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Fusion Protein:BAZ2A-PRIM1

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: BAZ2A-PRIM1
	FusionPDB ID: 9047
	FusionGDB2.0 ID: 9047
		Hgene	Tgene
	Gene symbol	BAZ2A	PRIM1
	Gene ID	11176	5557
	Gene name	bromodomain adjacent to zinc finger domain 2A	DNA primase subunit 1
	Synonyms	TIP5\|WALp3	p49
	Cytomap	12q13.3	12q13.3
	Type of gene	protein-coding	protein-coding
	Description	bromodomain adjacent to zinc finger domain protein 2ATTF-I interacting peptide 5TTF-I-interacting protein 5transcription termination factor I-interacting protein 5	DNA primase small subunitDNA primase 1DNA primase 49 kDa subunitDNA primase subunit 48primase (DNA) subunit 1primase p49 subunitprimase polypeptide 1, 49kDaprimase, DNA, polypeptide 1 (49kDa)
	Modification date	20200313	20200313
	UniProtAcc	Q9UIF9 Main function of 5'-partner protein: FUNCTION: Essential component of the NoRC (nucleolar remodeling complex) complex, a complex that mediates silencing of a fraction of rDNA by recruiting histone-modifying enzymes and DNA methyltransferases, leading to heterochromatin formation and transcriptional silencing. In the complex, it plays a central role by being recruited to rDNA and by targeting chromatin modifying enzymes such as HDAC1, leading to repress RNA polymerase I transcription. Recruited to rDNA via its interaction with TTF1 and its ability to recognize and bind histone H4 acetylated on 'Lys-16' (H4K16ac), leading to deacetylation of H4K5ac, H4K8ac, H4K12ac but not H4K16ac. Specifically binds pRNAs, 150-250 nucleotide RNAs that are complementary in sequence to the rDNA promoter; pRNA-binding is required for heterochromatin formation and rDNA silencing (By similarity). {ECO:0000250}.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000179765, ENST00000379441, ENST00000549884, ENST00000551812, ENST00000553222,	ENST00000552408, ENST00000338193,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	16 X 18 X 8=2304	11 X 10 X 7=770
	# samples	20	13
	** MAII score	log2(20/2304*10)=-3.52606881166759 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(13/770*10)=-2.56634682255381 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: BAZ2A [Title/Abstract] AND PRIM1 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: BAZ2A [Title/Abstract] AND PRIM1 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	BAZ2A(57006799)-PRIM1(57128029), # samples:2
Anticipated loss of major functional domain due to fusion event.	BAZ2A-PRIM1 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. BAZ2A-PRIM1 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. BAZ2A-PRIM1 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. BAZ2A-PRIM1 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. BAZ2A-PRIM1 seems lost the major protein functional domain in Hgene partner, which is a epigenetic factor due to the frame-shifted ORF. BAZ2A-PRIM1 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF. BAZ2A-PRIM1 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF. BAZ2A-PRIM1 seems lost the major protein functional domain in Hgene partner, which is a transcription factor due to the frame-shifted ORF. BAZ2A-PRIM1 seems lost the major protein functional domain in Tgene partner, which is a cell metabolism gene due to the frame-shifted ORF. BAZ2A-PRIM1 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.

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

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

Partner

Gene

GO ID

GO term

PubMed ID

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr12:57006799/chr12:57128029)
- 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 BAZ2A (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 PRIM1 (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)
ENST00000379441	BAZ2A	chr12	57006799	-	ENST00000338193	PRIM1	chr12	57128029	-	1444	1232	88	1350	420
ENST00000551812	BAZ2A	chr12	57006799	-	ENST00000338193	PRIM1	chr12	57128029	-	1547	1335	101	1453	450
ENST00000379441	BAZ2A	chr12	57008798	-	ENST00000338193	PRIM1	chr12	57128029	-	1039	827	88	945	285
ENST00000551812	BAZ2A	chr12	57008798	-	ENST00000338193	PRIM1	chr12	57128029	-	1142	930	101	1048	315
ENST00000379441	BAZ2A	chr12	57003520	-	ENST00000338193	PRIM1	chr12	57128029	-	2401	2189	88	2307	739
ENST00000551812	BAZ2A	chr12	57003520	-	ENST00000338193	PRIM1	chr12	57128029	-	2504	2292	101	2410	769

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
ENST00000379441	ENST00000338193	BAZ2A	chr12	57006799	-	PRIM1	chr12	57128029	-	0.001735151	0.99826485
ENST00000551812	ENST00000338193	BAZ2A	chr12	57006799	-	PRIM1	chr12	57128029	-	0.002654647	0.9973454
ENST00000379441	ENST00000338193	BAZ2A	chr12	57008798	-	PRIM1	chr12	57128029	-	0.004969502	0.9950305
ENST00000551812	ENST00000338193	BAZ2A	chr12	57008798	-	PRIM1	chr12	57128029	-	0.004028171	0.99597186
ENST00000379441	ENST00000338193	BAZ2A	chr12	57003520	-	PRIM1	chr12	57128029	-	0.004055264	0.9959447
ENST00000551812	ENST00000338193	BAZ2A	chr12	57003520	-	PRIM1	chr12	57128029	-	0.004709394	0.99529064

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 BAZ2A-PRIM1

+/-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
BAZ2A	chr12	57003520	PRIM1	chr12	57128029	2189	700	KTDNRPLKKLEAQDYKKTSLAPYVKV
BAZ2A	chr12	57003520	PRIM1	chr12	57128029	2292	730	KTDNRPLKKLEAQDYKKTSLAPYVKV
BAZ2A	chr12	57006799	PRIM1	chr12	57128029	1232	330	IDDTELMGAEDKLPLEDSPVISALDC
BAZ2A	chr12	57006799	PRIM1	chr12	57128029	1335	360	IDDTELMGAEDKLPLEDSPVISALDC
BAZ2A	chr12	57008798	PRIM1	chr12	57128029	827	246	GLVGSLELEEEQPDYKKTSLAPYVKV
BAZ2A	chr12	57008798	PRIM1	chr12	57128029	930	276	GLVGSLELEEEQPDYKKTSLAPYVKV

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Potential FusionNeoAntigen Information of BAZ2A-PRIM1 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.

BAZ2A-PRIM1_57003520_57128029.msa
BAZ2A-PRIM1_57006799_57128029.msa
BAZ2A-PRIM1_57008798_57128029.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)
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-B48:01	AQDYKKTSL	0.9973	0.5386	11	20
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-B39:24	AQDYKKTSL	0.9927	0.5761	11	20
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-B39:01	AQDYKKTSL	0.9744	0.9212	11	20
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-B08:09	AQDYKKTSL	0.9648	0.7589	11	20
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-B14:02	AQDYKKTSL	0.957	0.7476	11	20
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-B14:01	AQDYKKTSL	0.957	0.7476	11	20
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-B39:13	AQDYKKTSL	0.9368	0.9369	11	20
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-B38:02	AQDYKKTSL	0.9157	0.9703	11	20
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-B15:10	AQDYKKTSL	0.8663	0.6801	11	20
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-B15:03	AQDYKKTSL	0.7531	0.7867	11	20
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-B13:02	AQDYKKTSL	0.7114	0.713	11	20
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-B13:01	AQDYKKTSL	0.6075	0.9013	11	20
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-B47:01	AQDYKKTSL	0.569	0.5807	11	20
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-B15:37	AQDYKKTSL	0.5161	0.6575	11	20
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-B15:03	LKKLEAQDY	0.0631	0.6321	6	15
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-C05:09	AQDYKKTSL	0.9999	0.9482	11	20
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-C04:10	AQDYKKTSL	0.9999	0.8834	11	20
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-C04:07	AQDYKKTSL	0.9999	0.8918	11	20
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-C08:15	AQDYKKTSL	0.9997	0.9563	11	20
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-C01:17	AQDYKKTSL	0.9995	0.9563	11	20
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-C04:14	AQDYKKTSL	0.9905	0.8171	11	20
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-C04:06	AQDYKKTSL	0.9887	0.9316	11	20
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-C08:04	AQDYKKTSL	0.9867	0.9834	11	20
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-C08:13	AQDYKKTSL	0.9867	0.9834	11	20
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-B39:09	AQDYKKTSL	0.9815	0.6455	11	20
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-C07:13	AQDYKKTSL	0.973	0.9544	11	20
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-B39:12	AQDYKKTSL	0.9692	0.9328	11	20
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-B39:08	AQDYKKTSL	0.9641	0.8595	11	20
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-C07:29	AQDYKKTSL	0.9609	0.9605	11	20
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-C08:03	AQDYKKTSL	0.9525	0.9907	11	20
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-C01:30	AQDYKKTSL	0.952	0.9483	11	20
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-B14:03	AQDYKKTSL	0.936	0.6555	11	20
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-B39:05	AQDYKKTSL	0.9273	0.9149	11	20
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-B14:03	EAQDYKKTSL	0.9745	0.7962	10	20
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-B39:08	LEAQDYKKTSL	0.9979	0.8684	9	20
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-C04:01	AQDYKKTSL	0.9999	0.8918	11	20
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-C05:01	AQDYKKTSL	0.9999	0.9482	11	20
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-C04:03	AQDYKKTSL	0.9999	0.9319	11	20
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-C18:01	AQDYKKTSL	0.9998	0.9019	11	20
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-C01:03	AQDYKKTSL	0.9998	0.9435	11	20
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-C08:02	AQDYKKTSL	0.9997	0.9563	11	20
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-C01:02	AQDYKKTSL	0.9996	0.9544	11	20
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-C06:06	AQDYKKTSL	0.9954	0.9933	11	20
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-C04:04	AQDYKKTSL	0.988	0.9223	11	20
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-B39:02	AQDYKKTSL	0.9748	0.935	11	20
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-C07:04	AQDYKKTSL	0.969	0.9415	11	20
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-B39:31	AQDYKKTSL	0.9647	0.9319	11	20
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-B08:12	AQDYKKTSL	0.959	0.6278	11	20
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-B39:11	AQDYKKTSL	0.9586	0.8153	11	20
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-C08:01	AQDYKKTSL	0.9525	0.9907	11	20
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-C03:67	AQDYKKTSL	0.9443	0.9796	11	20
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-B07:13	AQDYKKTSL	0.7462	0.8334	11	20
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-B15:73	AQDYKKTSL	0.6968	0.8314	11	20
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-B15:09	AQDYKKTSL	0.6571	0.7377	11	20
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-B15:30	AQDYKKTSL	0.6204	0.921	11	20
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-A02:14	AQDYKKTSL	0.4857	0.5848	11	20
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-B15:54	LKKLEAQDY	0.051	0.741	6	15
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-B15:68	LKKLEAQDY	0.0156	0.5404	6	15
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-B08:12	EAQDYKKTSL	0.9387	0.5307	10	20
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	HLA-B41:03	LEAQDYKKTSL	0.9948	0.784	9	20
BAZ2A-PRIM1	chr12	57006799	chr12	57128029	1232	HLA-B51:01	LPLEDSPV	0.9947	0.6453	12	20
BAZ2A-PRIM1	chr12	57006799	chr12	57128029	1232	HLA-B51:02	LPLEDSPV	0.9846	0.6066	12	20
BAZ2A-PRIM1	chr12	57006799	chr12	57128029	1232	HLA-B35:04	LPLEDSPVI	0.9892	0.9549	12	21
BAZ2A-PRIM1	chr12	57006799	chr12	57128029	1232	HLA-B35:02	LPLEDSPVI	0.9892	0.9549	12	21
BAZ2A-PRIM1	chr12	57006799	chr12	57128029	1232	HLA-B35:03	LPLEDSPVI	0.983	0.8979	12	21
BAZ2A-PRIM1	chr12	57006799	chr12	57128029	1232	HLA-B35:01	LPLEDSPVI	0.9774	0.8946	12	21
BAZ2A-PRIM1	chr12	57006799	chr12	57128029	1232	HLA-B35:05	LPLEDSPVI	0.9763	0.5722	12	21
BAZ2A-PRIM1	chr12	57006799	chr12	57128029	1232	HLA-B35:08	LPLEDSPVI	0.9662	0.9007	12	21
BAZ2A-PRIM1	chr12	57006799	chr12	57128029	1232	HLA-A02:60	KLPLEDSPVI	0.6626	0.8362	11	21
BAZ2A-PRIM1	chr12	57006799	chr12	57128029	1232	HLA-A02:30	KLPLEDSPVI	0.6564	0.836	11	21
BAZ2A-PRIM1	chr12	57006799	chr12	57128029	1232	HLA-A02:24	KLPLEDSPVI	0.6564	0.836	11	21
BAZ2A-PRIM1	chr12	57006799	chr12	57128029	1232	HLA-A02:67	KLPLEDSPVI	0.6564	0.836	11	21
BAZ2A-PRIM1	chr12	57006799	chr12	57128029	1232	HLA-A02:27	KLPLEDSPVI	0.6401	0.8266	11	21
BAZ2A-PRIM1	chr12	57006799	chr12	57128029	1232	HLA-A02:16	KLPLEDSPVI	0.5378	0.7289	11	21
BAZ2A-PRIM1	chr12	57006799	chr12	57128029	1232	HLA-A02:35	KLPLEDSPVI	0.5178	0.8513	11	21
BAZ2A-PRIM1	chr12	57006799	chr12	57128029	1232	HLA-A02:29	KLPLEDSPVI	0.4678	0.8377	11	21
BAZ2A-PRIM1	chr12	57006799	chr12	57128029	1232	HLA-A02:20	KLPLEDSPVI	0.4441	0.8442	11	21
BAZ2A-PRIM1	chr12	57006799	chr12	57128029	1232	HLA-B78:01	LPLEDSPVI	0.9935	0.5427	12	21
BAZ2A-PRIM1	chr12	57006799	chr12	57128029	1232	HLA-B51:07	LPLEDSPVI	0.9933	0.7796	12	21
BAZ2A-PRIM1	chr12	57006799	chr12	57128029	1232	HLA-B35:12	LPLEDSPVI	0.9892	0.9549	12	21
BAZ2A-PRIM1	chr12	57006799	chr12	57128029	1232	HLA-B07:12	LPLEDSPVI	0.8253	0.5873	12	21
BAZ2A-PRIM1	chr12	57006799	chr12	57128029	1232	HLA-B39:10	LPLEDSPVI	0.6958	0.9398	12	21
BAZ2A-PRIM1	chr12	57006799	chr12	57128029	1232	HLA-B42:01	LPLEDSPVI	0.4513	0.8536	12	21
BAZ2A-PRIM1	chr12	57006799	chr12	57128029	1232	HLA-A02:01	KLPLEDSPVI	0.6564	0.836	11	21
BAZ2A-PRIM1	chr12	57006799	chr12	57128029	1232	HLA-B78:01	LPLEDSPVISA	0.9955	0.5845	12	23
BAZ2A-PRIM1	chr12	57006799	chr12	57128029	1232	HLA-B51:14	LPLEDSPV	0.9939	0.616	12	20
BAZ2A-PRIM1	chr12	57006799	chr12	57128029	1232	HLA-B51:09	LPLEDSPV	0.9851	0.5951	12	20
BAZ2A-PRIM1	chr12	57006799	chr12	57128029	1232	HLA-B51:21	LPLEDSPV	0.9711	0.6586	12	20
BAZ2A-PRIM1	chr12	57006799	chr12	57128029	1232	HLA-B59:01	LPLEDSPV	0.9003	0.5239	12	20
BAZ2A-PRIM1	chr12	57006799	chr12	57128029	1232	HLA-B78:02	LPLEDSPVI	0.995	0.5982	12	21
BAZ2A-PRIM1	chr12	57006799	chr12	57128029	1232	HLA-B35:09	LPLEDSPVI	0.9892	0.9549	12	21
BAZ2A-PRIM1	chr12	57006799	chr12	57128029	1232	HLA-B35:13	LPLEDSPVI	0.9836	0.9029	12	21
BAZ2A-PRIM1	chr12	57006799	chr12	57128029	1232	HLA-B35:23	LPLEDSPVI	0.9783	0.9007	12	21
BAZ2A-PRIM1	chr12	57006799	chr12	57128029	1232	HLA-B35:77	LPLEDSPVI	0.9774	0.8946	12	21
BAZ2A-PRIM1	chr12	57006799	chr12	57128029	1232	HLA-B35:30	LPLEDSPVI	0.9674	0.7186	12	21
BAZ2A-PRIM1	chr12	57006799	chr12	57128029	1232	HLA-B35:17	LPLEDSPVI	0.9674	0.7186	12	21
BAZ2A-PRIM1	chr12	57006799	chr12	57128029	1232	HLA-B35:24	LPLEDSPVI	0.9347	0.9051	12	21
BAZ2A-PRIM1	chr12	57006799	chr12	57128029	1232	HLA-B35:11	LPLEDSPVI	0.9069	0.933	12	21
BAZ2A-PRIM1	chr12	57006799	chr12	57128029	1232	HLA-B35:13	MGAEDKLPL	0.8937	0.9348	6	15
BAZ2A-PRIM1	chr12	57006799	chr12	57128029	1232	HLA-B67:01	LPLEDSPVI	0.8151	0.7435	12	21
BAZ2A-PRIM1	chr12	57006799	chr12	57128029	1232	HLA-B78:02	LPLEDSPVISA	0.9934	0.6147	12	23
BAZ2A-PRIM1	chr12	57006799	chr12	57128029	1232	HLA-B51:09	DKLPLEDSPVI	0.9474	0.5677	10	21
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	827	HLA-B08:09	QPDYKKTSL	0.9739	0.6386	11	20
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	827	HLA-B14:02	QPDYKKTSL	0.9429	0.6364	11	20
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	827	HLA-B14:01	QPDYKKTSL	0.9429	0.6364	11	20
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	827	HLA-B45:01	EEQPDYKKT	0.9356	0.7453	9	18
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	827	HLA-B39:01	QPDYKKTSL	0.8553	0.8981	11	20
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	827	HLA-B35:08	QPDYKKTSL	0.8236	0.9284	11	20
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	827	HLA-B35:01	QPDYKKTSL	0.799	0.9412	11	20
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	827	HLA-B35:03	QPDYKKTSL	0.7959	0.9379	11	20
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	827	HLA-B35:05	QPDYKKTSL	0.5405	0.6922	11	20
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	827	HLA-B35:02	QPDYKKTSL	0.5161	0.9531	11	20
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	827	HLA-B35:04	QPDYKKTSL	0.5161	0.9531	11	20
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	827	HLA-B44:03	EEQPDYKKTSL	0.9978	0.9457	9	20
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	827	HLA-C04:07	QPDYKKTSL	0.9993	0.8729	11	20
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	827	HLA-C04:10	QPDYKKTSL	0.9993	0.8696	11	20
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	827	HLA-C08:15	QPDYKKTSL	0.9975	0.9583	11	20
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	827	HLA-B14:03	QPDYKKTSL	0.9958	0.6402	11	20
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	827	HLA-B39:09	QPDYKKTSL	0.9117	0.5998	11	20
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	827	HLA-B39:08	QPDYKKTSL	0.8887	0.8599	11	20
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	827	HLA-B39:10	QPDYKKTSL	0.8534	0.8887	11	20
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	827	HLA-B39:12	QPDYKKTSL	0.8235	0.9123	11	20
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	827	HLA-C04:14	QPDYKKTSL	0.5495	0.8441	11	20
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	827	HLA-B35:12	QPDYKKTSL	0.5161	0.9531	11	20
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	827	HLA-B15:31	ELEEEQPDY	0.4324	0.907	6	15
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	827	HLA-B14:03	EQPDYKKTSL	0.9653	0.7296	10	20
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	827	HLA-B39:10	EQPDYKKTSL	0.9536	0.8495	10	20
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	827	HLA-B39:10	EEQPDYKKTSL	0.9964	0.8318	9	20
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	827	HLA-B07:13	QPDYKKTSL	0.9997	0.803	11	20
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	827	HLA-C04:01	QPDYKKTSL	0.9993	0.8729	11	20
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	827	HLA-C04:03	QPDYKKTSL	0.9992	0.9185	11	20
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	827	HLA-C18:01	QPDYKKTSL	0.9992	0.8892	11	20
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	827	HLA-C08:02	QPDYKKTSL	0.9975	0.9583	11	20
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	827	HLA-B08:12	QPDYKKTSL	0.9085	0.6534	11	20
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	827	HLA-B39:31	QPDYKKTSL	0.8554	0.9119	11	20
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	827	HLA-B39:11	QPDYKKTSL	0.8361	0.7984	11	20
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	827	HLA-B67:01	QPDYKKTSL	0.8231	0.8295	11	20
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	827	HLA-B35:77	QPDYKKTSL	0.799	0.9412	11	20
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	827	HLA-B35:23	QPDYKKTSL	0.7903	0.9406	11	20
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	827	HLA-B35:13	QPDYKKTSL	0.7658	0.9413	11	20
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	827	HLA-C04:04	QPDYKKTSL	0.6597	0.9176	11	20
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	827	HLA-C07:04	QPDYKKTSL	0.6577	0.9262	11	20
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	827	HLA-B35:11	QPDYKKTSL	0.6561	0.9255	11	20
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	827	HLA-B35:17	QPDYKKTSL	0.5794	0.8628	11	20
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	827	HLA-B35:30	QPDYKKTSL	0.5794	0.8628	11	20
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	827	HLA-B35:24	QPDYKKTSL	0.564	0.9139	11	20
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	827	HLA-B35:09	QPDYKKTSL	0.5161	0.9531	11	20
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	827	HLA-B15:09	QPDYKKTSL	0.4502	0.6943	11	20
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	827	HLA-B08:12	EQPDYKKTSL	0.9624	0.5177	10	20
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	827	HLA-B67:01	EQPDYKKTSL	0.9429	0.6794	10	20
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	827	HLA-B18:11	LELEEEQPDY	0.7467	0.9298	5	15
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	827	HLA-B44:07	EEQPDYKKTSL	0.9978	0.9457	9	20
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	827	HLA-B44:26	EEQPDYKKTSL	0.9978	0.9457	9	20
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	827	HLA-B44:13	EEQPDYKKTSL	0.9978	0.9457	9	20
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	827	HLA-B08:12	EEQPDYKKTSL	0.9963	0.5043	9	20

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Potential FusionNeoAntigen Information of BAZ2A-PRIM1 in HLA II

BAZ2A-PRIM1_57003520_57128029.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)
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1201	NRPLKKLEAQDYKKT	3	18
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1201	DNRPLKKLEAQDYKK	2	17
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1201	TDNRPLKKLEAQDYK	1	16
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1201	RPLKKLEAQDYKKTS	4	19
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1201	KTDNRPLKKLEAQDY	0	15
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1203	NRPLKKLEAQDYKKT	3	18
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1203	DNRPLKKLEAQDYKK	2	17
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1203	TDNRPLKKLEAQDYK	1	16
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1203	RPLKKLEAQDYKKTS	4	19
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1204	NRPLKKLEAQDYKKT	3	18
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1204	DNRPLKKLEAQDYKK	2	17
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1204	RPLKKLEAQDYKKTS	4	19
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1204	TDNRPLKKLEAQDYK	1	16
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1205	NRPLKKLEAQDYKKT	3	18
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1205	DNRPLKKLEAQDYKK	2	17
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1205	TDNRPLKKLEAQDYK	1	16
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1205	RPLKKLEAQDYKKTS	4	19
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1205	KTDNRPLKKLEAQDY	0	15
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1206	NRPLKKLEAQDYKKT	3	18
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1206	DNRPLKKLEAQDYKK	2	17
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1206	TDNRPLKKLEAQDYK	1	16
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1206	RPLKKLEAQDYKKTS	4	19
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1206	KTDNRPLKKLEAQDY	0	15
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1207	NRPLKKLEAQDYKKT	3	18
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1207	DNRPLKKLEAQDYKK	2	17
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1207	TDNRPLKKLEAQDYK	1	16
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1207	RPLKKLEAQDYKKTS	4	19
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1207	KTDNRPLKKLEAQDY	0	15
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1208	NRPLKKLEAQDYKKT	3	18
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1208	DNRPLKKLEAQDYKK	2	17
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1208	TDNRPLKKLEAQDYK	1	16
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1208	RPLKKLEAQDYKKTS	4	19
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1209	NRPLKKLEAQDYKKT	3	18
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1209	DNRPLKKLEAQDYKK	2	17
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1209	RPLKKLEAQDYKKTS	4	19
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1209	TDNRPLKKLEAQDYK	1	16
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1210	NRPLKKLEAQDYKKT	3	18
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1210	DNRPLKKLEAQDYKK	2	17
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1210	TDNRPLKKLEAQDYK	1	16
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1210	RPLKKLEAQDYKKTS	4	19
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1210	KTDNRPLKKLEAQDY	0	15
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1211	NRPLKKLEAQDYKKT	3	18
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1211	DNRPLKKLEAQDYKK	2	17
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1211	TDNRPLKKLEAQDYK	1	16
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1211	RPLKKLEAQDYKKTS	4	19
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1211	KTDNRPLKKLEAQDY	0	15
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1212	NRPLKKLEAQDYKKT	3	18
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1212	DNRPLKKLEAQDYKK	2	17
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1212	TDNRPLKKLEAQDYK	1	16
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1212	RPLKKLEAQDYKKTS	4	19
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1212	KTDNRPLKKLEAQDY	0	15
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1213	NRPLKKLEAQDYKKT	3	18
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1213	DNRPLKKLEAQDYKK	2	17
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1213	TDNRPLKKLEAQDYK	1	16
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1213	RPLKKLEAQDYKKTS	4	19
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1213	KTDNRPLKKLEAQDY	0	15
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1214	NRPLKKLEAQDYKKT	3	18
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1214	DNRPLKKLEAQDYKK	2	17
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1214	TDNRPLKKLEAQDYK	1	16
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1214	RPLKKLEAQDYKKTS	4	19
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1214	KTDNRPLKKLEAQDY	0	15
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1215	NRPLKKLEAQDYKKT	3	18
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1215	DNRPLKKLEAQDYKK	2	17
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1215	TDNRPLKKLEAQDYK	1	16
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1215	RPLKKLEAQDYKKTS	4	19
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1215	KTDNRPLKKLEAQDY	0	15
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1216	NRPLKKLEAQDYKKT	3	18
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1216	DNRPLKKLEAQDYKK	2	17
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1216	TDNRPLKKLEAQDYK	1	16
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1216	RPLKKLEAQDYKKTS	4	19
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1217	NRPLKKLEAQDYKKT	3	18
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1217	DNRPLKKLEAQDYKK	2	17
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1217	TDNRPLKKLEAQDYK	1	16
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1217	RPLKKLEAQDYKKTS	4	19
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1217	KTDNRPLKKLEAQDY	0	15
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1218	NRPLKKLEAQDYKKT	3	18
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1218	DNRPLKKLEAQDYKK	2	17
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1218	TDNRPLKKLEAQDYK	1	16
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1218	RPLKKLEAQDYKKTS	4	19
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1218	KTDNRPLKKLEAQDY	0	15
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1219	NRPLKKLEAQDYKKT	3	18
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1219	DNRPLKKLEAQDYKK	2	17
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1219	TDNRPLKKLEAQDYK	1	16
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1219	RPLKKLEAQDYKKTS	4	19
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1220	NRPLKKLEAQDYKKT	3	18
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1220	DNRPLKKLEAQDYKK	2	17
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1220	TDNRPLKKLEAQDYK	1	16
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1220	RPLKKLEAQDYKKTS	4	19
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1221	NRPLKKLEAQDYKKT	3	18
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1221	DNRPLKKLEAQDYKK	2	17
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1221	TDNRPLKKLEAQDYK	1	16
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1221	RPLKKLEAQDYKKTS	4	19
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1222	NRPLKKLEAQDYKKT	3	18
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1222	DNRPLKKLEAQDYKK	2	17
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1222	TDNRPLKKLEAQDYK	1	16
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1222	RPLKKLEAQDYKKTS	4	19
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1223	NRPLKKLEAQDYKKT	3	18
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1223	DNRPLKKLEAQDYKK	2	17
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1223	TDNRPLKKLEAQDYK	1	16
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1223	RPLKKLEAQDYKKTS	4	19
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB1-1223	KTDNRPLKKLEAQDY	0	15
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2189	DRB5-0205	NRPLKKLEAQDYKKT	3	18

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Fusion breakpoint peptide structures of BAZ2A-PRIM1

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
1880	ELEEEQPDYKKTSL	BAZ2A	PRIM1	chr12	57008798	chr12	57128029	827

File name	BPseq	Hgene	Tgene	Hchr	Hbp	Tchr	Tbp	AAlen
5163	LKKLEAQDYKKTSL	BAZ2A	PRIM1	chr12	57003520	chr12	57128029	2189

File name	BPseq	Hgene	Tgene	Hchr	Hbp	Tchr	Tbp	AAlen
5903	MGAEDKLPLEDSPV	BAZ2A	PRIM1	chr12	57006799	chr12	57128029	1232

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of BAZ2A-PRIM1

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	1880	ELEEEQPDYKKTSL	-5.8571	-5.9705
HLA-B14:02	3BVN	1880	ELEEEQPDYKKTSL	-4.7555	-5.7908
HLA-B52:01	3W39	1880	ELEEEQPDYKKTSL	-7.48776	-7.60116
HLA-B52:01	3W39	1880	ELEEEQPDYKKTSL	-4.30066	-5.33596
HLA-A24:02	5HGA	1880	ELEEEQPDYKKTSL	-6.00055	-6.11395
HLA-A24:02	5HGA	1880	ELEEEQPDYKKTSL	-5.71435	-6.74965
HLA-B44:05	3DX8	1880	ELEEEQPDYKKTSL	-5.22126	-5.33466
HLA-B44:05	3DX8	1880	ELEEEQPDYKKTSL	-4.75073	-5.78603
HLA-A02:01	6TDR	1880	ELEEEQPDYKKTSL	-7.35754	-8.39284
HLA-B14:02	3BVN	5163	LKKLEAQDYKKTSL	-5.49577	-5.60917
HLA-B14:02	3BVN	5163	LKKLEAQDYKKTSL	-4.37152	-5.40682
HLA-B52:01	3W39	5163	LKKLEAQDYKKTSL	-6.90336	-7.01676
HLA-B52:01	3W39	5163	LKKLEAQDYKKTSL	-4.80833	-5.84363
HLA-A11:01	4UQ2	5163	LKKLEAQDYKKTSL	-9.82261	-9.93601
HLA-A24:02	5HGA	5163	LKKLEAQDYKKTSL	-9.78612	-9.89952
HLA-A24:02	5HGA	5163	LKKLEAQDYKKTSL	-4.98992	-6.02522
HLA-B27:05	6PYJ	5163	LKKLEAQDYKKTSL	-5.31553	-6.35083
HLA-B44:05	3DX8	5163	LKKLEAQDYKKTSL	-5.70582	-5.81922
HLA-B44:05	3DX8	5163	LKKLEAQDYKKTSL	-4.32241	-5.35771
HLA-B14:02	3BVN	5903	MGAEDKLPLEDSPV	-7.38756	-7.50096
HLA-B14:02	3BVN	5903	MGAEDKLPLEDSPV	-6.17376	-7.20906
HLA-B52:01	3W39	5903	MGAEDKLPLEDSPV	-6.82178	-6.93518
HLA-B52:01	3W39	5903	MGAEDKLPLEDSPV	-5.12185	-6.15715
HLA-A11:01	4UQ2	5903	MGAEDKLPLEDSPV	-9.73713	-9.85053
HLA-A24:02	5HGA	5903	MGAEDKLPLEDSPV	-6.9463	-7.0597
HLA-A24:02	5HGA	5903	MGAEDKLPLEDSPV	-5.98739	-7.02269
HLA-B44:05	3DX8	5903	MGAEDKLPLEDSPV	-5.60116	-6.63646
HLA-B44:05	3DX8	5903	MGAEDKLPLEDSPV	-4.76903	-4.88243

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Vaccine Design for the FusionNeoAntigens of BAZ2A-PRIM1

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
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	10	20	EAQDYKKTSL	AGGCCCAAGATTATAAGAAGACCAGTCTAG
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	11	20	AQDYKKTSL	CCCAAGATTATAAGAAGACCAGTCTAG
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	6	15	LKKLEAQDY	TAAAGAAACTGGAGGCCCAAGATTATA
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	9	20	LEAQDYKKTSL	TGGAGGCCCAAGATTATAAGAAGACCAGTCTAG
BAZ2A-PRIM1	chr12	57006799	chr12	57128029	10	21	DKLPLEDSPVI	TCCTGCAAGATTATAAGAAGACCAGTCTAGCAC
BAZ2A-PRIM1	chr12	57006799	chr12	57128029	11	21	KLPLEDSPVI	TGCAAGATTATAAGAAGACCAGTCTAGCAC
BAZ2A-PRIM1	chr12	57006799	chr12	57128029	12	20	LPLEDSPV	AAGATTATAAGAAGACCAGTCTAG
BAZ2A-PRIM1	chr12	57006799	chr12	57128029	12	21	LPLEDSPVI	AAGATTATAAGAAGACCAGTCTAGCAC
BAZ2A-PRIM1	chr12	57006799	chr12	57128029	12	23	LPLEDSPVISA	AAGATTATAAGAAGACCAGTCTAGCACCTTATG
BAZ2A-PRIM1	chr12	57006799	chr12	57128029	6	15	MGAEDKLPL	TAGGGGAGTCTGTCCTGCAAGATTATA
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	10	20	EQPDYKKTSL	AGCAGCCAGATTATAAGAAGACCAGTCTAG
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	11	20	QPDYKKTSL	AGCCAGATTATAAGAAGACCAGTCTAG
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	5	15	LELEEEQPDY	TGGAGCTGGAAGAAGAGCAGCCAGATTATA
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	6	15	ELEEEQPDY	AGCTGGAAGAAGAGCAGCCAGATTATA
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	9	18	EEQPDYKKT	AAGAGCAGCCAGATTATAAGAAGACCA
BAZ2A-PRIM1	chr12	57008798	chr12	57128029	9	20	EEQPDYKKTSL	AAGAGCAGCCAGATTATAAGAAGACCAGTCTAG

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
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	0	15	KTDNRPLKKLEAQDY	AGACAGACAACCGCCCCCTAAAGAAACTGGAGGCCCAAGATTATA
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	1	16	TDNRPLKKLEAQDYK	CAGACAACCGCCCCCTAAAGAAACTGGAGGCCCAAGATTATAAGA
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	2	17	DNRPLKKLEAQDYKK	ACAACCGCCCCCTAAAGAAACTGGAGGCCCAAGATTATAAGAAGA
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	3	18	NRPLKKLEAQDYKKT	ACCGCCCCCTAAAGAAACTGGAGGCCCAAGATTATAAGAAGACCA
BAZ2A-PRIM1	chr12	57003520	chr12	57128029	4	19	RPLKKLEAQDYKKTS	GCCCCCTAAAGAAACTGGAGGCCCAAGATTATAAGAAGACCAGTC

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Information of the samples that have these potential fusion neoantigens of BAZ2A-PRIM1

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
BLCA	BAZ2A-PRIM1	chr12	57003520	ENST00000379441	chr12	57128029	ENST00000338193	TCGA-HQ-A2OE-01A
BRCA	BAZ2A-PRIM1	chr12	57006799	ENST00000379441	chr12	57128029	ENST00000338193	TCGA-D8-A140-01A
LUSC	BAZ2A-PRIM1	chr12	57008798	ENST00000379441	chr12	57128029	ENST00000338193	TCGA-60-2709-01A

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Potential target of CAR-T therapy development for BAZ2A-PRIM1

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 BAZ2A-PRIM1

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 BAZ2A-PRIM1

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)