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Fusion Protein:RCOR1-AMN

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: RCOR1-AMN
	FusionPDB ID: 73321
	FusionGDB2.0 ID: 73321
		Hgene	Tgene
	Gene symbol	RCOR1	AMN
	Gene ID	23186	81693
	Gene name	REST corepressor 1	amnion associated transmembrane protein
	Synonyms	COREST\|RCOR	PRO1028\|amnionless
	Cytomap	14q32.31-q32.32	14q32.32
	Type of gene	protein-coding	protein-coding
	Description	REST corepressor 1	protein amnionlessamnionless homologvisceral endoderm-specific type 1 transmembrane protein
	Modification date	20200313	20200313
	UniProtAcc	.	Q8IY45 Main function of 5'-partner protein:
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000262241, ENST00000570597,	ENST00000299155,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	10 X 9 X 10=900	3 X 5 X 3=45
	# samples	20	4
	** MAII score	log2(20/900*10)=-2.16992500144231 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(4/45*10)=-0.169925001442312 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: RCOR1 [Title/Abstract] AND AMN [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: RCOR1 [Title/Abstract] AND AMN [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	RCOR1(103059662)-AMN(103390048), # samples:2
Anticipated loss of major functional domain due to fusion event.	RCOR1-AMN 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. RCOR1-AMN 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. RCOR1-AMN 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. RCOR1-AMN 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. RCOR1-AMN seems lost the major protein functional domain in Hgene partner, which is a epigenetic factor due to the frame-shifted ORF. RCOR1-AMN seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF. RCOR1-AMN seems lost the major protein functional domain in Tgene partner, which is a cell metabolism gene due to the frame-shifted ORF. RCOR1-AMN 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	RCOR1	GO:0045892	negative regulation of transcription, DNA-templated	10449787
Hgene	RCOR1	GO:0070933	histone H4 deacetylation	17555596
Tgene	AMN	GO:0006898	receptor-mediated endocytosis	14576052
Tgene	AMN	GO:0015889	cobalamin transport	14576052
Tgene	AMN	GO:0043001	Golgi to plasma membrane protein transport	14576052

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr14:103059662/chr14:103390048)
- 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 RCOR1 (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 AMN (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)

ENST00000262241

RCOR1

chr14

103059662

ENST00000299155

AMN

chr14

103390048

2418

587

1905

626

ENST00000570597

RCOR1

chr14

103059662

ENST00000299155

AMN

chr14

103390048

2183

352

1670

556

ENST00000262241

RCOR1

chr14

103059662

ENST00000299155

AMN

chr14

103390047

2418

587

1905

626

ENST00000570597

RCOR1

chr14

103059662

ENST00000299155

AMN

chr14

103390047

2183

352

1670

556

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
ENST00000262241	ENST00000299155	RCOR1	chr14	103059662	+	AMN	chr14	103390048	+	0.06587295	0.934127
ENST00000570597	ENST00000299155	RCOR1	chr14	103059662	+	AMN	chr14	103390048	+	0.06324657	0.9367534
ENST00000262241	ENST00000299155	RCOR1	chr14	103059662	+	AMN	chr14	103390047	+	0.06587295	0.934127
ENST00000570597	ENST00000299155	RCOR1	chr14	103059662	+	AMN	chr14	103390047	+	0.06324657	0.9367534

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 RCOR1-AMN

+/-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
RCOR1	chr14	103059662	AMN	chr14	103390047	352	17	GPEVSGKRRGRNNAAASASAAAASAA
RCOR1	chr14	103059662	AMN	chr14	103390047	587	19	WGLEAAPRSARLGLPRLGLAPVGSRR
RCOR1	chr14	103059662	AMN	chr14	103390048	352	17	GPEVSGKRRGRNNAAASASAAAASAA
RCOR1	chr14	103059662	AMN	chr14	103390048	587	19	WGLEAAPRSARLGLPRLGLAPVGSRR

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Potential FusionNeoAntigen Information of RCOR1-AMN 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.

RCOR1-AMN_103059662_103390047.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)
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-B27:07	ARLGLPRL	0.9999	0.6562	9	17
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-B07:05	PRSARLGL	0.6196	0.5242	6	14
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-B07:02	PRSARLGL	0.5607	0.6477	6	14
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-B07:02	APRSARLGL	0.9998	0.6979	5	14
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-B07:05	APRSARLGL	0.9998	0.5431	5	14
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-B07:10	APRSARLGL	0.9998	0.7309	5	14
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-A74:09	RSARLGLPR	0.9952	0.7946	7	16
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-A74:11	RSARLGLPR	0.9952	0.7946	7	16
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-A74:03	RSARLGLPR	0.9952	0.7946	7	16
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-A31:06	RSARLGLPR	0.9677	0.7275	7	16
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-A11:04	RSARLGLPR	0.9378	0.6038	7	16
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-A31:02	RSARLGLPR	0.9354	0.8008	7	16
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-A03:12	RSARLGLPR	0.8904	0.7033	7	16
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-B08:09	APRSARLGL	0.7902	0.5348	5	14
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-B82:01	APRSARLGL	0.215	0.6474	5	14
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-B27:02	ARLGLPRLGL	0.9999	0.785	9	19
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-B27:04	ARLGLPRLGL	0.9999	0.8482	9	19
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-B27:07	ARLGLPRLGL	0.9999	0.7429	9	19
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-B27:05	ARLGLPRLGL	0.9999	0.9393	9	19
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-B07:02	APRSARLGLP	0.9962	0.625	5	15
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-B07:05	APRSARLGLP	0.996	0.6382	5	15
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-B07:02	AAPRSARLGL	0.9621	0.7044	4	14
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-B07:05	AAPRSARLGL	0.9615	0.5256	4	14
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-B07:02	EAAPRSARLGL	0.9974	0.6311	3	14
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-B07:04	PRSARLGL	0.9826	0.5802	6	14
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-C03:07	SARLGLPRL	0.996	0.9768	8	17
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-A31:01	RSARLGLPR	0.9947	0.7753	7	16
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-C03:19	SARLGLPRL	0.994	0.992	8	17
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-C03:08	SARLGLPRL	0.9927	0.9469	8	17
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-C15:06	SARLGLPRL	0.9922	0.9475	8	17
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-B07:12	APRSARLGL	0.9904	0.8346	5	14
RCOR1-AMN	chr14	103059662	chr14	103390047	352	HLA-B27:14	GRNNAAASA	0.9881	0.8581	9	18
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-A11:01	RSARLGLPR	0.9856	0.571	7	16
RCOR1-AMN	chr14	103059662	chr14	103390047	352	HLA-B73:01	GRNNAAASA	0.9829	0.7824	9	18
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-B07:04	SARLGLPRL	0.9747	0.5272	8	17
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-C02:06	SARLGLPRL	0.973	0.9825	8	17
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-C06:03	SARLGLPRL	0.9574	0.9963	8	17
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-C12:04	SARLGLPRL	0.9555	0.9972	8	17
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-C12:12	SARLGLPRL	0.9355	0.9367	8	17
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-B07:04	APRSARLGL	0.8951	0.6673	5	14
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-B39:10	APRSARLGL	0.2427	0.8091	5	14
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-B27:14	ARLGLPRLGL	0.9999	0.8954	9	19
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-B27:03	ARLGLPRLGL	0.9959	0.946	9	19
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-B07:04	AAPRSARLGL	0.9735	0.6948	4	14
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-B07:04	APRSARLGLP	0.9637	0.6122	5	15
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-B07:12	AAPRSARLGL	0.9564	0.8384	4	14
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-C01:17	AAPRSARLGL	0.9551	0.9506	4	14
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-B07:04	EAAPRSARLGL	0.9961	0.6202	3	14
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-B27:06	ARLGLPRL	0.9999	0.8772	9	17
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-B27:09	ARLGLPRL	0.9999	0.9402	9	17
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-B07:22	PRSARLGL	0.5607	0.6477	6	14
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-B07:22	APRSARLGL	0.9998	0.6979	5	14
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-B07:09	APRSARLGL	0.9997	0.6997	5	14
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-A74:01	RSARLGLPR	0.9952	0.7946	7	16
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-C03:05	SARLGLPRL	0.9895	0.9399	8	17
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-C03:17	SARLGLPRL	0.9865	0.9795	8	17
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-A11:02	RSARLGLPR	0.9856	0.571	7	16
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-C03:03	SARLGLPRL	0.9847	0.993	8	17
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-C03:04	SARLGLPRL	0.9847	0.993	8	17
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-B07:13	SARLGLPRL	0.9723	0.8882	8	17
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-C16:04	SARLGLPRL	0.9541	0.9797	8	17
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-C12:03	SARLGLPRL	0.9425	0.987	8	17
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-C16:02	SARLGLPRL	0.7888	0.9962	8	17
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-C16:01	SARLGLPRL	0.6598	0.9831	8	17
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-B67:01	APRSARLGL	0.2538	0.7107	5	14
RCOR1-AMN	chr14	103059662	chr14	103390047	352	HLA-B78:02	NAAASASAA	0.2499	0.8329	12	21
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-B82:02	APRSARLGL	0.215	0.6474	5	14
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-B27:09	ARLGLPRLGL	0.9999	0.9299	9	19
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-B27:10	ARLGLPRLGL	0.9999	0.9333	9	19
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-B27:06	ARLGLPRLGL	0.9999	0.8705	9	19
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-B27:08	ARLGLPRLGL	0.9999	0.8636	9	19
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-B07:22	APRSARLGLP	0.9962	0.625	5	15
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-B07:22	AAPRSARLGL	0.9621	0.7044	4	14
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-B07:09	AAPRSARLGL	0.9611	0.7166	4	14
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-C01:02	AAPRSARLGL	0.9537	0.9491	4	14
RCOR1-AMN	chr14	103059662	chr14	103390047	587	HLA-B07:22	EAAPRSARLGL	0.9974	0.6311	3	14

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Potential FusionNeoAntigen Information of RCOR1-AMN 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 RCOR1-AMN

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
4576	KRRGRNNAAASASA	RCOR1	AMN	chr14	103059662	chr14	103390047	352

File name	BPseq	Hgene	Tgene	Hchr	Hbp	Tchr	Tbp	AAlen
6966	PRSARLGLPRLGLA	RCOR1	AMN	chr14	103059662	chr14	103390047	587

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of RCOR1-AMN

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	4576	KRRGRNNAAASASA	-7.15543	-7.26883
HLA-B14:02	3BVN	4576	KRRGRNNAAASASA	-4.77435	-5.80965
HLA-B52:01	3W39	4576	KRRGRNNAAASASA	-6.80875	-6.92215
HLA-B52:01	3W39	4576	KRRGRNNAAASASA	-4.20386	-5.23916
HLA-A11:01	4UQ2	4576	KRRGRNNAAASASA	-7.5194	-8.5547
HLA-A11:01	4UQ2	4576	KRRGRNNAAASASA	-6.9601	-7.0735
HLA-A24:02	5HGA	4576	KRRGRNNAAASASA	-7.52403	-7.63743
HLA-A24:02	5HGA	4576	KRRGRNNAAASASA	-5.82433	-6.85963
HLA-B27:05	6PYJ	4576	KRRGRNNAAASASA	-3.28285	-4.31815
HLA-B44:05	3DX8	4576	KRRGRNNAAASASA	-5.91172	-6.94702
HLA-B44:05	3DX8	4576	KRRGRNNAAASASA	-4.24346	-4.35686
HLA-B14:02	3BVN	6966	PRSARLGLPRLGLA	-7.15543	-7.26883
HLA-B14:02	3BVN	6966	PRSARLGLPRLGLA	-4.77435	-5.80965
HLA-B52:01	3W39	6966	PRSARLGLPRLGLA	-6.80875	-6.92215
HLA-B52:01	3W39	6966	PRSARLGLPRLGLA	-4.20386	-5.23916
HLA-A11:01	4UQ2	6966	PRSARLGLPRLGLA	-7.5194	-8.5547
HLA-A11:01	4UQ2	6966	PRSARLGLPRLGLA	-6.9601	-7.0735
HLA-A24:02	5HGA	6966	PRSARLGLPRLGLA	-7.52403	-7.63743
HLA-A24:02	5HGA	6966	PRSARLGLPRLGLA	-5.82433	-6.85963
HLA-B27:05	6PYJ	6966	PRSARLGLPRLGLA	-3.28285	-4.31815
HLA-B44:05	3DX8	6966	PRSARLGLPRLGLA	-5.91172	-6.94702
HLA-B44:05	3DX8	6966	PRSARLGLPRLGLA	-4.24346	-4.35686

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Vaccine Design for the FusionNeoAntigens of RCOR1-AMN

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
RCOR1-AMN	chr14	103059662	chr14	103390047	12	21	NAAASASAA	CCGCACTGACCCAGGCGGTCTCCAAAC
RCOR1-AMN	chr14	103059662	chr14	103390047	3	14	EAAPRSARLGL	ACCAGGCGGTGGTGCCCGACTTCGACCCCGCAC
RCOR1-AMN	chr14	103059662	chr14	103390047	4	14	AAPRSARLGL	AGGCGGTGGTGCCCGACTTCGACCCCGCAC
RCOR1-AMN	chr14	103059662	chr14	103390047	5	14	APRSARLGL	CGGTGGTGCCCGACTTCGACCCCGCAC
RCOR1-AMN	chr14	103059662	chr14	103390047	5	15	APRSARLGLP	CGGTGGTGCCCGACTTCGACCCCGCACTGA
RCOR1-AMN	chr14	103059662	chr14	103390047	6	14	PRSARLGL	TGGTGCCCGACTTCGACCCCGCAC
RCOR1-AMN	chr14	103059662	chr14	103390047	7	16	RSARLGLPR	TGCCCGACTTCGACCCCGCACTGACCC
RCOR1-AMN	chr14	103059662	chr14	103390047	8	17	SARLGLPRL	CCGACTTCGACCCCGCACTGACCCAGG
RCOR1-AMN	chr14	103059662	chr14	103390047	9	17	ARLGLPRL	ACTTCGACCCCGCACTGACCCAGG
RCOR1-AMN	chr14	103059662	chr14	103390047	9	18	GRNNAAASA	ACTTCGACCCCGCACTGACCCAGGCGG
RCOR1-AMN	chr14	103059662	chr14	103390047	9	19	ARLGLPRLGL	ACTTCGACCCCGCACTGACCCAGGCGGTCT

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 RCOR1-AMN

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
STAD	RCOR1-AMN	chr14	103059662	ENST00000262241	chr14	103390047	ENST00000299155	TCGA-VQ-A928
STAD	RCOR1-AMN	chr14	103059662	ENST00000570597	chr14	103390047	ENST00000299155	TCGA-VQ-A928

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Potential target of CAR-T therapy development for RCOR1-AMN

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

AMN

chr14:103059662

chr14:103390047

ENST00000299155

358_378

454.0

Transmembrane

Helical

Tgene

AMN

chr14:103059662

chr14:103390048

ENST00000299155

358_378

454.0

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 RCOR1-AMN

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 RCOR1-AMN

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)