TASPGYSYF	0.9789	0.8975	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C16:04	TASPGYSYF	0.9756	0.9738	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C12:02	TASPGYSYF	0.9752	0.948	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-B58:06	TASPGYSYF	0.9726	0.9166	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-B35:24	TASPGYSYF	0.9673	0.9307	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C12:03	TASPGYSYF	0.9518	0.979	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-B15:12	TASPGYSYF	0.9415	0.9682	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C15:05	TASPGYSYF	0.9374	0.94	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-B35:13	TASPGYSYF	0.9325	0.9487	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C07:17	TASPGYSYF	0.9078	0.9701	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C07:22	TASPGYSYF	0.9069	0.7133	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C04:04	TASPGYSYF	0.8952	0.9291	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C06:06	TASPGYSYF	0.8925	0.9917	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-A25:01	TASPGYSYF	0.8904	0.8142	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C04:01	TASPGYSYF	0.8779	0.8179	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C04:03	TASPGYSYF	0.8572	0.8633	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C16:01	TASPGYSYF	0.8479	0.9629	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C05:01	TASPGYSYF	0.8432	0.9177	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C06:17	TASPGYSYF	0.8402	0.9957	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C06:02	TASPGYSYF	0.8402	0.9957	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C03:06	TASPGYSYF	0.8393	0.9836	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C18:01	TASPGYSYF	0.8375	0.8189	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C07:04	TASPGYSYF	0.8276	0.827	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C07:02	TASPGYSYF	0.8228	0.9629	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C07:01	TASPGYSYF	0.8078	0.7829	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C01:02	TASPGYSYF	0.7122	0.9135	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-B35:09	TASPGYSYF	0.684	0.9741	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C16:02	TASPGYSYF	0.5797	0.9957	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C02:10	TASPGYSYF	0.5649	0.9866	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C02:02	TASPGYSYF	0.5649	0.9866	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C08:02	TASPGYSYF	0.5478	0.9289	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-B07:13	TASPGYSYF	0.5345	0.8611	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C08:01	TASPGYSYF	0.4565	0.9436	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C06:08	TASPGYSYF	0.4216	0.9955	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C17:01	TASPGYSYF	0.0425	0.9724	6	15
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C14:02	SYFNSSDNNL	0.8764	0.9558	12	22
ROR1-ALG6	chr1	64516388	chr1	63867924	857	HLA-C14:03	SYFNSSDNNL	0.8764	0.9558	12	22

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Potential FusionNeoAntigen Information of ROR1-ALG6 in HLA II

ROR1-ALG6_64516388_63867924.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)
ROR1-ALG6	chr1	64516388	chr1	63867924	857	DRB1-0407	YSYFNSSDNNLQYWG	11	26
ROR1-ALG6	chr1	64516388	chr1	63867924	857	DRB1-0438	YSYFNSSDNNLQYWG	11	26
ROR1-ALG6	chr1	64516388	chr1	63867924	857	DRB1-0474	YSYFNSSDNNLQYWG	11	26

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Fusion breakpoint peptide structures of ROR1-ALG6

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
9251	TASPGYSYFNSSDN	ROR1	ALG6	chr1	64516388	chr1	63867924	857

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of ROR1-ALG6

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	9251	TASPGYSYFNSSDN	-7.9962	-8.1096
HLA-B14:02	3BVN	9251	TASPGYSYFNSSDN	-5.70842	-6.74372
HLA-B52:01	3W39	9251	TASPGYSYFNSSDN	-6.83737	-6.95077
HLA-B52:01	3W39	9251	TASPGYSYFNSSDN	-4.4836	-5.5189
HLA-A11:01	4UQ2	9251	TASPGYSYFNSSDN	-10.0067	-10.1201
HLA-A11:01	4UQ2	9251	TASPGYSYFNSSDN	-9.03915	-10.0745
HLA-A24:02	5HGA	9251	TASPGYSYFNSSDN	-6.56204	-6.67544
HLA-A24:02	5HGA	9251	TASPGYSYFNSSDN	-5.42271	-6.45801
HLA-B44:05	3DX8	9251	TASPGYSYFNSSDN	-7.85648	-8.89178
HLA-B44:05	3DX8	9251	TASPGYSYFNSSDN	-5.3978	-5.5112
HLA-A02:01	6TDR	9251	TASPGYSYFNSSDN	-3.37154	-4.40684

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Vaccine Design for the FusionNeoAntigens of ROR1-ALG6

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
ROR1-ALG6	chr1	64516388	chr1	63867924	12	22	SYFNSSDNNL	CTCGTATTTTAACAGCAGTGATAACAATTT
ROR1-ALG6	chr1	64516388	chr1	63867924	6	14	TASPGYSY	CACTGCAAGTCCAGGATACTCGTA
ROR1-ALG6	chr1	64516388	chr1	63867924	6	15	TASPGYSYF	CACTGCAAGTCCAGGATACTCGTATTT

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
ROR1-ALG6	chr1	64516388	chr1	63867924	11	26	YSYFNSSDNNLQYWG	ATACTCGTATTTTAACAGCAGTGATAACAATTTACAGTATTGGGG

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Information of the samples that have these potential fusion neoantigens of ROR1-ALG6

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	ROR1-ALG6	chr1	64516388	ENST00000371079	chr1	63867924	ENST00000263440	TCGA-13-0765

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Potential target of CAR-T therapy development for ROR1-ALG6

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

Tgene

ALG6

chr1:64516388

chr1:63867924

ENST00000371108

115_135

508.0

Transmembrane

Helical

Tgene

ALG6

chr1:64516388

chr1:63867924

ENST00000371108

144_164

508.0

Transmembrane

Helical

Tgene

ALG6

chr1:64516388

chr1:63867924

ENST00000371108

173_193

508.0

Transmembrane

Helical

Tgene

ALG6

chr1:64516388

chr1:63867924

ENST00000371108

227_247

508.0

Transmembrane

Helical

Tgene

ALG6

chr1:64516388

chr1:63867924

ENST00000371108

298_318

508.0

Transmembrane

Helical

Tgene

ALG6

chr1:64516388

chr1:63867924

ENST00000371108

324_344

508.0

Transmembrane

Helical

Tgene

ALG6

chr1:64516388

chr1:63867924

ENST00000371108

362_382

508.0

Transmembrane

Helical

Tgene

ALG6

chr1:64516388

chr1:63867924

ENST00000371108

388_408

508.0

Transmembrane

Helical

Tgene

ALG6

chr1:64516388

chr1:63867924

ENST00000371108

438_458

508.0

Transmembrane

Helical

Tgene

ALG6

chr1:64516388

chr1:63867924

ENST00000371108

473_493

508.0

Transmembrane

Helical

Tgene

ALG6

chr1:64516388

chr1:63902494

ENST00000371108

473_493

508.0

Transmembrane

Helical

Subcellular localization prediction of the transmembrane domain retained fusion proteins
* We used DeepLoc 1.0. The order of the X-axis of the barplot is as follows: Entry_ID, Localization, Type, Nucleus, Cytoplasm, Extracellular, Mitochondrion, Cell_membrane, Endoplasmic_reticulum, Plastid, Golgi.apparatus, Lysosome.Vacuole, Peroxisome. Y-axis is the output score of DeepLoc. Clicking the image will open a new tab with a large image.

Hgene

Hchr

Hbp

Henst

Tgene

Tchr

Tbp

Tenst

DeepLoc result

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Related Drugs to ROR1-ALG6

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 ROR1-ALG6

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)