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Fusion Protein:CARM1-NDUFS1

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: CARM1-NDUFS1
	FusionPDB ID: 13057
	FusionGDB2.0 ID: 13057
		Hgene	Tgene
	Gene symbol	CARM1	NDUFS1
	Gene ID	10498	4719
	Gene name	coactivator associated arginine methyltransferase 1	NADH:ubiquinone oxidoreductase core subunit S1
	Synonyms	PRMT4	CI-75Kd\|CI-75k\|MC1DN5\|PRO1304
	Cytomap	19p13.2	2q33.3
	Type of gene	protein-coding	protein-coding
	Description	histone-arginine methyltransferase CARM1protein arginine N-methyltransferase 4	NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrialNADH dehydrogenase (ubiquinone) Fe-S protein 1, 75kDa (NADH-coenzyme Q reductase)complex I 75kDa subunitcomplex I, mitochondrial respiratory chain, 75-kD subunitmitochondrial NADH-ubiquinone
	Modification date	20200313	20200313
	UniProtAcc	Q86X55 Main function of 5'-partner protein: FUNCTION: Methylates (mono- and asymmetric dimethylation) the guanidino nitrogens of arginyl residues in several proteins involved in DNA packaging, transcription regulation, pre-mRNA splicing, and mRNA stability. Recruited to promoters upon gene activation together with histone acetyltransferases from EP300/P300 and p160 families, methylates histone H3 at 'Arg-17' (H3R17me), forming mainly asymmetric dimethylarginine (H3R17me2a), leading to activate transcription via chromatin remodeling. During nuclear hormone receptor activation and TCF7L2/TCF4 activation, acts synergically with EP300/P300 and either one of the p160 histone acetyltransferases NCOA1/SRC1, NCOA2/GRIP1 and NCOA3/ACTR or CTNNB1/beta-catenin to activate transcription. During myogenic transcriptional activation, acts together with NCOA3/ACTR as a coactivator for MEF2C. During monocyte inflammatory stimulation, acts together with EP300/P300 as a coactivator for NF-kappa-B. Acts as coactivator for PPARG, promotes adipocyte differentiation and the accumulation of brown fat tissue. Plays a role in the regulation of pre-mRNA alternative splicing by methylation of splicing factors. Also seems to be involved in p53/TP53 transcriptional activation. Methylates EP300/P300, both at 'Arg-2142', which may loosen its interaction with NCOA2/GRIP1, and at 'Arg-580' and 'Arg-604' in the KIX domain, which impairs its interaction with CREB and inhibits CREB-dependent transcriptional activation. Also methylates arginine residues in RNA-binding proteins PABPC1, ELAVL1 and ELAV4, which may affect their mRNA-stabilizing properties and the half-life of their target mRNAs. {ECO:0000269\|PubMed:16497732, ECO:0000269\|PubMed:19405910}.	P28331 Main function of 5'-partner protein: FUNCTION: Core subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) which catalyzes electron transfer from NADH through the respiratory chain, using ubiquinone as an electron acceptor (PubMed:30879903, PubMed:31557978). Essential for catalysing the entry and efficient transfer of electrons within complex I (PubMed:31557978). Plays a key role in the assembly and stability of complex I and participates in the association of complex I with ubiquinol-cytochrome reductase complex (Complex III) to form supercomplexes (PubMed:30879903, PubMed:31557978). {ECO:0000269\|PubMed:30879903, ECO:0000269\|PubMed:31557978}.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000327064, ENST00000344150,	ENST00000233190, ENST00000423725, ENST00000432169, ENST00000440274, ENST00000449699, ENST00000455934, ENST00000457011,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	14 X 10 X 10=1400	7 X 7 X 6=294
	# samples	20	7
	** MAII score	log2(20/1400*10)=-2.8073549220576 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(7/294*10)=-2.0703893278914 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: CARM1 [Title/Abstract] AND NDUFS1 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: CARM1 [Title/Abstract] AND NDUFS1 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	CARM1(11019883)-NDUFS1(207007555), # samples:1
Anticipated loss of major functional domain due to fusion event.	CARM1-NDUFS1 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. CARM1-NDUFS1 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. CARM1-NDUFS1 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. CARM1-NDUFS1 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	CARM1	GO:0016571	histone methylation	19405910
Tgene	NDUFS1	GO:0008637	apoptotic mitochondrial changes	15186778

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr19:11019883/chr2:207007555)
- 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 CARM1 (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 NDUFS1 (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)
ENST00000327064	CARM1	chr19	11019883	+	ENST00000233190	NDUFS1	chr2	207007555	-	11313	748	46	1944	632
ENST00000327064	CARM1	chr19	11019883	+	ENST00000423725	NDUFS1	chr2	207007555	-	2311	748	46	1944	632
ENST00000327064	CARM1	chr19	11019883	+	ENST00000457011	NDUFS1	chr2	207007555	-	2185	748	46	1944	632
ENST00000327064	CARM1	chr19	11019883	+	ENST00000440274	NDUFS1	chr2	207007555	-	2174	748	46	1944	632
ENST00000327064	CARM1	chr19	11019883	+	ENST00000455934	NDUFS1	chr2	207007555	-	2031	748	46	1944	632
ENST00000327064	CARM1	chr19	11019883	+	ENST00000449699	NDUFS1	chr2	207007555	-	2029	748	46	1944	632
ENST00000327064	CARM1	chr19	11019883	+	ENST00000432169	NDUFS1	chr2	207007555	-	2029	748	46	1944	632
ENST00000344150	CARM1	chr19	11019883	+	ENST00000233190	NDUFS1	chr2	207007555	-	11123	558	0	1754	584
ENST00000344150	CARM1	chr19	11019883	+	ENST00000423725	NDUFS1	chr2	207007555	-	2121	558	0	1754	584
ENST00000344150	CARM1	chr19	11019883	+	ENST00000457011	NDUFS1	chr2	207007555	-	1995	558	0	1754	584
ENST00000344150	CARM1	chr19	11019883	+	ENST00000440274	NDUFS1	chr2	207007555	-	1984	558	0	1754	584
ENST00000344150	CARM1	chr19	11019883	+	ENST00000455934	NDUFS1	chr2	207007555	-	1841	558	0	1754	584
ENST00000344150	CARM1	chr19	11019883	+	ENST00000449699	NDUFS1	chr2	207007555	-	1839	558	0	1754	584
ENST00000344150	CARM1	chr19	11019883	+	ENST00000432169	NDUFS1	chr2	207007555	-	1839	558	0	1754	584

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
ENST00000327064	ENST00000233190	CARM1	chr19	11019883	+	NDUFS1	chr2	207007555	-	0.000547684	0.9994523
ENST00000327064	ENST00000423725	CARM1	chr19	11019883	+	NDUFS1	chr2	207007555	-	0.002164218	0.9978358
ENST00000327064	ENST00000457011	CARM1	chr19	11019883	+	NDUFS1	chr2	207007555	-	0.002909654	0.99709034
ENST00000327064	ENST00000440274	CARM1	chr19	11019883	+	NDUFS1	chr2	207007555	-	0.002945814	0.9970542
ENST00000327064	ENST00000455934	CARM1	chr19	11019883	+	NDUFS1	chr2	207007555	-	0.00462303	0.99537694
ENST00000327064	ENST00000449699	CARM1	chr19	11019883	+	NDUFS1	chr2	207007555	-	0.004705091	0.99529487
ENST00000327064	ENST00000432169	CARM1	chr19	11019883	+	NDUFS1	chr2	207007555	-	0.004705091	0.99529487
ENST00000344150	ENST00000233190	CARM1	chr19	11019883	+	NDUFS1	chr2	207007555	-	0.000472588	0.99952745
ENST00000344150	ENST00000423725	CARM1	chr19	11019883	+	NDUFS1	chr2	207007555	-	0.001617535	0.99838245
ENST00000344150	ENST00000457011	CARM1	chr19	11019883	+	NDUFS1	chr2	207007555	-	0.002199118	0.9978009
ENST00000344150	ENST00000440274	CARM1	chr19	11019883	+	NDUFS1	chr2	207007555	-	0.002206436	0.99779356
ENST00000344150	ENST00000455934	CARM1	chr19	11019883	+	NDUFS1	chr2	207007555	-	0.003503812	0.99649626
ENST00000344150	ENST00000449699	CARM1	chr19	11019883	+	NDUFS1	chr2	207007555	-	0.003567459	0.99643254
ENST00000344150	ENST00000432169	CARM1	chr19	11019883	+	NDUFS1	chr2	207007555	-	0.003567459	0.99643254

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 CARM1-NDUFS1

+/-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
CARM1	chr19	11019883	NDUFS1	chr2	207007555	558	186	RAILQNHTDFKDKLQSFQGKDVAAIA
CARM1	chr19	11019883	NDUFS1	chr2	207007555	748	234	RAILQNHTDFKDKLQSFQGKDVAAIA

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Potential FusionNeoAntigen Information of CARM1-NDUFS1 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.

CARM1-NDUFS1_11019883_207007555.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)
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	HLA-B39:01	NHTDFKDKL	0.9975	0.722	5	14
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	HLA-B38:01	NHTDFKDKL	0.9956	0.8089	5	14
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	HLA-B38:02	NHTDFKDKL	0.9955	0.8129	5	14
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	HLA-B39:06	NHTDFKDKL	0.988	0.5752	5	14
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	HLA-B15:18	NHTDFKDKL	0.4971	0.5162	5	14
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	HLA-B39:01	QNHTDFKDKL	0.7209	0.7797	4	14
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	HLA-B38:01	QNHTDFKDKL	0.6104	0.8358	4	14
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	HLA-B38:02	QNHTDFKDKL	0.6092	0.8398	4	14
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	HLA-B38:01	LQNHTDFKDKL	0.9106	0.9605	3	14
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	HLA-C08:15	HTDFKDKL	1	0.9765	6	14
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	HLA-C05:09	HTDFKDKL	1	0.9143	6	14
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	HLA-B39:12	NHTDFKDKL	0.9968	0.729	5	14
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	HLA-B39:05	NHTDFKDKL	0.9953	0.7007	5	14
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	HLA-C12:16	DFKDKLQSF	0.6855	0.9373	8	17
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	HLA-B15:21	DFKDKLQSF	0.6563	0.8732	8	17
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	HLA-C07:13	NHTDFKDKL	0.3995	0.8631	5	14
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	HLA-C07:05	DFKDKLQSF	0.3539	0.9194	8	17
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	HLA-C07:95	DFKDKLQSF	0.3155	0.582	8	17
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	HLA-C07:19	DFKDKLQSF	0.2845	0.5467	8	17
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	HLA-C07:27	DFKDKLQSF	0.2808	0.9235	8	17
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	HLA-C07:10	DFKDKLQSF	0.2767	0.9528	8	17
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	HLA-C07:80	DFKDKLQSF	0.2766	0.9214	8	17
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	HLA-C07:67	DFKDKLQSF	0.2766	0.9214	8	17
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	HLA-B14:03	NHTDFKDKL	0.2685	0.6695	5	14
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	HLA-C07:46	DFKDKLQSF	0.2138	0.8244	8	17
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	HLA-B39:05	QNHTDFKDKL	0.6067	0.7576	4	14
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	HLA-C05:09	HTDFKDKLQSF	1	0.8652	6	17
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	HLA-C04:03	HTDFKDKL	1	0.8046	6	14
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	HLA-C08:02	HTDFKDKL	1	0.9765	6	14
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	HLA-C05:01	HTDFKDKL	1	0.9143	6	14
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	HLA-C18:01	FKDKLQSF	0.9998	0.6461	9	17
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	HLA-C07:17	FKDKLQSF	0.9985	0.9533	9	17
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	HLA-B39:31	NHTDFKDKL	0.9975	0.7214	5	14
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	HLA-B38:05	NHTDFKDKL	0.9956	0.8089	5	14
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	HLA-B39:11	NHTDFKDKL	0.8234	0.6765	5	14
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	HLA-C07:22	DFKDKLQSF	0.6091	0.6141	8	17
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	HLA-B18:07	DFKDKLQSF	0.5575	0.8513	8	17
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	HLA-A25:01	DFKDKLQSF	0.5572	0.8641	8	17
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	HLA-B18:03	DFKDKLQSF	0.4741	0.9001	8	17
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	HLA-C07:17	DFKDKLQSF	0.3319	0.9544	8	17
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	HLA-C14:02	DFKDKLQSF	0.3307	0.9413	8	17
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	HLA-C14:03	DFKDKLQSF	0.3307	0.9413	8	17
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	HLA-C06:06	DFKDKLQSF	0.2911	0.986	8	17
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	HLA-C07:01	DFKDKLQSF	0.2891	0.5512	8	17
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	HLA-C07:02	DFKDKLQSF	0.2766	0.9214	8	17
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	HLA-B39:11	QNHTDFKDKL	0.7791	0.797	4	14
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	HLA-B38:05	QNHTDFKDKL	0.6104	0.8358	4	14
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	HLA-C05:01	HTDFKDKLQSF	1	0.8652	6	17
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	HLA-B58:06	HTDFKDKLQSF	0.9998	0.7783	6	17
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	HLA-B57:02	HTDFKDKLQSF	0.9997	0.9367	6	17
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	HLA-A25:01	HTDFKDKLQSF	0.9703	0.849	6	17
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	HLA-B38:05	LQNHTDFKDKL	0.9106	0.9605	3	14

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Potential FusionNeoAntigen Information of CARM1-NDUFS1 in HLA II

CARM1-NDUFS1_11019883_207007555.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)
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1457	RAILQNHTDFKDKLQ	0	15
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1501	KDKLQSFQGKDVAAI	10	25
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1501	FKDKLQSFQGKDVAA	9	24
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1501	DFKDKLQSFQGKDVA	8	23
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1502	KDKLQSFQGKDVAAI	10	25
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1502	FKDKLQSFQGKDVAA	9	24
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1503	FKDKLQSFQGKDVAA	9	24
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1503	KDKLQSFQGKDVAAI	10	25
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1504	FKDKLQSFQGKDVAA	9	24
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1504	KDKLQSFQGKDVAAI	10	25
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1504	DFKDKLQSFQGKDVA	8	23
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1505	FKDKLQSFQGKDVAA	9	24
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1505	KDKLQSFQGKDVAAI	10	25
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1505	DFKDKLQSFQGKDVA	8	23
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1506	KDKLQSFQGKDVAAI	10	25
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1506	FKDKLQSFQGKDVAA	9	24
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1506	DFKDKLQSFQGKDVA	8	23
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1507	KDKLQSFQGKDVAAI	10	25
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1507	FKDKLQSFQGKDVAA	9	24
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1507	DFKDKLQSFQGKDVA	8	23
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1508	KDKLQSFQGKDVAAI	10	25
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1508	FKDKLQSFQGKDVAA	9	24
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1509	KDKLQSFQGKDVAAI	10	25
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1509	FKDKLQSFQGKDVAA	9	24
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1509	DFKDKLQSFQGKDVA	8	23
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1510	KDKLQSFQGKDVAAI	10	25
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1510	FKDKLQSFQGKDVAA	9	24
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1510	DFKDKLQSFQGKDVA	8	23
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1511	KDKLQSFQGKDVAAI	10	25
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1511	FKDKLQSFQGKDVAA	9	24
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1512	FKDKLQSFQGKDVAA	9	24
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1512	KDKLQSFQGKDVAAI	10	25
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1512	DFKDKLQSFQGKDVA	8	23
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1513	KDKLQSFQGKDVAAI	10	25
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1513	FKDKLQSFQGKDVAA	9	24
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1513	DFKDKLQSFQGKDVA	8	23
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1514	KDKLQSFQGKDVAAI	10	25
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1514	FKDKLQSFQGKDVAA	9	24
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1515	KDKLQSFQGKDVAAI	10	25
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1515	FKDKLQSFQGKDVAA	9	24
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1516	KDKLQSFQGKDVAAI	10	25
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1516	FKDKLQSFQGKDVAA	9	24
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1516	DFKDKLQSFQGKDVA	8	23
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1518	KDKLQSFQGKDVAAI	10	25
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1518	FKDKLQSFQGKDVAA	9	24
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1518	DFKDKLQSFQGKDVA	8	23
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1519	KDKLQSFQGKDVAAI	10	25
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1519	FKDKLQSFQGKDVAA	9	24
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1520	KDKLQSFQGKDVAAI	10	25
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1520	FKDKLQSFQGKDVAA	9	24
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1520	DFKDKLQSFQGKDVA	8	23
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1521	KDKLQSFQGKDVAAI	10	25
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1521	FKDKLQSFQGKDVAA	9	24
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1521	DFKDKLQSFQGKDVA	8	23
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1522	KDKLQSFQGKDVAAI	10	25
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1522	FKDKLQSFQGKDVAA	9	24
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1522	DFKDKLQSFQGKDVA	8	23
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1523	FKDKLQSFQGKDVAA	9	24
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1523	KDKLQSFQGKDVAAI	10	25
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1524	KDKLQSFQGKDVAAI	10	25
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1524	FKDKLQSFQGKDVAA	9	24
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1524	DFKDKLQSFQGKDVA	8	23
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1526	KDKLQSFQGKDVAAI	10	25
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1526	FKDKLQSFQGKDVAA	9	24
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1528	KDKLQSFQGKDVAAI	10	25
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1528	FKDKLQSFQGKDVAA	9	24
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1529	FKDKLQSFQGKDVAA	9	24
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1529	KDKLQSFQGKDVAAI	10	25
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1530	KDKLQSFQGKDVAAI	10	25
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1530	FKDKLQSFQGKDVAA	9	24
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1531	KDKLQSFQGKDVAAI	10	25
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1531	FKDKLQSFQGKDVAA	9	24
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1532	KDKLQSFQGKDVAAI	10	25
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1532	FKDKLQSFQGKDVAA	9	24
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1532	DFKDKLQSFQGKDVA	8	23
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1533	KDKLQSFQGKDVAAI	10	25
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1533	FKDKLQSFQGKDVAA	9	24
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1533	DFKDKLQSFQGKDVA	8	23
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1535	KDKLQSFQGKDVAAI	10	25
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1535	FKDKLQSFQGKDVAA	9	24
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1536	KDKLQSFQGKDVAAI	10	25
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1536	FKDKLQSFQGKDVAA	9	24
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1537	KDKLQSFQGKDVAAI	10	25
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1537	FKDKLQSFQGKDVAA	9	24
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1537	DFKDKLQSFQGKDVA	8	23
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1538	KDKLQSFQGKDVAAI	10	25
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1538	FKDKLQSFQGKDVAA	9	24
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1539	KDKLQSFQGKDVAAI	10	25
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1539	FKDKLQSFQGKDVAA	9	24
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1540	KDKLQSFQGKDVAAI	10	25
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1540	FKDKLQSFQGKDVAA	9	24
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1540	DFKDKLQSFQGKDVA	8	23
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1541	KDKLQSFQGKDVAAI	10	25
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1541	FKDKLQSFQGKDVAA	9	24
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1541	DFKDKLQSFQGKDVA	8	23
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1542	KDKLQSFQGKDVAAI	10	25
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1542	FKDKLQSFQGKDVAA	9	24
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1542	DFKDKLQSFQGKDVA	8	23
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1543	KDKLQSFQGKDVAAI	10	25
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1543	FKDKLQSFQGKDVAA	9	24
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1543	DFKDKLQSFQGKDVA	8	23
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1544	KDKLQSFQGKDVAAI	10	25
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1544	FKDKLQSFQGKDVAA	9	24
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1545	KDKLQSFQGKDVAAI	10	25
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1545	FKDKLQSFQGKDVAA	9	24
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1545	DFKDKLQSFQGKDVA	8	23
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1546	KDKLQSFQGKDVAAI	10	25
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1546	FKDKLQSFQGKDVAA	9	24
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1546	DFKDKLQSFQGKDVA	8	23
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1547	KDKLQSFQGKDVAAI	10	25
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1547	FKDKLQSFQGKDVAA	9	24
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1548	KDKLQSFQGKDVAAI	10	25
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1548	FKDKLQSFQGKDVAA	9	24
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1548	DFKDKLQSFQGKDVA	8	23
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1549	FKDKLQSFQGKDVAA	9	24
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1549	KDKLQSFQGKDVAAI	10	25
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1549	DFKDKLQSFQGKDVA	8	23
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1615	KDKLQSFQGKDVAAI	10	25
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB1-1615	FKDKLQSFQGKDVAA	9	24
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB5-0204	KDKLQSFQGKDVAAI	10	25
CARM1-NDUFS1	chr19	11019883	chr2	207007555	748	DRB5-0204	FKDKLQSFQGKDVAA	9	24

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Fusion breakpoint peptide structures of CARM1-NDUFS1

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
3516	HTDFKDKLQSFQGK	CARM1	NDUFS1	chr19	11019883	chr2	207007555	748

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of CARM1-NDUFS1

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	3516	HTDFKDKLQSFQGK	-7.15543	-7.26883
HLA-B14:02	3BVN	3516	HTDFKDKLQSFQGK	-4.77435	-5.80965
HLA-B52:01	3W39	3516	HTDFKDKLQSFQGK	-6.80875	-6.92215
HLA-B52:01	3W39	3516	HTDFKDKLQSFQGK	-4.20386	-5.23916
HLA-A11:01	4UQ2	3516	HTDFKDKLQSFQGK	-7.5194	-8.5547
HLA-A11:01	4UQ2	3516	HTDFKDKLQSFQGK	-6.9601	-7.0735
HLA-A24:02	5HGA	3516	HTDFKDKLQSFQGK	-7.52403	-7.63743
HLA-A24:02	5HGA	3516	HTDFKDKLQSFQGK	-5.82433	-6.85963
HLA-B27:05	6PYJ	3516	HTDFKDKLQSFQGK	-3.28285	-4.31815
HLA-B44:05	3DX8	3516	HTDFKDKLQSFQGK	-5.91172	-6.94702
HLA-B44:05	3DX8	3516	HTDFKDKLQSFQGK	-4.24346	-4.35686

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Vaccine Design for the FusionNeoAntigens of CARM1-NDUFS1

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
CARM1-NDUFS1	chr19	11019883	chr2	207007555	3	14	LQNHTDFKDKL	CTGCAAAACCACACCGACTTCAAGGACAAGTTG
CARM1-NDUFS1	chr19	11019883	chr2	207007555	4	14	QNHTDFKDKL	CAAAACCACACCGACTTCAAGGACAAGTTG
CARM1-NDUFS1	chr19	11019883	chr2	207007555	5	14	NHTDFKDKL	AACCACACCGACTTCAAGGACAAGTTG
CARM1-NDUFS1	chr19	11019883	chr2	207007555	6	14	HTDFKDKL	CACACCGACTTCAAGGACAAGTTG
CARM1-NDUFS1	chr19	11019883	chr2	207007555	6	17	HTDFKDKLQSF	CACACCGACTTCAAGGACAAGTTGCAGAGTTTT
CARM1-NDUFS1	chr19	11019883	chr2	207007555	8	17	DFKDKLQSF	GACTTCAAGGACAAGTTGCAGAGTTTT
CARM1-NDUFS1	chr19	11019883	chr2	207007555	9	17	FKDKLQSF	TTCAAGGACAAGTTGCAGAGTTTT

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
CARM1-NDUFS1	chr19	11019883	chr2	207007555	0	15	RAILQNHTDFKDKLQ	CGCGCCATCCTGCAAAACCACACCGACTTCAAGGACAAGTTGCAG
CARM1-NDUFS1	chr19	11019883	chr2	207007555	10	25	KDKLQSFQGKDVAAI	AAGGACAAGTTGCAGAGTTTTCAAGGCAAAGATGTGGCAGCAATT
CARM1-NDUFS1	chr19	11019883	chr2	207007555	8	23	DFKDKLQSFQGKDVA	GACTTCAAGGACAAGTTGCAGAGTTTTCAAGGCAAAGATGTGGCA
CARM1-NDUFS1	chr19	11019883	chr2	207007555	9	24	FKDKLQSFQGKDVAA	TTCAAGGACAAGTTGCAGAGTTTTCAAGGCAAAGATGTGGCAGCA

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Information of the samples that have these potential fusion neoantigens of CARM1-NDUFS1

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
ESCA	CARM1-NDUFS1	chr19	11019883	ENST00000327064	chr2	207007555	ENST00000233190	TCGA-JY-A93F

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Potential target of CAR-T therapy development for CARM1-NDUFS1

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 CARM1-NDUFS1

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 CARM1-NDUFS1

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)