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Fusion Protein:RPS19-CEACAM5

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: RPS19-CEACAM5
	FusionPDB ID: 77528
	FusionGDB2.0 ID: 77528
		Hgene	Tgene
	Gene symbol	RPS19	CEACAM5
	Gene ID	6223	1048
	Gene name	ribosomal protein S19	CEA cell adhesion molecule 5
	Synonyms	DBA\|DBA1\|LOH19CR1\|S19\|eS19	CD66e\|CEA
	Cytomap	19q13.2	19q13.2
	Type of gene	protein-coding	protein-coding
	Description	40S ribosomal protein S19loss of heterozygosity on chromosome 19, region 1loss of heterozygosity, 19, chromosomal region 1small ribosomal subunit protein eS19	carcinoembryonic antigen-related cell adhesion molecule 5carcinoembryonic antigen related cell adhesion molecule 5meconium antigen 100
	Modification date	20200313	20200313
	UniProtAcc	.	P06731 Main function of 5'-partner protein: FUNCTION: Cell surface glycoprotein that plays a role in cell adhesion, intracellular signaling and tumor progression (PubMed:2803308, PubMed:10910050, PubMed:10864933). Mediates homophilic and heterophilic cell adhesion with other carcinoembryonic antigen-related cell adhesion molecules, such as CEACAM6 (PubMed:2803308). Plays a role as an oncogene by promoting tumor progression; induces resistance to anoikis of colorectal carcinoma cells (PubMed:10910050). {ECO:0000269\|PubMed:10864933, ECO:0000269\|PubMed:10910050, ECO:0000269\|PubMed:2803308}.; FUNCTION: (Microbial infection) Receptor for E.coli Dr adhesins. Binding of E.coli Dr adhesins leads to dissociation of the homodimer. {ECO:0000269\|PubMed:18086185}.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000221975, ENST00000593863, ENST00000598742,	ENST00000221992, ENST00000398599, ENST00000405816,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	21 X 12 X 11=2772	11 X 16 X 6=1056
	# samples	26	14
	** MAII score	log2(26/2772*10)=-3.41434372910876 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(14/1056*10)=-2.91511110241349 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: RPS19 [Title/Abstract] AND CEACAM5 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: RPS19 [Title/Abstract] AND CEACAM5 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	RPS19(42365281)-CEACAM5(42231154), # samples:2
Anticipated loss of major functional domain due to fusion event.	RPS19-CEACAM5 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. RPS19-CEACAM5 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. RPS19-CEACAM5 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. RPS19-CEACAM5 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. RPS19-CEACAM5 seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF. RPS19-CEACAM5 seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target 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	RPS19	GO:0002548	monocyte chemotaxis	11226885
Hgene	RPS19	GO:0031640	killing of cells of other organism	15019208
Hgene	RPS19	GO:0050829	defense response to Gram-negative bacterium	15019208
Hgene	RPS19	GO:0060265	positive regulation of respiratory burst involved in inflammatory response	15750715
Hgene	RPS19	GO:0060266	negative regulation of respiratory burst involved in inflammatory response	15750715
Hgene	RPS19	GO:0061844	antimicrobial humoral immune response mediated by antimicrobial peptide	15019208
Tgene	CEACAM5	GO:0010832	negative regulation of myotube differentiation	8408226\|10931872
Tgene	CEACAM5	GO:0034109	homotypic cell-cell adhesion	10864933
Tgene	CEACAM5	GO:0043066	negative regulation of apoptotic process	11448920
Tgene	CEACAM5	GO:2000811	negative regulation of anoikis	10910050

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr19:42365281/chr19:42231154)
- 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 RPS19 (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 CEACAM5 (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)
ENST00000598742	RPS19	chr19	42365281	+	ENST00000398599	CEACAM5	chr19	42224841	+	1080	544	372	881	169
ENST00000598742	RPS19	chr19	42365281	+	ENST00000221992	CEACAM5	chr19	42224841	+	1533	544	372	881	169
ENST00000598742	RPS19	chr19	42365281	+	ENST00000405816	CEACAM5	chr19	42224841	+	1044	544	372	881	169
ENST00000593863	RPS19	chr19	42365281	+	ENST00000398599	CEACAM5	chr19	42224841	+	757	221	49	558	169
ENST00000593863	RPS19	chr19	42365281	+	ENST00000221992	CEACAM5	chr19	42224841	+	1210	221	49	558	169
ENST00000593863	RPS19	chr19	42365281	+	ENST00000405816	CEACAM5	chr19	42224841	+	721	221	49	558	169
ENST00000598742	RPS19	chr19	42365281	+	ENST00000398599	CEACAM5	chr19	42213598	+	2784	544	372	2585	737
ENST00000598742	RPS19	chr19	42365281	+	ENST00000221992	CEACAM5	chr19	42213598	+	3240	544	372	2588	738
ENST00000598742	RPS19	chr19	42365281	+	ENST00000405816	CEACAM5	chr19	42213598	+	2751	544	372	2588	738
ENST00000593863	RPS19	chr19	42365281	+	ENST00000398599	CEACAM5	chr19	42213598	+	2461	221	49	2262	737
ENST00000593863	RPS19	chr19	42365281	+	ENST00000221992	CEACAM5	chr19	42213598	+	2917	221	49	2265	738
ENST00000593863	RPS19	chr19	42365281	+	ENST00000405816	CEACAM5	chr19	42213598	+	2428	221	49	2265	738
ENST00000598742	RPS19	chr19	42365281	+	ENST00000398599	CEACAM5	chr19	42224842	+	1080	544	372	881	169
ENST00000598742	RPS19	chr19	42365281	+	ENST00000221992	CEACAM5	chr19	42224842	+	1533	544	372	881	169
ENST00000598742	RPS19	chr19	42365281	+	ENST00000405816	CEACAM5	chr19	42224842	+	1044	544	372	881	169
ENST00000593863	RPS19	chr19	42365281	+	ENST00000398599	CEACAM5	chr19	42224842	+	757	221	49	558	169
ENST00000593863	RPS19	chr19	42365281	+	ENST00000221992	CEACAM5	chr19	42224842	+	1210	221	49	558	169
ENST00000593863	RPS19	chr19	42365281	+	ENST00000405816	CEACAM5	chr19	42224842	+	721	221	49	558	169
ENST00000598742	RPS19	chr19	42365281	+	ENST00000398599	CEACAM5	chr19	42213599	+	2784	544	372	2585	737
ENST00000598742	RPS19	chr19	42365281	+	ENST00000221992	CEACAM5	chr19	42213599	+	3240	544	372	2588	738
ENST00000598742	RPS19	chr19	42365281	+	ENST00000405816	CEACAM5	chr19	42213599	+	2751	544	372	2588	738
ENST00000593863	RPS19	chr19	42365281	+	ENST00000398599	CEACAM5	chr19	42213599	+	2461	221	49	2262	737
ENST00000593863	RPS19	chr19	42365281	+	ENST00000221992	CEACAM5	chr19	42213599	+	2917	221	49	2265	738
ENST00000593863	RPS19	chr19	42365281	+	ENST00000405816	CEACAM5	chr19	42213599	+	2428	221	49	2265	738
ENST00000598742	RPS19	chr19	42365280	+	ENST00000398599	CEACAM5	chr19	42224841	+	1080	544	372	881	169
ENST00000598742	RPS19	chr19	42365280	+	ENST00000221992	CEACAM5	chr19	42224841	+	1533	544	372	881	169
ENST00000598742	RPS19	chr19	42365280	+	ENST00000405816	CEACAM5	chr19	42224841	+	1044	544	372	881	169
ENST00000593863	RPS19	chr19	42365280	+	ENST00000398599	CEACAM5	chr19	42224841	+	757	221	49	558	169
ENST00000593863	RPS19	chr19	42365280	+	ENST00000221992	CEACAM5	chr19	42224841	+	1210	221	49	558	169
ENST00000593863	RPS19	chr19	42365280	+	ENST00000405816	CEACAM5	chr19	42224841	+	721	221	49	558	169

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
ENST00000598742	ENST00000398599	RPS19	chr19	42365281	+	CEACAM5	chr19	42224841	+	0.023521826	0.9764782
ENST00000598742	ENST00000221992	RPS19	chr19	42365281	+	CEACAM5	chr19	42224841	+	0.01210477	0.98789525
ENST00000598742	ENST00000405816	RPS19	chr19	42365281	+	CEACAM5	chr19	42224841	+	0.021583902	0.9784161
ENST00000593863	ENST00000398599	RPS19	chr19	42365281	+	CEACAM5	chr19	42224841	+	0.010175486	0.9898245
ENST00000593863	ENST00000221992	RPS19	chr19	42365281	+	CEACAM5	chr19	42224841	+	0.007750218	0.99224985
ENST00000593863	ENST00000405816	RPS19	chr19	42365281	+	CEACAM5	chr19	42224841	+	0.009473232	0.9905268
ENST00000598742	ENST00000398599	RPS19	chr19	42365281	+	CEACAM5	chr19	42213598	+	0.002205203	0.99779487
ENST00000598742	ENST00000221992	RPS19	chr19	42365281	+	CEACAM5	chr19	42213598	+	0.0014765	0.99852353
ENST00000598742	ENST00000405816	RPS19	chr19	42365281	+	CEACAM5	chr19	42213598	+	0.00227485	0.9977252
ENST00000593863	ENST00000398599	RPS19	chr19	42365281	+	CEACAM5	chr19	42213598	+	0.002171798	0.9978282
ENST00000593863	ENST00000221992	RPS19	chr19	42365281	+	CEACAM5	chr19	42213598	+	0.001429667	0.9985703
ENST00000593863	ENST00000405816	RPS19	chr19	42365281	+	CEACAM5	chr19	42213598	+	0.00226052	0.99773943
ENST00000598742	ENST00000398599	RPS19	chr19	42365281	+	CEACAM5	chr19	42224842	+	0.023521826	0.9764782
ENST00000598742	ENST00000221992	RPS19	chr19	42365281	+	CEACAM5	chr19	42224842	+	0.01210477	0.98789525
ENST00000598742	ENST00000405816	RPS19	chr19	42365281	+	CEACAM5	chr19	42224842	+	0.021583902	0.9784161
ENST00000593863	ENST00000398599	RPS19	chr19	42365281	+	CEACAM5	chr19	42224842	+	0.010175486	0.9898245
ENST00000593863	ENST00000221992	RPS19	chr19	42365281	+	CEACAM5	chr19	42224842	+	0.007750218	0.99224985
ENST00000593863	ENST00000405816	RPS19	chr19	42365281	+	CEACAM5	chr19	42224842	+	0.009473232	0.9905268
ENST00000598742	ENST00000398599	RPS19	chr19	42365281	+	CEACAM5	chr19	42213599	+	0.002205203	0.99779487
ENST00000598742	ENST00000221992	RPS19	chr19	42365281	+	CEACAM5	chr19	42213599	+	0.0014765	0.99852353
ENST00000598742	ENST00000405816	RPS19	chr19	42365281	+	CEACAM5	chr19	42213599	+	0.00227485	0.9977252
ENST00000593863	ENST00000398599	RPS19	chr19	42365281	+	CEACAM5	chr19	42213599	+	0.002171798	0.9978282
ENST00000593863	ENST00000221992	RPS19	chr19	42365281	+	CEACAM5	chr19	42213599	+	0.001429667	0.9985703
ENST00000593863	ENST00000405816	RPS19	chr19	42365281	+	CEACAM5	chr19	42213599	+	0.00226052	0.99773943
ENST00000598742	ENST00000398599	RPS19	chr19	42365280	+	CEACAM5	chr19	42224841	+	0.023521826	0.9764782
ENST00000598742	ENST00000221992	RPS19	chr19	42365280	+	CEACAM5	chr19	42224841	+	0.01210477	0.98789525
ENST00000598742	ENST00000405816	RPS19	chr19	42365280	+	CEACAM5	chr19	42224841	+	0.021583902	0.9784161
ENST00000593863	ENST00000398599	RPS19	chr19	42365280	+	CEACAM5	chr19	42224841	+	0.010175486	0.9898245
ENST00000593863	ENST00000221992	RPS19	chr19	42365280	+	CEACAM5	chr19	42224841	+	0.007750218	0.99224985
ENST00000593863	ENST00000405816	RPS19	chr19	42365280	+	CEACAM5	chr19	42224841	+	0.009473232	0.9905268

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 RPS19-CEACAM5

+/-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
RPS19	chr19	42365280	CEACAM5	chr19	42224841	221	57	LAPYDENWFYTRADGPDTPIISPPDS
RPS19	chr19	42365280	CEACAM5	chr19	42224841	544	57	LAPYDENWFYTRADGPDTPIISPPDS
RPS19	chr19	42365281	CEACAM5	chr19	42213598	221	57	LAPYDENWFYTRAASLLTFWNPPTTA
RPS19	chr19	42365281	CEACAM5	chr19	42213598	544	57	LAPYDENWFYTRAASLLTFWNPPTTA
RPS19	chr19	42365281	CEACAM5	chr19	42213599	221	57	LAPYDENWFYTRAASLLTFWNPPTTA
RPS19	chr19	42365281	CEACAM5	chr19	42213599	544	57	LAPYDENWFYTRAASLLTFWNPPTTA
RPS19	chr19	42365281	CEACAM5	chr19	42224841	221	57	LAPYDENWFYTRADGPDTPIISPPDS
RPS19	chr19	42365281	CEACAM5	chr19	42224841	544	57	LAPYDENWFYTRADGPDTPIISPPDS
RPS19	chr19	42365281	CEACAM5	chr19	42224842	221	57	LAPYDENWFYTRADGPDTPIISPPDS
RPS19	chr19	42365281	CEACAM5	chr19	42224842	544	57	LAPYDENWFYTRADGPDTPIISPPDS

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Potential FusionNeoAntigen Information of RPS19-CEACAM5 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.

RPS19-CEACAM5_42365280_42224841.msa
RPS19-CEACAM5_42365281_42213598.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)
RPS19-CEACAM5	chr19	42365280	chr19	42224841	221	HLA-C05:09	RADGPDTPI	0.9999	0.9746	11	20
RPS19-CEACAM5	chr19	42365280	chr19	42224841	221	HLA-C08:15	RADGPDTPI	0.9996	0.9834	11	20
RPS19-CEACAM5	chr19	42365280	chr19	42224841	221	HLA-C04:06	RADGPDTPI	0.933	0.948	11	20
RPS19-CEACAM5	chr19	42365280	chr19	42224841	221	HLA-C08:13	RADGPDTPI	0.7571	0.9723	11	20
RPS19-CEACAM5	chr19	42365280	chr19	42224841	221	HLA-C08:04	RADGPDTPI	0.7571	0.9723	11	20
RPS19-CEACAM5	chr19	42365280	chr19	42224841	221	HLA-B73:01	TRADGPDTP	0.5757	0.8391	10	19
RPS19-CEACAM5	chr19	42365280	chr19	42224841	221	HLA-C08:03	RADGPDTPI	0.4948	0.9844	11	20
RPS19-CEACAM5	chr19	42365280	chr19	42224841	221	HLA-C05:09	RADGPDTPII	0.9999	0.9639	11	21
RPS19-CEACAM5	chr19	42365280	chr19	42224841	221	HLA-C08:15	RADGPDTPII	0.9997	0.9773	11	21
RPS19-CEACAM5	chr19	42365280	chr19	42224841	221	HLA-C08:15	YTRADGPDTPI	0.9841	0.9753	9	20
RPS19-CEACAM5	chr19	42365280	chr19	42224841	221	HLA-C05:01	RADGPDTPI	0.9999	0.9746	11	20
RPS19-CEACAM5	chr19	42365280	chr19	42224841	221	HLA-C04:03	RADGPDTPI	0.9999	0.9488	11	20
RPS19-CEACAM5	chr19	42365280	chr19	42224841	221	HLA-C08:02	RADGPDTPI	0.9996	0.9834	11	20
RPS19-CEACAM5	chr19	42365280	chr19	42224841	221	HLA-C03:06	RADGPDTPI	0.7209	0.982	11	20
RPS19-CEACAM5	chr19	42365280	chr19	42224841	221	HLA-C08:01	RADGPDTPI	0.4948	0.9844	11	20
RPS19-CEACAM5	chr19	42365280	chr19	42224841	221	HLA-B35:13	RADGPDTPI	0.398	0.8336	11	20
RPS19-CEACAM5	chr19	42365280	chr19	42224841	221	HLA-B07:13	RADGPDTPI	0.3223	0.8592	11	20
RPS19-CEACAM5	chr19	42365280	chr19	42224841	221	HLA-C05:01	RADGPDTPII	0.9999	0.9639	11	21
RPS19-CEACAM5	chr19	42365280	chr19	42224841	221	HLA-C08:02	RADGPDTPII	0.9997	0.9773	11	21
RPS19-CEACAM5	chr19	42365280	chr19	42224841	221	HLA-C08:02	YTRADGPDTPI	0.9841	0.9753	9	20
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B58:01	AASLLTFW	0.9989	0.9874	12	20
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B15:16	RAASLLTF	0.9988	0.927	11	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B27:04	TRAASLLTF	0.9997	0.7784	10	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B57:01	RAASLLTFW	0.9997	0.9865	11	20
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B27:05	TRAASLLTF	0.9997	0.7454	10	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B58:02	RAASLLTFW	0.9993	0.9752	11	20
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B58:01	RAASLLTFW	0.9993	0.9741	11	20
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B15:17	RAASLLTFW	0.9982	0.9657	11	20
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B27:07	TRAASLLTF	0.9978	0.6248	10	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-A31:08	RAASLLTFW	0.9967	0.7015	11	20
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B15:16	RAASLLTFW	0.996	0.9614	11	20
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B39:24	TRAASLLTF	0.9958	0.6484	10	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B08:01	WFYTRAASL	0.9955	0.5844	7	16
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B57:03	RAASLLTFW	0.9954	0.9944	11	20
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B14:01	TRAASLLTF	0.9948	0.8403	10	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B14:02	TRAASLLTF	0.9948	0.8403	10	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B14:01	WFYTRAASL	0.9947	0.7245	7	16
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B14:02	WFYTRAASL	0.9947	0.7245	7	16
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-A32:13	RAASLLTFW	0.9929	0.9691	11	20
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B08:09	WFYTRAASL	0.9914	0.7322	7	16
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B39:01	TRAASLLTF	0.9908	0.8906	10	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B38:02	TRAASLLTF	0.9821	0.9586	10	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B38:01	TRAASLLTF	0.9799	0.9571	10	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B53:01	RAASLLTFW	0.9565	0.5916	11	20
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B15:10	TRAASLLTF	0.7707	0.6269	10	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B15:18	TRAASLLTF	0.7643	0.7669	10	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B15:03	TRAASLLTF	0.6916	0.803	10	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B15:37	TRAASLLTF	0.6746	0.7173	10	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B57:01	YTRAASLLTF	0.9996	0.959	9	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B27:04	YTRAASLLTF	0.9977	0.7706	9	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B15:17	YTRAASLLTF	0.9977	0.8476	9	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B27:05	YTRAASLLTF	0.9974	0.7355	9	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B15:16	YTRAASLLTF	0.9973	0.8208	9	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B57:01	TRAASLLTFW	0.9972	0.9835	10	20
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B57:03	YTRAASLLTF	0.9941	0.9721	9	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B15:18	YTRAASLLTF	0.9828	0.6073	9	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B58:02	TRAASLLTFW	0.9823	0.971	10	20
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B57:03	TRAASLLTFW	0.9808	0.9925	10	20
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B27:07	YTRAASLLTF	0.9806	0.5327	9	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B58:01	TRAASLLTFW	0.9715	0.967	10	20
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B57:01	YTRAASLLTFW	0.9999	0.9713	9	20
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B58:02	YTRAASLLTFW	0.9996	0.9324	9	20
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B58:01	YTRAASLLTFW	0.9988	0.952	9	20
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B57:03	YTRAASLLTFW	0.9984	0.9886	9	20
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B15:17	YTRAASLLTFW	0.9976	0.9092	9	20
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C07:13	FYTRAASL	0.932	0.8392	8	16
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C07:29	FYTRAASL	0.8897	0.9019	8	16
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B27:14	TRAASLLTF	0.9996	0.7028	10	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C07:05	TRAASLLTF	0.9994	0.9576	10	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C07:95	TRAASLLTF	0.9994	0.6876	10	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C07:27	TRAASLLTF	0.9991	0.9512	10	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C07:29	TRAASLLTF	0.9986	0.9143	10	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C07:13	TRAASLLTF	0.9972	0.9424	10	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B27:03	TRAASLLTF	0.9959	0.7631	10	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B39:09	TRAASLLTF	0.9928	0.8019	10	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B39:12	TRAASLLTF	0.9902	0.8968	10	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B14:03	WFYTRAASL	0.9298	0.7674	7	16
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C07:46	TRAASLLTF	0.8422	0.9274	10	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C07:19	TRAASLLTF	0.8258	0.8301	10	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C07:67	TRAASLLTF	0.8191	0.9589	10	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C07:80	TRAASLLTF	0.8191	0.9589	10	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C07:10	TRAASLLTF	0.8152	0.9725	10	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C07:05	WFYTRAASL	0.6761	0.9705	7	16
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C07:13	WFYTRAASL	0.673	0.9261	7	16
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C07:67	WFYTRAASL	0.6007	0.9494	7	16
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C07:80	WFYTRAASL	0.6007	0.9494	7	16
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C07:29	WFYTRAASL	0.5941	0.9327	7	16
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C07:10	WFYTRAASL	0.5625	0.9753	7	16
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B14:03	TRAASLLTF	0.4463	0.7795	10	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C07:05	FYTRAASLL	0.4028	0.959	8	17
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B44:08	RAASLLTFW	0.3903	0.797	11	20
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C07:13	FYTRAASLL	0.3763	0.8886	8	17
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C07:29	FYTRAASLL	0.3728	0.9008	8	17
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C07:10	FYTRAASLL	0.3141	0.9624	8	17
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C07:27	FYTRAASLL	0.3099	0.9295	8	17
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C12:16	TRAASLLTF	0.3071	0.9422	10	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C07:80	FYTRAASLL	0.303	0.9145	8	17
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C07:67	FYTRAASLL	0.303	0.9145	8	17
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C07:46	FYTRAASLL	0.2914	0.8461	8	17
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C07:19	FYTRAASLL	0.2654	0.7021	8	17
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C04:14	FYTRAASLL	0.1486	0.7809	8	17
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C04:10	FYTRAASLL	0.0566	0.69	8	17
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C12:16	YTRAASLLTF	0.9998	0.9337	9	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C07:27	YTRAASLLTF	0.9945	0.9136	9	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C07:05	YTRAASLLTF	0.9939	0.9385	9	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C07:95	YTRAASLLTF	0.9934	0.5493	9	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C07:67	YTRAASLLTF	0.9925	0.9307	9	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C07:80	YTRAASLLTF	0.9925	0.9307	9	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C07:19	YTRAASLLTF	0.9894	0.7327	9	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C07:10	YTRAASLLTF	0.9858	0.9479	9	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C07:46	YTRAASLLTF	0.9832	0.8827	9	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B27:03	YTRAASLLTF	0.929	0.7525	9	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C03:02	RAASLLTF	0.9997	0.9665	11	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B57:04	AASLLTFW	0.9994	0.8202	12	20
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C16:01	RAASLLTF	0.9992	0.983	11	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C16:02	RAASLLTF	0.9951	0.9948	11	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C03:67	FYTRAASL	0.9722	0.9743	8	16
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C14:02	FYTRAASL	0.876	0.9449	8	16
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C14:03	FYTRAASL	0.876	0.9449	8	16
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B27:08	TRAASLLTF	0.9997	0.6476	10	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B27:06	TRAASLLTF	0.9997	0.8114	10	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B27:10	TRAASLLTF	0.9997	0.8673	10	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B57:10	RAASLLTFW	0.9997	0.9865	11	20
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C07:01	TRAASLLTF	0.9995	0.6932	10	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B57:04	RAASLLTFW	0.9993	0.7786	11	20
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B58:06	RAASLLTFW	0.999	0.9752	11	20
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B27:09	TRAASLLTF	0.9973	0.7268	10	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-A32:01	RAASLLTFW	0.9971	0.9796	11	20
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C07:17	TRAASLLTF	0.9959	0.9621	10	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B08:18	WFYTRAASL	0.9955	0.5844	7	16
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B39:31	TRAASLLTF	0.993	0.8918	10	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B57:02	RAASLLTFW	0.9929	0.9301	11	20
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B15:13	RAASLLTFW	0.9818	0.966	11	20
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B38:05	TRAASLLTF	0.9799	0.9571	10	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B08:12	WFYTRAASL	0.9741	0.7761	7	16
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C06:08	TRAASLLTF	0.9677	0.9825	10	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C07:22	TRAASLLTF	0.9073	0.6401	10	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C03:67	WFYTRAASL	0.8613	0.9769	7	16
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C07:04	TRAASLLTF	0.8596	0.9248	10	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B15:24	RAASLLTFW	0.8354	0.9865	11	20
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C07:02	TRAASLLTF	0.8191	0.9589	10	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C07:04	WFYTRAASL	0.7345	0.9154	7	16
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B48:02	TRAASLLTF	0.7193	0.9223	10	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C03:67	FYTRAASLL	0.6348	0.9707	8	17
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C06:06	WFYTRAASL	0.6276	0.9786	7	16
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B53:02	RAASLLTFW	0.6237	0.5288	11	20
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C03:67	TRAASLLTF	0.6196	0.9828	10	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C07:02	WFYTRAASL	0.6007	0.9494	7	16
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C07:17	WFYTRAASL	0.5693	0.9596	7	16
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C04:04	WFYTRAASL	0.4631	0.7958	7	16
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C06:06	TRAASLLTF	0.4027	0.99	10	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C14:03	WFYTRAASL	0.4002	0.9529	7	16
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C14:02	WFYTRAASL	0.4002	0.9529	7	16
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C07:17	FYTRAASLL	0.3398	0.9405	8	17
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C07:02	FYTRAASLL	0.303	0.9145	8	17
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B15:68	TRAASLLTF	0.29	0.6858	10	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B15:54	TRAASLLTF	0.2799	0.8187	10	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C07:04	FYTRAASLL	0.2641	0.8493	8	17
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C06:02	TRAASLLTF	0.2243	0.9871	10	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C06:17	TRAASLLTF	0.2243	0.9871	10	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C04:04	FYTRAASLL	0.2185	0.7455	8	17
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C06:06	FYTRAASLL	0.1924	0.97	8	17
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C14:02	FYTRAASLL	0.1651	0.9431	8	17
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C14:03	FYTRAASLL	0.1651	0.9431	8	17
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C18:01	FYTRAASLL	0.0878	0.6857	8	17
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B57:10	YTRAASLLTF	0.9996	0.959	9	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B58:06	YTRAASLLTF	0.9994	0.8085	9	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B57:04	YTRAASLLTF	0.9993	0.706	9	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B27:10	YTRAASLLTF	0.9978	0.8565	9	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C07:22	YTRAASLLTF	0.9976	0.5416	9	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B27:08	YTRAASLLTF	0.9974	0.6053	9	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B57:10	TRAASLLTFW	0.9972	0.9835	10	20
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B57:04	TRAASLLTFW	0.9938	0.7772	10	20
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C07:01	YTRAASLLTF	0.9936	0.5533	9	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B27:06	YTRAASLLTF	0.993	0.8032	9	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B57:02	YTRAASLLTF	0.9928	0.8995	9	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-C07:02	YTRAASLLTF	0.9925	0.9307	9	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B27:09	YTRAASLLTF	0.9794	0.7309	9	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B57:02	TRAASLLTFW	0.9651	0.9458	10	20
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B57:10	YTRAASLLTFW	0.9999	0.9713	9	20
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B57:04	YTRAASLLTFW	0.9997	0.7791	9	20
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B58:06	YTRAASLLTFW	0.9996	0.9552	9	20
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B57:02	YTRAASLLTFW	0.9975	0.9458	9	20
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	HLA-B27:08	FYTRAASLLTF	0.9953	0.653	8	19

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Potential FusionNeoAntigen Information of RPS19-CEACAM5 in HLA II

RPS19-CEACAM5_42365281_42213598.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)
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0701	YDENWFYTRAASLLT	3	18
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0701	DENWFYTRAASLLTF	4	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0701	PYDENWFYTRAASLL	2	17
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0701	APYDENWFYTRAASL	1	16
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0703	YDENWFYTRAASLLT	3	18
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0703	DENWFYTRAASLLTF	4	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0703	PYDENWFYTRAASLL	2	17
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0703	APYDENWFYTRAASL	1	16
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0704	YDENWFYTRAASLLT	3	18
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0704	DENWFYTRAASLLTF	4	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0704	PYDENWFYTRAASLL	2	17
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0705	YDENWFYTRAASLLT	3	18
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0705	DENWFYTRAASLLTF	4	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0705	PYDENWFYTRAASLL	2	17
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0705	APYDENWFYTRAASL	1	16
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0706	YDENWFYTRAASLLT	3	18
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0706	DENWFYTRAASLLTF	4	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0706	PYDENWFYTRAASLL	2	17
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0706	APYDENWFYTRAASL	1	16
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0707	YDENWFYTRAASLLT	3	18
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0707	DENWFYTRAASLLTF	4	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0707	PYDENWFYTRAASLL	2	17
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0707	APYDENWFYTRAASL	1	16
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0708	YDENWFYTRAASLLT	3	18
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0708	DENWFYTRAASLLTF	4	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0708	PYDENWFYTRAASLL	2	17
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0708	APYDENWFYTRAASL	1	16
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0709	YDENWFYTRAASLLT	3	18
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0709	DENWFYTRAASLLTF	4	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0709	PYDENWFYTRAASLL	2	17
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0709	APYDENWFYTRAASL	1	16
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0711	YDENWFYTRAASLLT	3	18
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0711	DENWFYTRAASLLTF	4	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0711	PYDENWFYTRAASLL	2	17
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0711	APYDENWFYTRAASL	1	16
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0712	YDENWFYTRAASLLT	3	18
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0712	DENWFYTRAASLLTF	4	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0712	PYDENWFYTRAASLL	2	17
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0712	APYDENWFYTRAASL	1	16
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0713	YDENWFYTRAASLLT	3	18
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0713	DENWFYTRAASLLTF	4	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0713	PYDENWFYTRAASLL	2	17
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0713	APYDENWFYTRAASL	1	16
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0714	YDENWFYTRAASLLT	3	18
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0714	DENWFYTRAASLLTF	4	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0714	PYDENWFYTRAASLL	2	17
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0714	APYDENWFYTRAASL	1	16
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0715	YDENWFYTRAASLLT	3	18
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0715	DENWFYTRAASLLTF	4	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0715	PYDENWFYTRAASLL	2	17
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0715	APYDENWFYTRAASL	1	16
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0716	YDENWFYTRAASLLT	3	18
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0716	DENWFYTRAASLLTF	4	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0716	PYDENWFYTRAASLL	2	17
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0716	APYDENWFYTRAASL	1	16
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0717	YDENWFYTRAASLLT	3	18
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0717	DENWFYTRAASLLTF	4	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0717	PYDENWFYTRAASLL	2	17
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0717	APYDENWFYTRAASL	1	16
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0719	YDENWFYTRAASLLT	3	18
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0719	DENWFYTRAASLLTF	4	19
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0719	PYDENWFYTRAASLL	2	17
RPS19-CEACAM5	chr19	42365281	chr19	42213598	221	DRB1-0719	APYDENWFYTRAASL	1	16

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Fusion breakpoint peptide structures of RPS19-CEACAM5

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
6457	NWFYTRAASLLTFW	RPS19	CEACAM5	chr19	42365281	chr19	42213598	221

File name	BPseq	Hgene	Tgene	Hchr	Hbp	Tchr	Tbp	AAlen
6458	NWFYTRADGPDTPI	RPS19	CEACAM5	chr19	42365280	chr19	42224841	221

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of RPS19-CEACAM5

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	6457	NWFYTRAASLLTFW	-7.9962	-8.1096
HLA-B14:02	3BVN	6457	NWFYTRAASLLTFW	-5.70842	-6.74372
HLA-B52:01	3W39	6457	NWFYTRAASLLTFW	-6.83737	-6.95077
HLA-B52:01	3W39	6457	NWFYTRAASLLTFW	-4.4836	-5.5189
HLA-A11:01	4UQ2	6457	NWFYTRAASLLTFW	-10.0067	-10.1201
HLA-A11:01	4UQ2	6457	NWFYTRAASLLTFW	-9.03915	-10.0745
HLA-A24:02	5HGA	6457	NWFYTRAASLLTFW	-6.56204	-6.67544
HLA-A24:02	5HGA	6457	NWFYTRAASLLTFW	-5.42271	-6.45801
HLA-B44:05	3DX8	6457	NWFYTRAASLLTFW	-7.85648	-8.89178
HLA-B44:05	3DX8	6457	NWFYTRAASLLTFW	-5.3978	-5.5112
HLA-A02:01	6TDR	6457	NWFYTRAASLLTFW	-3.37154	-4.40684
HLA-B14:02	3BVN	6458	NWFYTRADGPDTPI	-6.73939	-6.85279
HLA-B14:02	3BVN	6458	NWFYTRADGPDTPI	-5.8572	-6.8925
HLA-B52:01	3W39	6458	NWFYTRADGPDTPI	-6.06811	-6.18151
HLA-B52:01	3W39	6458	NWFYTRADGPDTPI	-4.01521	-5.05051
HLA-A24:02	5HGA	6458	NWFYTRADGPDTPI	-6.11611	-7.15141
HLA-A24:02	5HGA	6458	NWFYTRADGPDTPI	-5.72969	-5.84309
HLA-B27:05	6PYJ	6458	NWFYTRADGPDTPI	-6.42433	-7.45963
HLA-B44:05	3DX8	6458	NWFYTRADGPDTPI	-5.79012	-5.90352
HLA-B44:05	3DX8	6458	NWFYTRADGPDTPI	-3.82099	-4.85629

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Vaccine Design for the FusionNeoAntigens of RPS19-CEACAM5

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
RPS19-CEACAM5	chr19	42365280	chr19	42224841	10	19	TRADGPDTP	CGCGAGCTGATGGGCCGGACACCCCCA
RPS19-CEACAM5	chr19	42365280	chr19	42224841	11	20	RADGPDTPI	GAGCTGATGGGCCGGACACCCCCATCA
RPS19-CEACAM5	chr19	42365280	chr19	42224841	11	21	RADGPDTPII	GAGCTGATGGGCCGGACACCCCCATCATTT
RPS19-CEACAM5	chr19	42365280	chr19	42224841	9	20	YTRADGPDTPI	ACACGCGAGCTGATGGGCCGGACACCCCCATCA
RPS19-CEACAM5	chr19	42365281	chr19	42213598	10	19	TRAASLLTF	CGCGAGCTGCCTCACTTCTAACCTTCT
RPS19-CEACAM5	chr19	42365281	chr19	42213598	10	20	TRAASLLTFW	CGCGAGCTGCCTCACTTCTAACCTTCTGGA
RPS19-CEACAM5	chr19	42365281	chr19	42213598	11	19	RAASLLTF	GAGCTGCCTCACTTCTAACCTTCT
RPS19-CEACAM5	chr19	42365281	chr19	42213598	11	20	RAASLLTFW	GAGCTGCCTCACTTCTAACCTTCTGGA
RPS19-CEACAM5	chr19	42365281	chr19	42213598	12	20	AASLLTFW	CTGCCTCACTTCTAACCTTCTGGA
RPS19-CEACAM5	chr19	42365281	chr19	42213598	7	16	WFYTRAASL	GGTTCTACACGCGAGCTGCCTCACTTC
RPS19-CEACAM5	chr19	42365281	chr19	42213598	8	16	FYTRAASL	TCTACACGCGAGCTGCCTCACTTC
RPS19-CEACAM5	chr19	42365281	chr19	42213598	8	17	FYTRAASLL	TCTACACGCGAGCTGCCTCACTTCTAA
RPS19-CEACAM5	chr19	42365281	chr19	42213598	8	19	FYTRAASLLTF	TCTACACGCGAGCTGCCTCACTTCTAACCTTCT
RPS19-CEACAM5	chr19	42365281	chr19	42213598	9	19	YTRAASLLTF	ACACGCGAGCTGCCTCACTTCTAACCTTCT
RPS19-CEACAM5	chr19	42365281	chr19	42213598	9	20	YTRAASLLTFW	ACACGCGAGCTGCCTCACTTCTAACCTTCTGGA

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
RPS19-CEACAM5	chr19	42365281	chr19	42213598	1	16	APYDENWFYTRAASL	CTCCCTACGATGAGAACTGGTTCTACACGCGAGCTGCCTCACTTC
RPS19-CEACAM5	chr19	42365281	chr19	42213598	2	17	PYDENWFYTRAASLL	CCTACGATGAGAACTGGTTCTACACGCGAGCTGCCTCACTTCTAA
RPS19-CEACAM5	chr19	42365281	chr19	42213598	3	18	YDENWFYTRAASLLT	ACGATGAGAACTGGTTCTACACGCGAGCTGCCTCACTTCTAACCT
RPS19-CEACAM5	chr19	42365281	chr19	42213598	4	19	DENWFYTRAASLLTF	ATGAGAACTGGTTCTACACGCGAGCTGCCTCACTTCTAACCTTCT

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Information of the samples that have these potential fusion neoantigens of RPS19-CEACAM5

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
LUSC	RPS19-CEACAM5	chr19	42365280	ENST00000593863	chr19	42224841	ENST00000221992	TCGA-58-8387-01A
READ	RPS19-CEACAM5	chr19	42365281	ENST00000593863	chr19	42213598	ENST00000221992	TCGA-EI-6506

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Potential target of CAR-T therapy development for RPS19-CEACAM5

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 RPS19-CEACAM5

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 RPS19-CEACAM5

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)