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Fusion Protein:RBL1-CSTA

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: RBL1-CSTA
	FusionPDB ID: 72720
	FusionGDB2.0 ID: 72720
		Hgene	Tgene
	Gene symbol	RBL1	CSTA
	Gene ID	5933	1475
	Gene name	RB transcriptional corepressor like 1	cystatin A
	Synonyms	CP107\|PRB1\|p107	AREI\|PSS4\|STF1\|STFA
	Cytomap	20q11.23	3q21.1
	Type of gene	protein-coding	protein-coding
	Description	retinoblastoma-like protein 1107 kDa retinoblastoma-associated proteinretinoblastoma-like 1	cystatin-Acystatin A (stefin A)cystatin AS
	Modification date	20200313	20200313
	UniProtAcc	.	P01040 Main function of 5'-partner protein: FUNCTION: This is an intracellular thiol proteinase inhibitor. Has an important role in desmosome-mediated cell-cell adhesion in the lower levels of the epidermis. {ECO:0000269\|PubMed:21944047}.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000344359, ENST00000373664, ENST00000598590,	ENST00000264474, ENST00000479204,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	13 X 9 X 7=819	9 X 10 X 4=360
	# samples	15	9
	** MAII score	log2(15/819*10)=-2.44890095114513 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(9/360*10)=-2 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: RBL1 [Title/Abstract] AND CSTA [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: RBL1 [Title/Abstract] AND CSTA [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	RBL1(35717392)-CSTA(122056394), # samples:2
Anticipated loss of major functional domain due to fusion event.	RBL1-CSTA 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. RBL1-CSTA 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. RBL1-CSTA 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. RBL1-CSTA 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. RBL1-CSTA seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor 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	RBL1	GO:0043550	regulation of lipid kinase activity	16286473
Tgene	CSTA	GO:0010466	negative regulation of peptidase activity	6203523
Tgene	CSTA	GO:0018149	peptide cross-linking	10908733
Tgene	CSTA	GO:0030216	keratinocyte differentiation	10908733
Tgene	CSTA	GO:0045861	negative regulation of proteolysis	3488317

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr20:35717392/chr3:122056394)
- 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 RBL1 (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 CSTA (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)

ENST00000373664

RBL1

chr20

35717392

ENST00000479204

CSTA

chr3

122056394

1081

357

513

148

ENST00000344359

RBL1

chr20

35717392

ENST00000479204

CSTA

chr3

122056394

1075

351

507

148

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
ENST00000373664	ENST00000479204	RBL1	chr20	35717392	-	CSTA	chr3	122056394	+	0.007653671	0.9923463
ENST00000344359	ENST00000479204	RBL1	chr20	35717392	-	CSTA	chr3	122056394	+	0.008294845	0.9917052

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 RBL1-CSTA

+/-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
RBL1	chr20	35717392	CSTA	chr3	122056394	351	96	CVSLTRILRSAKLRLNHSLKKKQMRL
RBL1	chr20	35717392	CSTA	chr3	122056394	357	96	CVSLTRILRSAKLRLNHSLKKKQMRL

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Potential FusionNeoAntigen Information of RBL1-CSTA 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.

RBL1-CSTA_35717392_122056394.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)
RBL1-CSTA	chr20	35717392	chr3	122056394	351	HLA-B27:05	LRLNHSLKK	0.9991	0.8556	12	21
RBL1-CSTA	chr20	35717392	chr3	122056394	351	HLA-A30:08	KLRLNHSLK	0.9987	0.6664	11	20
RBL1-CSTA	chr20	35717392	chr3	122056394	351	HLA-B27:04	LRLNHSLKK	0.9951	0.5943	12	21
RBL1-CSTA	chr20	35717392	chr3	122056394	351	HLA-A74:09	RILRSAKLR	0.9807	0.5988	5	14
RBL1-CSTA	chr20	35717392	chr3	122056394	351	HLA-A74:03	RILRSAKLR	0.9807	0.5988	5	14
RBL1-CSTA	chr20	35717392	chr3	122056394	351	HLA-A74:11	RILRSAKLR	0.9807	0.5988	5	14
RBL1-CSTA	chr20	35717392	chr3	122056394	351	HLA-B39:01	AKLRLNHSL	0.9652	0.7953	10	19
RBL1-CSTA	chr20	35717392	chr3	122056394	351	HLA-A31:02	RILRSAKLR	0.8766	0.5392	5	14
RBL1-CSTA	chr20	35717392	chr3	122056394	351	HLA-B39:13	AKLRLNHSL	0.8674	0.7783	10	19
RBL1-CSTA	chr20	35717392	chr3	122056394	351	HLA-B15:03	AKLRLNHSL	0.4633	0.576	10	19
RBL1-CSTA	chr20	35717392	chr3	122056394	351	HLA-A30:08	KLRLNHSLKK	0.9979	0.6898	11	21
RBL1-CSTA	chr20	35717392	chr3	122056394	351	HLA-B27:05	KLRLNHSLKK	0.9596	0.8156	11	21
RBL1-CSTA	chr20	35717392	chr3	122056394	351	HLA-A74:11	KLRLNHSLKK	0.9554	0.5186	11	21
RBL1-CSTA	chr20	35717392	chr3	122056394	351	HLA-A74:09	KLRLNHSLKK	0.9554	0.5186	11	21
RBL1-CSTA	chr20	35717392	chr3	122056394	351	HLA-A74:03	KLRLNHSLKK	0.9554	0.5186	11	21
RBL1-CSTA	chr20	35717392	chr3	122056394	351	HLA-B27:07	TRILRSAKLRL	0.9998	0.5246	4	15
RBL1-CSTA	chr20	35717392	chr3	122056394	351	HLA-B27:05	AKLRLNHSLKK	0.9983	0.8876	10	21
RBL1-CSTA	chr20	35717392	chr3	122056394	351	HLA-B27:14	LRLNHSLKK	0.9973	0.8102	12	21
RBL1-CSTA	chr20	35717392	chr3	122056394	351	HLA-B39:12	AKLRLNHSL	0.9774	0.8016	10	19
RBL1-CSTA	chr20	35717392	chr3	122056394	351	HLA-B27:03	LRLNHSLKK	0.9301	0.8823	12	21
RBL1-CSTA	chr20	35717392	chr3	122056394	351	HLA-B39:05	AKLRLNHSL	0.8013	0.7731	10	19
RBL1-CSTA	chr20	35717392	chr3	122056394	351	HLA-B15:04	ILRSAKLRL	0.6719	0.8414	6	15
RBL1-CSTA	chr20	35717392	chr3	122056394	351	HLA-B14:03	AKLRLNHSL	0.4867	0.6414	10	19
RBL1-CSTA	chr20	35717392	chr3	122056394	351	HLA-B27:14	KLRLNHSLKK	0.9176	0.7583	11	21
RBL1-CSTA	chr20	35717392	chr3	122056394	351	HLA-B27:03	KLRLNHSLKK	0.4942	0.8599	11	21
RBL1-CSTA	chr20	35717392	chr3	122056394	351	HLA-B27:14	AKLRLNHSLKK	0.998	0.8188	10	21
RBL1-CSTA	chr20	35717392	chr3	122056394	351	HLA-B27:03	AKLRLNHSLKK	0.8239	0.9121	10	21
RBL1-CSTA	chr20	35717392	chr3	122056394	351	HLA-A30:01	KLRLNHSLK	0.9987	0.8532	11	20
RBL1-CSTA	chr20	35717392	chr3	122056394	351	HLA-B27:10	LRLNHSLKK	0.9986	0.7932	12	21
RBL1-CSTA	chr20	35717392	chr3	122056394	351	HLA-A74:01	RILRSAKLR	0.9807	0.5988	5	14
RBL1-CSTA	chr20	35717392	chr3	122056394	351	HLA-B39:02	AKLRLNHSL	0.9763	0.7822	10	19
RBL1-CSTA	chr20	35717392	chr3	122056394	351	HLA-B39:31	AKLRLNHSL	0.9589	0.8004	10	19
RBL1-CSTA	chr20	35717392	chr3	122056394	351	HLA-B48:02	AKLRLNHSL	0.331	0.7802	10	19
RBL1-CSTA	chr20	35717392	chr3	122056394	351	HLA-A30:01	KLRLNHSLKK	0.9977	0.8372	11	21
RBL1-CSTA	chr20	35717392	chr3	122056394	351	HLA-B08:12	SAKLRLNHSL	0.9826	0.571	9	19
RBL1-CSTA	chr20	35717392	chr3	122056394	351	HLA-A74:01	KLRLNHSLKK	0.9554	0.5186	11	21
RBL1-CSTA	chr20	35717392	chr3	122056394	351	HLA-B27:10	KLRLNHSLKK	0.8829	0.7615	11	21
RBL1-CSTA	chr20	35717392	chr3	122056394	351	HLA-B27:06	TRILRSAKLRL	0.9999	0.7089	4	15
RBL1-CSTA	chr20	35717392	chr3	122056394	351	HLA-B27:09	TRILRSAKLRL	0.9997	0.7918	4	15
RBL1-CSTA	chr20	35717392	chr3	122056394	351	HLA-B27:10	AKLRLNHSLKK	0.9984	0.8603	10	21

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Potential FusionNeoAntigen Information of RBL1-CSTA in HLA II

RBL1-CSTA_35717392_122056394.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)
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-0303	RSAKLRLNHSLKKKQ	8	23
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-0303	SAKLRLNHSLKKKQM	9	24
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-0303	LRSAKLRLNHSLKKK	7	22
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1113	LTRILRSAKLRLNHS	3	18
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1113	SLTRILRSAKLRLNH	2	17
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1117	LTRILRSAKLRLNHS	3	18
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1117	SLTRILRSAKLRLNH	2	17
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1117	TRILRSAKLRLNHSL	4	19
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1152	LTRILRSAKLRLNHS	3	18
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1152	SLTRILRSAKLRLNH	2	17
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1152	TRILRSAKLRLNHSL	4	19
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1186	RSAKLRLNHSLKKKQ	8	23
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1186	SAKLRLNHSLKKKQM	9	24
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1189	LTRILRSAKLRLNHS	3	18
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1189	SLTRILRSAKLRLNH	2	17
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1316	RSAKLRLNHSLKKKQ	8	23
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1316	SAKLRLNHSLKKKQM	9	24
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1341	RSAKLRLNHSLKKKQ	8	23
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1341	SAKLRLNHSLKKKQM	9	24
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1367	RSAKLRLNHSLKKKQ	8	23
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1367	SAKLRLNHSLKKKQM	9	24
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1396	RSAKLRLNHSLKKKQ	8	23
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1396	SAKLRLNHSLKKKQM	9	24
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1401	LTRILRSAKLRLNHS	3	18
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1401	SLTRILRSAKLRLNH	2	17
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1401	VSLTRILRSAKLRLN	1	16
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1401	TRILRSAKLRLNHSL	4	19
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1404	LTRILRSAKLRLNHS	3	18
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1404	SLTRILRSAKLRLNH	2	17
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1405	LTRILRSAKLRLNHS	3	18
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1405	SLTRILRSAKLRLNH	2	17
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1405	TRILRSAKLRLNHSL	4	19
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1407	LTRILRSAKLRLNHS	3	18
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1407	SLTRILRSAKLRLNH	2	17
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1408	LTRILRSAKLRLNHS	3	18
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1408	SLTRILRSAKLRLNH	2	17
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1408	TRILRSAKLRLNHSL	4	19
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1411	LTRILRSAKLRLNHS	3	18
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1411	SLTRILRSAKLRLNH	2	17
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1416	LTRILRSAKLRLNHS	3	18
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1418	LTRILRSAKLRLNHS	3	18
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1418	SLTRILRSAKLRLNH	2	17
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1418	TRILRSAKLRLNHSL	4	19
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1418	VSLTRILRSAKLRLN	1	16
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1419	RSAKLRLNHSLKKKQ	8	23
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1419	SAKLRLNHSLKKKQM	9	24
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1423	LTRILRSAKLRLNHS	3	18
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1423	SLTRILRSAKLRLNH	2	17
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1423	TRILRSAKLRLNHSL	4	19
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1424	RSAKLRLNHSLKKKQ	8	23
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1424	SAKLRLNHSLKKKQM	9	24
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1426	LTRILRSAKLRLNHS	3	18
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1426	SLTRILRSAKLRLNH	2	17
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1426	VSLTRILRSAKLRLN	1	16
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1426	TRILRSAKLRLNHSL	4	19
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1428	LTRILRSAKLRLNHS	3	18
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1428	SLTRILRSAKLRLNH	2	17
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1428	VSLTRILRSAKLRLN	1	16
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1431	LTRILRSAKLRLNHS	3	18
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1432	LTRILRSAKLRLNHS	3	18
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1432	SLTRILRSAKLRLNH	2	17
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1434	LTRILRSAKLRLNHS	3	18
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1434	SLTRILRSAKLRLNH	2	17
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1435	LTRILRSAKLRLNHS	3	18
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1435	SLTRILRSAKLRLNH	2	17
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1435	VSLTRILRSAKLRLN	1	16
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1435	TRILRSAKLRLNHSL	4	19
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1438	LTRILRSAKLRLNHS	3	18
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1438	SLTRILRSAKLRLNH	2	17
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1438	VSLTRILRSAKLRLN	1	16
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1438	TRILRSAKLRLNHSL	4	19
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1439	LTRILRSAKLRLNHS	3	18
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1443	LTRILRSAKLRLNHS	3	18
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1443	SLTRILRSAKLRLNH	2	17
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1443	TRILRSAKLRLNHSL	4	19
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1445	LTRILRSAKLRLNHS	3	18
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1445	SLTRILRSAKLRLNH	2	17
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1445	TRILRSAKLRLNHSL	4	19
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1445	VSLTRILRSAKLRLN	1	16
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1447	RSAKLRLNHSLKKKQ	8	23
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1447	SAKLRLNHSLKKKQM	9	24
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1447	LRSAKLRLNHSLKKK	7	22
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1450	LTRILRSAKLRLNHS	3	18
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1450	SLTRILRSAKLRLNH	2	17
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1450	VSLTRILRSAKLRLN	1	16
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1454	LTRILRSAKLRLNHS	3	18
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1454	SLTRILRSAKLRLNH	2	17
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1454	VSLTRILRSAKLRLN	1	16
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1454	TRILRSAKLRLNHSL	4	19
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1455	LTRILRSAKLRLNHS	3	18
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1455	SLTRILRSAKLRLNH	2	17
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1456	LTRILRSAKLRLNHS	3	18
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1456	SLTRILRSAKLRLNH	2	17
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1456	TRILRSAKLRLNHSL	4	19
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1458	LTRILRSAKLRLNHS	3	18
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1458	SLTRILRSAKLRLNH	2	17
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1458	VSLTRILRSAKLRLN	1	16
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1458	TRILRSAKLRLNHSL	4	19
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1459	LTRILRSAKLRLNHS	3	18
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1459	SLTRILRSAKLRLNH	2	17
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1459	TRILRSAKLRLNHSL	4	19
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1460	LTRILRSAKLRLNHS	3	18
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1460	SLTRILRSAKLRLNH	2	17
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1460	VSLTRILRSAKLRLN	1	16
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1460	TRILRSAKLRLNHSL	4	19
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1461	LTRILRSAKLRLNHS	3	18
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1461	SLTRILRSAKLRLNH	2	17
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1462	LTRILRSAKLRLNHS	3	18
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1462	SLTRILRSAKLRLNH	2	17
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1462	VSLTRILRSAKLRLN	1	16
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1462	TRILRSAKLRLNHSL	4	19
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1464	LTRILRSAKLRLNHS	3	18
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1464	SLTRILRSAKLRLNH	2	17
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1464	TRILRSAKLRLNHSL	4	19
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1465	LTRILRSAKLRLNHS	3	18
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1465	SLTRILRSAKLRLNH	2	17
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1470	LTRILRSAKLRLNHS	3	18
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1470	SLTRILRSAKLRLNH	2	17
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1471	LTRILRSAKLRLNHS	3	18
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1471	SLTRILRSAKLRLNH	2	17
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1472	LTRILRSAKLRLNHS	3	18
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1472	SLTRILRSAKLRLNH	2	17
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1472	TRILRSAKLRLNHSL	4	19
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1475	LTRILRSAKLRLNHS	3	18
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1475	SLTRILRSAKLRLNH	2	17
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1475	VSLTRILRSAKLRLN	1	16
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1475	TRILRSAKLRLNHSL	4	19
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1481	LTRILRSAKLRLNHS	3	18
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1481	SLTRILRSAKLRLNH	2	17
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1482	LTRILRSAKLRLNHS	3	18
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1482	SLTRILRSAKLRLNH	2	17
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1482	VSLTRILRSAKLRLN	1	16
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1482	TRILRSAKLRLNHSL	4	19
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1486	LTRILRSAKLRLNHS	3	18
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1486	SLTRILRSAKLRLNH	2	17
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1486	VSLTRILRSAKLRLN	1	16
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1486	TRILRSAKLRLNHSL	4	19
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1487	LTRILRSAKLRLNHS	3	18
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1487	SLTRILRSAKLRLNH	2	17
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1487	VSLTRILRSAKLRLN	1	16
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1487	TRILRSAKLRLNHSL	4	19
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1488	LTRILRSAKLRLNHS	3	18
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1488	SLTRILRSAKLRLNH	2	17
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1488	VSLTRILRSAKLRLN	1	16
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1488	TRILRSAKLRLNHSL	4	19
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1490	LTRILRSAKLRLNHS	3	18
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1490	SLTRILRSAKLRLNH	2	17
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1490	VSLTRILRSAKLRLN	1	16
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1490	TRILRSAKLRLNHSL	4	19
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1491	LTRILRSAKLRLNHS	3	18
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1491	SLTRILRSAKLRLNH	2	17
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1491	TRILRSAKLRLNHSL	4	19
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1495	LTRILRSAKLRLNHS	3	18
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1495	SLTRILRSAKLRLNH	2	17
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1495	TRILRSAKLRLNHSL	4	19
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1496	LTRILRSAKLRLNHS	3	18
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1496	SLTRILRSAKLRLNH	2	17
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1496	TRILRSAKLRLNHSL	4	19
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1497	LTRILRSAKLRLNHS	3	18
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1497	SLTRILRSAKLRLNH	2	17
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1497	VSLTRILRSAKLRLN	1	16
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1497	TRILRSAKLRLNHSL	4	19
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1498	SAKLRLNHSLKKKQM	9	24
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1498	RSAKLRLNHSLKKKQ	8	23
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1499	LTRILRSAKLRLNHS	3	18
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1499	SLTRILRSAKLRLNH	2	17
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1499	VSLTRILRSAKLRLN	1	16
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB1-1499	TRILRSAKLRLNHSL	4	19
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB3-0204	RSAKLRLNHSLKKKQ	8	23
RBL1-CSTA	chr20	35717392	chr3	122056394	351	DRB3-0204	SAKLRLNHSLKKKQM	9	24

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Fusion breakpoint peptide structures of RBL1-CSTA

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
3816	ILRSAKLRLNHSLK	RBL1	CSTA	chr20	35717392	chr3	122056394	351

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of RBL1-CSTA

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	3816	ILRSAKLRLNHSLK	-7.15543	-7.26883
HLA-B14:02	3BVN	3816	ILRSAKLRLNHSLK	-4.77435	-5.80965
HLA-B52:01	3W39	3816	ILRSAKLRLNHSLK	-6.80875	-6.92215
HLA-B52:01	3W39	3816	ILRSAKLRLNHSLK	-4.20386	-5.23916
HLA-A11:01	4UQ2	3816	ILRSAKLRLNHSLK	-7.5194	-8.5547
HLA-A11:01	4UQ2	3816	ILRSAKLRLNHSLK	-6.9601	-7.0735
HLA-A24:02	5HGA	3816	ILRSAKLRLNHSLK	-7.52403	-7.63743
HLA-A24:02	5HGA	3816	ILRSAKLRLNHSLK	-5.82433	-6.85963
HLA-B27:05	6PYJ	3816	ILRSAKLRLNHSLK	-3.28285	-4.31815
HLA-B44:05	3DX8	3816	ILRSAKLRLNHSLK	-5.91172	-6.94702
HLA-B44:05	3DX8	3816	ILRSAKLRLNHSLK	-4.24346	-4.35686

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Vaccine Design for the FusionNeoAntigens of RBL1-CSTA

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
RBL1-CSTA	chr20	35717392	chr3	122056394	10	19	AKLRLNHSL	TAAATTAAGGTTAAACCACAGCTTGAA
RBL1-CSTA	chr20	35717392	chr3	122056394	10	21	AKLRLNHSLKK	TAAATTAAGGTTAAACCACAGCTTGAAGAAAAA
RBL1-CSTA	chr20	35717392	chr3	122056394	11	20	KLRLNHSLK	ATTAAGGTTAAACCACAGCTTGAAGAA
RBL1-CSTA	chr20	35717392	chr3	122056394	11	21	KLRLNHSLKK	ATTAAGGTTAAACCACAGCTTGAAGAAAAA
RBL1-CSTA	chr20	35717392	chr3	122056394	12	21	LRLNHSLKK	AAGGTTAAACCACAGCTTGAAGAAAAA
RBL1-CSTA	chr20	35717392	chr3	122056394	4	15	TRILRSAKLRL	CAGAATACTACGTTCAGCTAAATTAAGGTTAAA
RBL1-CSTA	chr20	35717392	chr3	122056394	5	14	RILRSAKLR	AATACTACGTTCAGCTAAATTAAGGTT
RBL1-CSTA	chr20	35717392	chr3	122056394	6	15	ILRSAKLRL	ACTACGTTCAGCTAAATTAAGGTTAAA
RBL1-CSTA	chr20	35717392	chr3	122056394	9	19	SAKLRLNHSL	AGCTAAATTAAGGTTAAACCACAGCTTGAA

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
RBL1-CSTA	chr20	35717392	chr3	122056394	1	16	VSLTRILRSAKLRLN	TTCACTTACCAGAATACTACGTTCAGCTAAATTAAGGTTAAACCA
RBL1-CSTA	chr20	35717392	chr3	122056394	2	17	SLTRILRSAKLRLNH	ACTTACCAGAATACTACGTTCAGCTAAATTAAGGTTAAACCACAG
RBL1-CSTA	chr20	35717392	chr3	122056394	3	18	LTRILRSAKLRLNHS	TACCAGAATACTACGTTCAGCTAAATTAAGGTTAAACCACAGCTT
RBL1-CSTA	chr20	35717392	chr3	122056394	4	19	TRILRSAKLRLNHSL	CAGAATACTACGTTCAGCTAAATTAAGGTTAAACCACAGCTTGAA
RBL1-CSTA	chr20	35717392	chr3	122056394	7	22	LRSAKLRLNHSLKKK	ACGTTCAGCTAAATTAAGGTTAAACCACAGCTTGAAGAAAAAACA
RBL1-CSTA	chr20	35717392	chr3	122056394	8	23	RSAKLRLNHSLKKKQ	TTCAGCTAAATTAAGGTTAAACCACAGCTTGAAGAAAAAACAAAT
RBL1-CSTA	chr20	35717392	chr3	122056394	9	24	SAKLRLNHSLKKKQM	AGCTAAATTAAGGTTAAACCACAGCTTGAAGAAAAAACAAATGAG

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Information of the samples that have these potential fusion neoantigens of RBL1-CSTA

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	RBL1-CSTA	chr20	35717392	ENST00000344359	chr3	122056394	ENST00000479204	TCGA-61-2111-01A

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Potential target of CAR-T therapy development for RBL1-CSTA

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 RBL1-CSTA

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 RBL1-CSTA

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)