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Fusion Protein:BCL2L11-MERTK

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: BCL2L11-MERTK
	FusionPDB ID: 9344
	FusionGDB2.0 ID: 9344
		Hgene	Tgene
	Gene symbol	BCL2L11	MERTK
	Gene ID	10018	10461
	Gene name	BCL2 like 11	MER proto-oncogene, tyrosine kinase
	Synonyms	BAM\|BIM\|BOD	MER\|RP38\|Tyro12\|c-Eyk\|c-mer
	Cytomap	2q13	2q13
	Type of gene	protein-coding	protein-coding
	Description	bcl-2-like protein 11BCL2-like 11 (apoptosis facilitator)bcl-2 interacting mediator of cell deathbcl-2 interacting protein Bimbcl-2-related ovarian death agonist	tyrosine-protein kinase MerMER receptor tyrosine kinaseSTK kinasec-mer proto-oncogene tyrosine kinaseproto-oncogene c-Merreceptor tyrosine kinase MerTK
	Modification date	20200313	20200329
	UniProtAcc	O43521 Main function of 5'-partner protein: FUNCTION: Induces apoptosis and anoikis. Isoform BimL is more potent than isoform BimEL. Isoform Bim-alpha1, isoform Bim-alpha2 and isoform Bim-alpha3 induce apoptosis, although less potent than isoform BimEL, isoform BimL and isoform BimS. Isoform Bim-gamma induces apoptosis. Isoform Bim-alpha3 induces apoptosis possibly through a caspase-mediated pathway. Isoform BimAC and isoform BimABC lack the ability to induce apoptosis. {ECO:0000269\|PubMed:11997495, ECO:0000269\|PubMed:15486195, ECO:0000269\|PubMed:9430630}.	Q12866 Main function of 5'-partner protein: FUNCTION: Receptor tyrosine kinase that transduces signals from the extracellular matrix into the cytoplasm by binding to several ligands including LGALS3, TUB, TULP1 or GAS6. Regulates many physiological processes including cell survival, migration, differentiation, and phagocytosis of apoptotic cells (efferocytosis). Ligand binding at the cell surface induces autophosphorylation of MERTK on its intracellular domain that provides docking sites for downstream signaling molecules. Following activation by ligand, interacts with GRB2 or PLCG2 and induces phosphorylation of MAPK1, MAPK2, FAK/PTK2 or RAC1. MERTK signaling plays a role in various processes such as macrophage clearance of apoptotic cells, platelet aggregation, cytoskeleton reorganization and engulfment. Functions in the retinal pigment epithelium (RPE) as a regulator of rod outer segments fragments phagocytosis. Plays also an important role in inhibition of Toll-like receptors (TLRs)-mediated innate immune response by activating STAT1, which selectively induces production of suppressors of cytokine signaling SOCS1 and SOCS3. {ECO:0000269\|PubMed:17005688}.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000308659, ENST00000357757, ENST00000393253, ENST00000393256, ENST00000337565, ENST00000405953,	ENST00000295408, ENST00000409780, ENST00000421804,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	7 X 4 X 6=168	7 X 10 X 8=560
	# samples	9	13
	** MAII score	log2(9/168*10)=-0.900464326449086 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(13/560*10)=-2.10691520391651 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: BCL2L11 [Title/Abstract] AND MERTK [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: BCL2L11 [Title/Abstract] AND MERTK [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	BCL2L11(111907724)-MERTK(112751827), # samples:1 BCL2L11(111907724)-MERTK(112751828), # samples:1
Anticipated loss of major functional domain due to fusion event.	BCL2L11-MERTK 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. BCL2L11-MERTK 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. BCL2L11-MERTK 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. BCL2L11-MERTK seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.

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

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

Partner	Gene	GO ID	GO term	PubMed ID
Hgene	BCL2L11	GO:0008630	intrinsic apoptotic signaling pathway in response to DNA damage	11546872
Hgene	BCL2L11	GO:0031334	positive regulation of protein complex assembly	21041309
Hgene	BCL2L11	GO:0034976	response to endoplasmic reticulum stress	22761832
Hgene	BCL2L11	GO:2000271	positive regulation of fibroblast apoptotic process	11997495
Tgene	MERTK	GO:0050766	positive regulation of phagocytosis	18395422

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr2:111907724/chr2:112751827)
- 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 BCL2L11 (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 MERTK (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)
ENST00000393253	BCL2L11	chr2	111907724	+	ENST00000295408	MERTK	chr2	112751827	+	2917	516	126	2219	697
ENST00000393253	BCL2L11	chr2	111907724	+	ENST00000421804	MERTK	chr2	112751827	+	2692	516	126	2219	697
ENST00000393253	BCL2L11	chr2	111907724	+	ENST00000409780	MERTK	chr2	112751827	+	2723	516	126	2219	697
ENST00000357757	BCL2L11	chr2	111907724	+	ENST00000295408	MERTK	chr2	112751827	+	3187	786	126	2489	787
ENST00000357757	BCL2L11	chr2	111907724	+	ENST00000421804	MERTK	chr2	112751827	+	2962	786	126	2489	787
ENST00000357757	BCL2L11	chr2	111907724	+	ENST00000409780	MERTK	chr2	112751827	+	2993	786	126	2489	787
ENST00000308659	BCL2L11	chr2	111907724	+	ENST00000295408	MERTK	chr2	112751827	+	3007	606	126	2309	727
ENST00000308659	BCL2L11	chr2	111907724	+	ENST00000421804	MERTK	chr2	112751827	+	2782	606	126	2309	727
ENST00000308659	BCL2L11	chr2	111907724	+	ENST00000409780	MERTK	chr2	112751827	+	2813	606	126	2309	727
ENST00000393256	BCL2L11	chr2	111907724	+	ENST00000295408	MERTK	chr2	112751827	+	3172	771	111	2474	787
ENST00000393256	BCL2L11	chr2	111907724	+	ENST00000421804	MERTK	chr2	112751827	+	2947	771	111	2474	787
ENST00000393256	BCL2L11	chr2	111907724	+	ENST00000409780	MERTK	chr2	112751827	+	2978	771	111	2474	787
ENST00000393253	BCL2L11	chr2	111907724	+	ENST00000295408	MERTK	chr2	112751828	+	2917	516	126	2219	697
ENST00000393253	BCL2L11	chr2	111907724	+	ENST00000421804	MERTK	chr2	112751828	+	2692	516	126	2219	697
ENST00000393253	BCL2L11	chr2	111907724	+	ENST00000409780	MERTK	chr2	112751828	+	2723	516	126	2219	697
ENST00000357757	BCL2L11	chr2	111907724	+	ENST00000295408	MERTK	chr2	112751828	+	3187	786	126	2489	787
ENST00000357757	BCL2L11	chr2	111907724	+	ENST00000421804	MERTK	chr2	112751828	+	2962	786	126	2489	787
ENST00000357757	BCL2L11	chr2	111907724	+	ENST00000409780	MERTK	chr2	112751828	+	2993	786	126	2489	787
ENST00000308659	BCL2L11	chr2	111907724	+	ENST00000295408	MERTK	chr2	112751828	+	3007	606	126	2309	727
ENST00000308659	BCL2L11	chr2	111907724	+	ENST00000421804	MERTK	chr2	112751828	+	2782	606	126	2309	727
ENST00000308659	BCL2L11	chr2	111907724	+	ENST00000409780	MERTK	chr2	112751828	+	2813	606	126	2309	727
ENST00000393256	BCL2L11	chr2	111907724	+	ENST00000295408	MERTK	chr2	112751828	+	3172	771	111	2474	787
ENST00000393256	BCL2L11	chr2	111907724	+	ENST00000421804	MERTK	chr2	112751828	+	2947	771	111	2474	787
ENST00000393256	BCL2L11	chr2	111907724	+	ENST00000409780	MERTK	chr2	112751828	+	2978	771	111	2474	787

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
ENST00000393253	ENST00000295408	BCL2L11	chr2	111907724	+	MERTK	chr2	112751827	+	0.00144963	0.99855036
ENST00000393253	ENST00000421804	BCL2L11	chr2	111907724	+	MERTK	chr2	112751827	+	0.002027541	0.9979724
ENST00000393253	ENST00000409780	BCL2L11	chr2	111907724	+	MERTK	chr2	112751827	+	0.001866313	0.9981337
ENST00000357757	ENST00000295408	BCL2L11	chr2	111907724	+	MERTK	chr2	112751827	+	0.001931925	0.99806803
ENST00000357757	ENST00000421804	BCL2L11	chr2	111907724	+	MERTK	chr2	112751827	+	0.002545598	0.99745435
ENST00000357757	ENST00000409780	BCL2L11	chr2	111907724	+	MERTK	chr2	112751827	+	0.00238232	0.99761766
ENST00000308659	ENST00000295408	BCL2L11	chr2	111907724	+	MERTK	chr2	112751827	+	0.002063098	0.99793696
ENST00000308659	ENST00000421804	BCL2L11	chr2	111907724	+	MERTK	chr2	112751827	+	0.002854994	0.997145
ENST00000308659	ENST00000409780	BCL2L11	chr2	111907724	+	MERTK	chr2	112751827	+	0.0026363	0.99736375
ENST00000393256	ENST00000295408	BCL2L11	chr2	111907724	+	MERTK	chr2	112751827	+	0.001870162	0.9981299
ENST00000393256	ENST00000421804	BCL2L11	chr2	111907724	+	MERTK	chr2	112751827	+	0.002473051	0.99752694
ENST00000393256	ENST00000409780	BCL2L11	chr2	111907724	+	MERTK	chr2	112751827	+	0.002315902	0.9976841
ENST00000393253	ENST00000295408	BCL2L11	chr2	111907724	+	MERTK	chr2	112751828	+	0.00144963	0.99855036
ENST00000393253	ENST00000421804	BCL2L11	chr2	111907724	+	MERTK	chr2	112751828	+	0.002027541	0.9979724
ENST00000393253	ENST00000409780	BCL2L11	chr2	111907724	+	MERTK	chr2	112751828	+	0.001866313	0.9981337
ENST00000357757	ENST00000295408	BCL2L11	chr2	111907724	+	MERTK	chr2	112751828	+	0.001931925	0.99806803
ENST00000357757	ENST00000421804	BCL2L11	chr2	111907724	+	MERTK	chr2	112751828	+	0.002545598	0.99745435
ENST00000357757	ENST00000409780	BCL2L11	chr2	111907724	+	MERTK	chr2	112751828	+	0.00238232	0.99761766
ENST00000308659	ENST00000295408	BCL2L11	chr2	111907724	+	MERTK	chr2	112751828	+	0.002063098	0.99793696
ENST00000308659	ENST00000421804	BCL2L11	chr2	111907724	+	MERTK	chr2	112751828	+	0.002854994	0.997145
ENST00000308659	ENST00000409780	BCL2L11	chr2	111907724	+	MERTK	chr2	112751828	+	0.0026363	0.99736375
ENST00000393256	ENST00000295408	BCL2L11	chr2	111907724	+	MERTK	chr2	112751828	+	0.001870162	0.9981299
ENST00000393256	ENST00000421804	BCL2L11	chr2	111907724	+	MERTK	chr2	112751828	+	0.002473051	0.99752694
ENST00000393256	ENST00000409780	BCL2L11	chr2	111907724	+	MERTK	chr2	112751828	+	0.002315902	0.9976841

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 BCL2L11-MERTK

+/-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
BCL2L11	chr2	111907724	MERTK	chr2	112751827	606	160	RIGDEFNAYYARRKELLEEVGQNGSR
BCL2L11	chr2	111907724	MERTK	chr2	112751827	771	220	RIGDEFNAYYARRKELLEEVGQNGSR
BCL2L11	chr2	111907724	MERTK	chr2	112751827	786	220	RIGDEFNAYYARRKELLEEVGQNGSR
BCL2L11	chr2	111907724	MERTK	chr2	112751828	606	160	RIGDEFNAYYARRKELLEEVGQNGSR
BCL2L11	chr2	111907724	MERTK	chr2	112751828	771	220	RIGDEFNAYYARRKELLEEVGQNGSR
BCL2L11	chr2	111907724	MERTK	chr2	112751828	786	220	RIGDEFNAYYARRKELLEEVGQNGSR

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Potential FusionNeoAntigen Information of BCL2L11-MERTK 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.

BCL2L11-MERTK_111907724_112751827.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)
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-B27:02	RRKELLEEV	0.9989	0.7008	11	20
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-B27:07	RRKELLEEV	0.9989	0.8871	11	20
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-B27:05	RRKELLEEV	0.9988	0.8249	11	20
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-B27:04	RRKELLEEV	0.9987	0.8884	11	20
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-B14:02	AYYARRKEL	0.9052	0.7488	7	16
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-B14:01	AYYARRKEL	0.9052	0.7488	7	16
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C07:05	YYARRKEL	0.7478	0.9188	8	16
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C07:29	YYARRKEL	0.6807	0.9279	8	16
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C07:13	YYARRKEL	0.632	0.8928	8	16
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C07:80	YYARRKEL	0.6187	0.9376	8	16
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C07:67	YYARRKEL	0.6187	0.9376	8	16
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C07:10	YYARRKEL	0.6013	0.9532	8	16
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-B27:14	RRKELLEEV	0.999	0.809	11	20
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-B73:01	RRKELLEEV	0.9896	0.8232	11	20
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C07:05	RRKELLEEV	0.958	0.9798	11	20
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-B27:03	RRKELLEEV	0.9154	0.8391	11	20
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C07:27	RRKELLEEV	0.8975	0.9742	11	20
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C07:95	RRKELLEEV	0.7958	0.9017	11	20
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C07:46	RRKELLEEV	0.7416	0.9622	11	20
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C07:19	RRKELLEEV	0.6833	0.9184	11	20
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-B39:12	RRKELLEEV	0.6568	0.9502	11	20
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-B14:03	AYYARRKEL	0.3806	0.7609	7	16
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C07:19	YYARRKELL	0.3033	0.6172	8	17
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C07:46	YYARRKELL	0.2971	0.8197	8	17
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C07:05	YYARRKELL	0.2929	0.9263	8	17
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C07:67	YYARRKELL	0.2899	0.923	8	17
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C07:80	YYARRKELL	0.2899	0.923	8	17
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-B14:03	YYARRKELL	0.2876	0.7091	8	17
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C07:19	AYYARRKEL	0.2868	0.835	7	16
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C07:10	YYARRKELL	0.2829	0.954	8	17
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C07:46	AYYARRKEL	0.2454	0.9253	7	16
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C07:29	YYARRKELL	0.2396	0.9158	8	17
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C12:16	AYYARRKEL	0.2134	0.9666	7	16
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C07:67	AYYARRKEL	0.206	0.9608	7	16
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C07:80	AYYARRKEL	0.206	0.9608	7	16
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C07:10	AYYARRKEL	0.1941	0.9692	7	16
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C07:05	AYYARRKEL	0.1934	0.9566	7	16
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C07:29	AYYARRKEL	0.1782	0.9484	7	16
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C12:16	YYARRKELL	0.1667	0.9544	8	17
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C07:27	YYARRKELL	0.1572	0.9225	8	17
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C07:13	YYARRKELL	0.1248	0.8772	8	17
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C07:13	AYYARRKEL	0.114	0.9236	7	16
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C07:95	YYARRKELL	0.1103	0.6296	8	17
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C07:27	AYYARRKEL	0.1052	0.9603	7	16
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C04:14	YYARRKELL	0.0654	0.6894	8	17
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C12:16	RRKELLEEV	0.0083	0.977	11	20
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C16:04	YARRKELL	0.9286	0.9785	9	17
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C16:01	YARRKELL	0.7946	0.9734	9	17
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C07:04	YYARRKEL	0.791	0.8339	8	16
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C06:06	YYARRKEL	0.7774	0.9798	8	16
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C03:67	YYARRKEL	0.7746	0.973	8	16
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C14:03	YYARRKEL	0.7083	0.9438	8	16
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C14:02	YYARRKEL	0.7083	0.9438	8	16
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C07:02	YYARRKEL	0.6187	0.9376	8	16
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-B27:06	RRKELLEEV	0.9992	0.9194	11	20
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-B27:09	RRKELLEEV	0.999	0.7931	11	20
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-B27:10	RRKELLEEV	0.9987	0.9178	11	20
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-B27:08	RRKELLEEV	0.9987	0.7966	11	20
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C06:08	RRKELLEEV	0.9353	0.9899	11	20
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C07:01	RRKELLEEV	0.8448	0.8906	11	20
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C07:04	RRKELLEEV	0.6509	0.9811	11	20
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C07:22	RRKELLEEV	0.6096	0.9052	11	20
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C07:22	YYARRKELL	0.4231	0.6847	8	17
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C07:22	AYYARRKEL	0.3565	0.7721	7	16
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C06:17	AYYARRKEL	0.3249	0.9943	7	16
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C06:02	AYYARRKEL	0.3249	0.9943	7	16
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C07:02	YYARRKELL	0.2899	0.923	8	17
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C07:04	AYYARRKEL	0.2751	0.9307	7	16
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C07:17	YYARRKELL	0.2719	0.9641	8	17
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C03:67	YYARRKELL	0.2571	0.9769	8	17
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C06:17	YYARRKELL	0.2536	0.9925	8	17
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C06:02	YYARRKELL	0.2536	0.9925	8	17
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C07:04	YYARRKELL	0.2374	0.8177	8	17
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C07:02	AYYARRKEL	0.206	0.9608	7	16
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C03:67	AYYARRKEL	0.2043	0.9787	7	16
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C07:17	AYYARRKEL	0.1913	0.9675	7	16
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C06:06	YYARRKELL	0.1642	0.9818	8	17
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C07:01	YYARRKELL	0.1427	0.6028	8	17
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C07:01	AYYARRKEL	0.1409	0.7352	7	16
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C14:02	AYYARRKEL	0.1258	0.9648	7	16
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C14:03	AYYARRKEL	0.1258	0.9648	7	16
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C14:03	YYARRKELL	0.1153	0.9434	8	17
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C14:02	YYARRKELL	0.1153	0.9434	8	17
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C06:06	AYYARRKEL	0.1147	0.9911	7	16
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C06:17	RRKELLEEV	0.1113	0.9935	11	20
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C06:02	RRKELLEEV	0.1113	0.9935	11	20
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C04:04	YYARRKELL	0.0443	0.7693	8	17
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C18:01	YYARRKELL	0.041	0.6578	8	17
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C06:08	YYARRKELL	0.0406	0.9894	8	17
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	HLA-C06:08	AYYARRKEL	0.0274	0.9944	7	16

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Potential FusionNeoAntigen Information of BCL2L11-MERTK in HLA II

BCL2L11-MERTK_111907724_112751827.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)
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	DRB1-0801	NAYYARRKELLEEVG	6	21
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	DRB1-0816	NAYYARRKELLEEVG	6	21
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	DRB1-0826	NAYYARRKELLEEVG	6	21
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	DRB1-0837	NAYYARRKELLEEVG	6	21
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	DRB1-0837	FNAYYARRKELLEEV	5	20
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	DRB1-0839	NAYYARRKELLEEVG	6	21
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	DRB5-0102	IGDEFNAYYARRKEL	1	16
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	DRB5-0102	RIGDEFNAYYARRKE	0	15
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	DRB5-0102	GDEFNAYYARRKELL	2	17
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	DRB5-0103	IGDEFNAYYARRKEL	1	16
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	DRB5-0103	RIGDEFNAYYARRKE	0	15
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	DRB5-0103	GDEFNAYYARRKELL	2	17
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	DRB5-0103	DEFNAYYARRKELLE	3	18
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	DRB5-0104	IGDEFNAYYARRKEL	1	16
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	DRB5-0104	RIGDEFNAYYARRKE	0	15
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	DRB5-0104	GDEFNAYYARRKELL	2	17
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	DRB5-0108N	IGDEFNAYYARRKEL	1	16
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	DRB5-0108N	RIGDEFNAYYARRKE	0	15
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	DRB5-0108N	GDEFNAYYARRKELL	2	17
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	DRB5-0111	IGDEFNAYYARRKEL	1	16
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	DRB5-0111	RIGDEFNAYYARRKE	0	15
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	DRB5-0111	GDEFNAYYARRKELL	2	17
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	DRB5-0111	DEFNAYYARRKELLE	3	18
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	DRB5-0203	IGDEFNAYYARRKEL	1	16
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	DRB5-0203	GDEFNAYYARRKELL	2	17
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	DRB5-0203	RIGDEFNAYYARRKE	0	15
BCL2L11-MERTK	chr2	111907724	chr2	112751827	606	DRB5-0203	DEFNAYYARRKELLE	3	18

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Fusion breakpoint peptide structures of BCL2L11-MERTK

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
6095	NAYYARRKELLEEV	BCL2L11	MERTK	chr2	111907724	chr2	112751827	606

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of BCL2L11-MERTK

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	6095	NAYYARRKELLEEV	-7.9962	-8.1096
HLA-B14:02	3BVN	6095	NAYYARRKELLEEV	-5.70842	-6.74372
HLA-B52:01	3W39	6095	NAYYARRKELLEEV	-6.83737	-6.95077
HLA-B52:01	3W39	6095	NAYYARRKELLEEV	-4.4836	-5.5189
HLA-A11:01	4UQ2	6095	NAYYARRKELLEEV	-10.0067	-10.1201
HLA-A11:01	4UQ2	6095	NAYYARRKELLEEV	-9.03915	-10.0745
HLA-A24:02	5HGA	6095	NAYYARRKELLEEV	-6.56204	-6.67544
HLA-A24:02	5HGA	6095	NAYYARRKELLEEV	-5.42271	-6.45801
HLA-B44:05	3DX8	6095	NAYYARRKELLEEV	-7.85648	-8.89178
HLA-B44:05	3DX8	6095	NAYYARRKELLEEV	-5.3978	-5.5112
HLA-A02:01	6TDR	6095	NAYYARRKELLEEV	-3.37154	-4.40684

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Vaccine Design for the FusionNeoAntigens of BCL2L11-MERTK

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
BCL2L11-MERTK	chr2	111907724	chr2	112751827	11	20	RRKELLEEV	AGGAGGAAAGAGCTCTTGGAGGAAGTT
BCL2L11-MERTK	chr2	111907724	chr2	112751827	7	16	AYYARRKEL	GCTTACTATGCAAGGAGGAAAGAGCTC
BCL2L11-MERTK	chr2	111907724	chr2	112751827	8	16	YYARRKEL	TACTATGCAAGGAGGAAAGAGCTC
BCL2L11-MERTK	chr2	111907724	chr2	112751827	8	17	YYARRKELL	TACTATGCAAGGAGGAAAGAGCTCTTG
BCL2L11-MERTK	chr2	111907724	chr2	112751827	9	17	YARRKELL	TATGCAAGGAGGAAAGAGCTCTTG

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
BCL2L11-MERTK	chr2	111907724	chr2	112751827	0	15	RIGDEFNAYYARRKE	CGTATTGGAGACGAGTTTAACGCTTACTATGCAAGGAGGAAAGAG
BCL2L11-MERTK	chr2	111907724	chr2	112751827	1	16	IGDEFNAYYARRKEL	ATTGGAGACGAGTTTAACGCTTACTATGCAAGGAGGAAAGAGCTC
BCL2L11-MERTK	chr2	111907724	chr2	112751827	2	17	GDEFNAYYARRKELL	GGAGACGAGTTTAACGCTTACTATGCAAGGAGGAAAGAGCTCTTG
BCL2L11-MERTK	chr2	111907724	chr2	112751827	3	18	DEFNAYYARRKELLE	GACGAGTTTAACGCTTACTATGCAAGGAGGAAAGAGCTCTTGGAG
BCL2L11-MERTK	chr2	111907724	chr2	112751827	5	20	FNAYYARRKELLEEV	TTTAACGCTTACTATGCAAGGAGGAAAGAGCTCTTGGAGGAAGTT
BCL2L11-MERTK	chr2	111907724	chr2	112751827	6	21	NAYYARRKELLEEVG	AACGCTTACTATGCAAGGAGGAAAGAGCTCTTGGAGGAAGTTGGC

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Information of the samples that have these potential fusion neoantigens of BCL2L11-MERTK

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
HNSC	BCL2L11-MERTK	chr2	111907724	ENST00000308659	chr2	112751827	ENST00000295408	TCGA-DQ-7594

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Potential target of CAR-T therapy development for BCL2L11-MERTK

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

MERTK

chr2:111907724

chr2:112751827

ENST00000295408

506_526

1000.0

Transmembrane

Helical

Tgene

MERTK

chr2:111907724

chr2:112751827

ENST00000421804

506_526

951.3333333333334

Transmembrane

Helical

Tgene

MERTK

chr2:111907724

chr2:112751828

ENST00000295408

506_526

1000.0

Transmembrane

Helical

Tgene

MERTK

chr2:111907724

chr2:112751828

ENST00000421804

506_526

951.3333333333334

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 BCL2L11-MERTK

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 BCL2L11-MERTK

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)