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Fusion Protein:RB1-FNDC3A

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: RB1-FNDC3A
	FusionPDB ID: 72560
	FusionGDB2.0 ID: 72560
		Hgene	Tgene
	Gene symbol	RB1	FNDC3A
	Gene ID	5925	22862
	Gene name	RB transcriptional corepressor 1	fibronectin type III domain containing 3A
	Synonyms	OSRC\|PPP1R130\|RB\|p105-Rb\|p110-RB1\|pRb\|pp110	FNDC3\|HUGO\|bA203I16.1\|bA203I16.5
	Cytomap	13q14.2	13q14.2
	Type of gene	protein-coding	protein-coding
	Description	retinoblastoma-associated proteinGOS563 exon 17 substitution mutation causes premature stopexon 17 tumor GOS561 substitution mutation causes premature stopprepro-retinoblastoma-associated proteinprotein phosphatase 1, regulatory subunit 130retinoblas	fibronectin type-III domain-containing protein 3Ahuman gene expressed in odontoblasts
	Modification date	20200329	20200313
	UniProtAcc	RB1CC1 Main function of 5'-partner protein: 1594	Q9Y2H6 Main function of 5'-partner protein: FUNCTION: Mediates spermatid-Sertoli adhesion during spermatogenesis. {ECO:0000250}.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000267163, ENST00000484879,	ENST00000398316, ENST00000492622, ENST00000541916,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	23 X 9 X 13=2691	9 X 10 X 4=360
	# samples	27	10
	** MAII score	log2(27/2691*10)=-3.31711107858959 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(10/360*10)=-1.84799690655495 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: RB1 [Title/Abstract] AND FNDC3A [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: RB1 [Title/Abstract] AND FNDC3A [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	FNDC3A(49688867)-RB1(49037867), # samples:2 RB1(48942740)-FNDC3A(49742748), # samples:1
Anticipated loss of major functional domain due to fusion event.	FNDC3A-RB1 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. FNDC3A-RB1 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. RB1-FNDC3A 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. RB1-FNDC3A 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. RB1-FNDC3A 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. RB1-FNDC3A 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	RB1	GO:0043550	regulation of lipid kinase activity	16286473
Hgene	RB1	GO:0045892	negative regulation of transcription, DNA-templated	10783144\|12065415\|19223331
Hgene	RB1	GO:2000679	positive regulation of transcription regulatory region DNA binding	25100735

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr13:49688867/chr13:49037867)
- 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 RB1 (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 FNDC3A (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)

ENST00000267163

RB1

chr13

48942740

ENST00000492622

FNDC3A

chr13

49742748

6209

1265

138

3824

1228

ENST00000267163

RB1

chr13

48942740

ENST00000541916

FNDC3A

chr13

49742748

4804

1265

138

3824

1228

ENST00000267163

RB1

chr13

48942740

ENST00000398316

FNDC3A

chr13

49742748

6023

1265

138

3824

1228

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
ENST00000267163	ENST00000492622	RB1	chr13	48942740	+	FNDC3A	chr13	49742748	+	0.000127759	0.9998722
ENST00000267163	ENST00000541916	RB1	chr13	48942740	+	FNDC3A	chr13	49742748	+	0.00015647	0.9998435
ENST00000267163	ENST00000398316	RB1	chr13	48942740	+	FNDC3A	chr13	49742748	+	0.000135434	0.9998646

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 RB1-FNDC3A

+/-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
RB1	chr13	48942740	FNDC3A	chr13	49742748	1265	375	DEEVNVIPPHTPVRVQAEYNSIKGTP

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Potential FusionNeoAntigen Information of RB1-FNDC3A 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.

RB1-FNDC3A_48942740_49742748.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)
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-B39:06	HTPVRVQA	0.9303	0.9332	9	17
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-B35:01	TPVRVQAEY	0.995	0.8213	10	19
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-B35:08	TPVRVQAEY	0.9877	0.821	10	19
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-B39:06	PHTPVRVQA	0.9663	0.9087	8	17
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-B15:02	TPVRVQAEY	0.9617	0.8801	10	19
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-A68:06	VIPPHTPVR	0.9515	0.6942	5	14
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-A34:02	VIPPHTPVR	0.9381	0.6212	5	14
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-A68:08	VIPPHTPVR	0.9371	0.6737	5	14
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-A34:05	VIPPHTPVR	0.9349	0.699	5	14
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-A34:01	VIPPHTPVR	0.9349	0.699	5	14
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-A31:02	VIPPHTPVR	0.9323	0.8736	5	14
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-A68:03	VIPPHTPVR	0.9253	0.6666	5	14
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-A68:05	VIPPHTPVR	0.9199	0.6691	5	14
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-A74:03	VIPPHTPVR	0.9185	0.8364	5	14
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-A74:11	VIPPHTPVR	0.9185	0.8364	5	14
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-A74:09	VIPPHTPVR	0.9185	0.8364	5	14
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-A31:06	VIPPHTPVR	0.894	0.7506	5	14
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-A66:01	VIPPHTPVR	0.8792	0.8101	5	14
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-B35:05	TPVRVQAEY	0.8383	0.5135	10	19
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-B35:04	IPPHTPVRV	0.7891	0.9264	6	15
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-B35:02	IPPHTPVRV	0.7891	0.9264	6	15
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-A66:03	VIPPHTPVR	0.7375	0.7262	5	14
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-B35:03	TPVRVQAEY	0.5615	0.8025	10	19
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-A26:03	VIPPHTPVR	0.4978	0.8061	5	14
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-B35:04	TPVRVQAEY	0.1276	0.8705	10	19
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-B35:02	TPVRVQAEY	0.1276	0.8705	10	19
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-A68:24	NVIPPHTPVR	0.9967	0.6491	4	14
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-A68:03	NVIPPHTPVR	0.996	0.6282	4	14
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-A68:06	NVIPPHTPVR	0.9955	0.5482	4	14
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-A66:01	NVIPPHTPVR	0.995	0.813	4	14
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-A68:08	NVIPPHTPVR	0.9876	0.6329	4	14
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-A68:05	NVIPPHTPVR	0.9859	0.6327	4	14
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-A34:01	NVIPPHTPVR	0.9829	0.6137	4	14
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-A34:05	NVIPPHTPVR	0.9829	0.6137	4	14
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-B35:08	HTPVRVQAEY	0.9561	0.7359	9	19
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-A26:03	NVIPPHTPVR	0.9559	0.8319	4	14
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-A66:03	NVIPPHTPVR	0.9522	0.6108	4	14
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-A31:02	NVIPPHTPVR	0.9494	0.87	4	14
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-A33:05	NVIPPHTPVR	0.9487	0.857	4	14
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-A33:01	NVIPPHTPVR	0.9487	0.857	4	14
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-A31:06	NVIPPHTPVR	0.9348	0.7808	4	14
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-A74:03	NVIPPHTPVR	0.9262	0.876	4	14
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-A74:11	NVIPPHTPVR	0.9262	0.876	4	14
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-A74:09	NVIPPHTPVR	0.9262	0.876	4	14
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-B35:01	HTPVRVQAEY	0.9208	0.7007	9	19
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-B15:31	TPVRVQAEY	0.9946	0.7904	10	19
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-B51:07	IPPHTPVRV	0.99	0.8247	6	15
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-B15:21	TPVRVQAEY	0.9669	0.8637	10	19
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-A33:03	VIPPHTPVR	0.9452	0.5906	5	14
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-A31:01	VIPPHTPVR	0.9406	0.8331	5	14
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-B54:01	IPPHTPVRV	0.9234	0.5415	6	15
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-B35:12	IPPHTPVRV	0.7891	0.9264	6	15
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-C01:30	IPPHTPVRV	0.1609	0.9796	6	15
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-B35:12	TPVRVQAEY	0.1276	0.8705	10	19
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-B39:10	IPPHTPVRV	0.0352	0.965	6	15
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-C01:17	IPPHTPVRV	0.0135	0.9662	6	15
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-A68:01	NVIPPHTPVR	0.9967	0.6491	4	14
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-A31:01	NVIPPHTPVR	0.9489	0.851	4	14
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-B15:31	HTPVRVQAEY	0.9229	0.663	9	19
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-A02:07	VIPPHTPVRV	0.7964	0.7007	5	15
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-C01:17	VIPPHTPVRV	0.5343	0.9508	5	15
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-C01:30	VIPPHTPVRV	0.4752	0.9758	5	15
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-B54:01	IPPHTPVRVQA	0.9949	0.7678	6	17
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-B35:77	TPVRVQAEY	0.995	0.8213	10	19
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-B35:23	TPVRVQAEY	0.9947	0.8428	10	19
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-B35:20	TPVRVQAEY	0.9944	0.8657	10	19
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-B35:24	TPVRVQAEY	0.975	0.8415	10	19
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-B35:11	TPVRVQAEY	0.9615	0.8563	10	19
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-B35:17	TPVRVQAEY	0.9548	0.6949	10	19
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-B35:30	TPVRVQAEY	0.9548	0.6949	10	19
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-A74:01	VIPPHTPVR	0.9185	0.8364	5	14
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-A66:02	VIPPHTPVR	0.846	0.6821	5	14
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-B35:09	IPPHTPVRV	0.7891	0.9264	6	15
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-B15:13	TPVRVQAEY	0.7648	0.759	10	19
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-B18:04	TPVRVQAEY	0.6544	0.6561	10	19
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-B15:08	TPVRVQAEY	0.5294	0.7099	10	19
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-B15:11	TPVRVQAEY	0.5179	0.7204	10	19
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-B35:43	TPVRVQAEY	0.4871	0.7215	10	19
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-B18:07	TPVRVQAEY	0.3223	0.6034	10	19
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-B18:03	TPVRVQAEY	0.286	0.6244	10	19
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-B18:06	TPVRVQAEY	0.2815	0.6422	10	19
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-B18:08	TPVRVQAEY	0.2667	0.6584	10	19
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-B35:09	TPVRVQAEY	0.1276	0.8705	10	19
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-C01:02	IPPHTPVRV	0.0075	0.9647	6	15
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-C01:03	IPPHTPVRV	0.0048	0.9519	6	15
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-B15:11	HTPVRVQAEY	0.995	0.7242	9	19
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-B15:08	HTPVRVQAEY	0.9935	0.7203	9	19
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-B35:43	HTPVRVQAEY	0.9918	0.7267	9	19
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-B35:11	HTPVRVQAEY	0.9845	0.812	9	19
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-A66:02	NVIPPHTPVR	0.9766	0.5897	4	14
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-B35:30	HTPVRVQAEY	0.9441	0.5957	9	19
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-B35:17	HTPVRVQAEY	0.9441	0.5957	9	19
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-A74:01	NVIPPHTPVR	0.9262	0.876	4	14
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-B35:77	HTPVRVQAEY	0.9208	0.7007	9	19
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-B35:23	HTPVRVQAEY	0.9181	0.7534	9	19
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-B35:20	HTPVRVQAEY	0.9143	0.7603	9	19
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-A25:01	HTPVRVQAEY	0.8063	0.7402	9	19
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-B35:24	HTPVRVQAEY	0.7095	0.7978	9	19
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-C01:02	VIPPHTPVRV	0.5681	0.9493	5	15
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-C01:03	VIPPHTPVRV	0.55	0.9275	5	15
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-A68:02	NVIPPHTPVRV	0.9931	0.7676	4	15
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-A69:01	NVIPPHTPVRV	0.9828	0.8464	4	15
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-B56:05	IPPHTPVRVQA	0.9693	0.5539	6	17
RB1-FNDC3A	chr13	48942740	chr13	49742748	1265	HLA-B55:02	IPPHTPVRVQA	0.9638	0.6202	6	17

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Potential FusionNeoAntigen Information of RB1-FNDC3A 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 RB1-FNDC3A

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
3894	IPPHTPVRVQAEYN	RB1	FNDC3A	chr13	48942740	chr13	49742748	1265

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of RB1-FNDC3A

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	3894	IPPHTPVRVQAEYN	-7.15543	-7.26883
HLA-B14:02	3BVN	3894	IPPHTPVRVQAEYN	-4.77435	-5.80965
HLA-B52:01	3W39	3894	IPPHTPVRVQAEYN	-6.80875	-6.92215
HLA-B52:01	3W39	3894	IPPHTPVRVQAEYN	-4.20386	-5.23916
HLA-A11:01	4UQ2	3894	IPPHTPVRVQAEYN	-7.5194	-8.5547
HLA-A11:01	4UQ2	3894	IPPHTPVRVQAEYN	-6.9601	-7.0735
HLA-A24:02	5HGA	3894	IPPHTPVRVQAEYN	-7.52403	-7.63743
HLA-A24:02	5HGA	3894	IPPHTPVRVQAEYN	-5.82433	-6.85963
HLA-B27:05	6PYJ	3894	IPPHTPVRVQAEYN	-3.28285	-4.31815
HLA-B44:05	3DX8	3894	IPPHTPVRVQAEYN	-5.91172	-6.94702
HLA-B44:05	3DX8	3894	IPPHTPVRVQAEYN	-4.24346	-4.35686

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Vaccine Design for the FusionNeoAntigens of RB1-FNDC3A

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
RB1-FNDC3A	chr13	48942740	chr13	49742748	10	19	TPVRVQAEY	TCCAGTTAGAGTCCAGGCAGAATATAA
RB1-FNDC3A	chr13	48942740	chr13	49742748	4	14	NVIPPHTPVR	TGTAATTCCTCCACACACTCCAGTTAGAGT
RB1-FNDC3A	chr13	48942740	chr13	49742748	4	15	NVIPPHTPVRV	TGTAATTCCTCCACACACTCCAGTTAGAGTCCA
RB1-FNDC3A	chr13	48942740	chr13	49742748	5	14	VIPPHTPVR	AATTCCTCCACACACTCCAGTTAGAGT
RB1-FNDC3A	chr13	48942740	chr13	49742748	5	15	VIPPHTPVRV	AATTCCTCCACACACTCCAGTTAGAGTCCA
RB1-FNDC3A	chr13	48942740	chr13	49742748	6	15	IPPHTPVRV	TCCTCCACACACTCCAGTTAGAGTCCA
RB1-FNDC3A	chr13	48942740	chr13	49742748	6	17	IPPHTPVRVQA	TCCTCCACACACTCCAGTTAGAGTCCAGGCAGA
RB1-FNDC3A	chr13	48942740	chr13	49742748	8	17	PHTPVRVQA	ACACACTCCAGTTAGAGTCCAGGCAGA
RB1-FNDC3A	chr13	48942740	chr13	49742748	9	17	HTPVRVQA	CACTCCAGTTAGAGTCCAGGCAGA
RB1-FNDC3A	chr13	48942740	chr13	49742748	9	19	HTPVRVQAEY	CACTCCAGTTAGAGTCCAGGCAGAATATAA

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 RB1-FNDC3A

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	RB1-FNDC3A	chr13	48942740	ENST00000267163	chr13	49742748	ENST00000398316	TCGA-04-1365

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Potential target of CAR-T therapy development for RB1-FNDC3A

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

FNDC3A

chr13:48942740

chr13:49742748

ENST00000398316

1177_1197

1143.0

Transmembrane

Helical

Tgene

FNDC3A

chr13:48942740

chr13:49742748

ENST00000492622

1177_1197

1199.0

Transmembrane

Helical

Tgene

FNDC3A

chr13:48942740

chr13:49742748

ENST00000541916

1177_1197

1199.0

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 RB1-FNDC3A

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 RB1-FNDC3A

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)