Home

Download

Statistics

Examples

Help

Contact

Fusion Protein:C21orf59-BACE2

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: C21orf59-BACE2
	FusionPDB ID: 11531
	FusionGDB2.0 ID: 11531
		Hgene	Tgene
	Gene symbol	C21orf59	BACE2
	Gene ID	56683	25825
	Gene name	cilia and flagella associated protein 298	beta-secretase 2
	Synonyms	C21orf48\|C21orf59\|CILD26\|FBB18\|Kur	AEPLC\|ALP56\|ASP1\|ASP21\|BAE2\|CDA13\|CEAP1\|DRAP
	Cytomap	21q22.11	21q22.2-q22.3
	Type of gene	protein-coding	protein-coding
	Description	cilia- and flagella-associated protein 298UPF0769 protein C21orf59kurly homologprostate cancer upregulated protein 1protein kurly homolog	beta-secretase 256 kDa aspartic-like proteaseDown syndrome region aspartic proteaseSLCO3A1/BACE2 fusionaspartyl protease 1beta-site APP-cleaving enzyme 2beta-site amyloid beta A4 precursor protein-cleaving enzyme 2memapsin-1membrane-associated asp
	Modification date	20200313	20200313
	UniProtAcc	.	Q9Y5Z0 Main function of 5'-partner protein: FUNCTION: Responsible for the proteolytic processing of the amyloid precursor protein (APP). Cleaves APP, between residues 690 and 691, leading to the generation and extracellular release of beta-cleaved soluble APP, and a corresponding cell-associated C-terminal fragment which is later released by gamma-secretase. It has also been shown that it can cleave APP between residues 671 and 672. Responsible also for the proteolytic processing of CLTRN in pancreatic beta cells (PubMed:21907142). {ECO:0000269\|PubMed:10591213, ECO:0000269\|PubMed:11083922, ECO:0000269\|PubMed:11423558, ECO:0000269\|PubMed:15857888, ECO:0000269\|PubMed:16816112, ECO:0000269\|PubMed:21907142}.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000290155, ENST00000382549, ENST00000540881,	ENST00000466122, ENST00000328735, ENST00000330333, ENST00000347667,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	3 X 3 X 3=27	14 X 9 X 8=1008
	# samples	4	14
	** MAII score	log2(4/27*10)=0.567040592723894 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0	log2(14/1008*10)=-2.84799690655495 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: C21orf59 [Title/Abstract] AND BACE2 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: C21orf59 [Title/Abstract] AND BACE2 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	C21orf59(33975471)-BACE2(42598193), # samples:1
Anticipated loss of major functional domain due to fusion event.	C21orf59-BACE2 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. C21orf59-BACE2 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
Tgene	BACE2	GO:0006509	membrane protein ectodomain proteolysis	10591213

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr21:33975471/chr21:42598193)
- 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 C21orf59 (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 BACE2 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Top

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)
ENST00000290155	C21orf59	chr21	33975471	-	ENST00000328735	BACE2	chr21	42598193	+	3338	1289	32	2167	711
ENST00000290155	C21orf59	chr21	33975471	-	ENST00000330333	BACE2	chr21	42598193	+	3507	1289	32	2533	833
ENST00000290155	C21orf59	chr21	33975471	-	ENST00000347667	BACE2	chr21	42598193	+	9278	1289	32	2383	783

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
ENST00000290155	ENST00000328735	C21orf59	chr21	33975471	-	BACE2	chr21	42598193	+	0.005825276	0.9941748
ENST00000290155	ENST00000330333	C21orf59	chr21	33975471	-	BACE2	chr21	42598193	+	0.002423911	0.99757606
ENST00000290155	ENST00000347667	C21orf59	chr21	33975471	-	BACE2	chr21	42598193	+	0.000936345	0.9990637

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

Top

Fusion Protein Breakpoint Sequences for C21orf59-BACE2

+/-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
C21orf59	chr21	33975471	BACE2	chr21	42598193	1289	419	KNEKTKIIAKIQQLQILVDTGSSNFA

Top

Potential FusionNeoAntigen Information of C21orf59-BACE2 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.

C21orf59-BACE2_33975471_42598193.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)
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-B13:02	IQQLQILV	0.9884	0.6411	10	18
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-B52:01	IQQLQILV	0.96	0.9174	10	18
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-A02:04	KIIAKIQQL	0.9895	0.7607	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-B52:01	IAKIQQLQI	0.9894	0.8955	7	16
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-A02:38	KIIAKIQQL	0.9878	0.7016	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-A02:11	KIIAKIQQL	0.9878	0.7283	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-A02:60	KIIAKIQQL	0.9873	0.6387	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-A02:24	KIIAKIQQL	0.9872	0.6815	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-A02:67	KIIAKIQQL	0.9872	0.6815	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-A02:30	KIIAKIQQL	0.9872	0.6815	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-A02:21	KIIAKIQQL	0.9846	0.7935	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-A02:13	KIIAKIQQL	0.9803	0.6544	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-A02:27	KIIAKIQQL	0.9795	0.5418	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-A30:08	KIIAKIQQL	0.9779	0.7921	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-B39:24	AKIQQLQIL	0.9737	0.642	8	17
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-A02:21	KIQQLQILV	0.9504	0.6604	9	18
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-A02:35	KIIAKIQQL	0.9503	0.72	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-B15:16	IAKIQQLQI	0.9431	0.639	7	16
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-A02:04	KIQQLQILV	0.9341	0.72	9	18
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-A02:60	KIQQLQILV	0.9333	0.5203	9	18
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-A32:13	KIIAKIQQL	0.9281	0.9662	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-A02:11	KIQQLQILV	0.9277	0.5556	9	18
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-A02:29	KIIAKIQQL	0.9117	0.687	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-B39:13	AKIQQLQIL	0.9062	0.9619	8	17
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-A02:27	KIQQLQILV	0.9051	0.5063	9	18
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-A02:20	KIIAKIQQL	0.8857	0.6826	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-B08:09	IAKIQQLQI	0.8646	0.5523	7	16
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-A02:29	KIQQLQILV	0.8062	0.5312	9	18
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-A02:20	KIQQLQILV	0.7892	0.5309	9	18
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-A02:35	KIQQLQILV	0.7862	0.5667	9	18
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-B15:03	AKIQQLQIL	0.4519	0.714	8	17
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-B13:02	KIQQLQILV	0.3886	0.649	9	18
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-B13:01	KIIAKIQQL	0.1324	0.8352	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C15:04	KIIAKIQQL	0.9998	0.9476	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C15:06	KIIAKIQQL	0.9997	0.9513	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C03:07	KIIAKIQQL	0.9997	0.9783	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C03:19	KIIAKIQQL	0.9995	0.9857	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C03:08	KIIAKIQQL	0.9992	0.8227	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C12:04	KIIAKIQQL	0.9988	0.9978	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C06:03	KIIAKIQQL	0.9988	0.997	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C04:06	KIIAKIQQL	0.9979	0.9402	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C12:12	KIIAKIQQL	0.9968	0.9631	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C15:06	IAKIQQLQI	0.9962	0.8918	7	16
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C04:14	KIIAKIQQL	0.9944	0.8998	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-B51:07	IAKIQQLQI	0.9908	0.8578	7	16
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-B15:04	KIIAKIQQL	0.989	0.802	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-A02:07	KIIAKIQQL	0.9882	0.7098	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-A02:01	KIIAKIQQL	0.9872	0.6815	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-B15:07	KIIAKIQQL	0.9838	0.6575	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-B39:09	AKIQQLQIL	0.9808	0.7908	8	17
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C12:16	KIIAKIQQL	0.9756	0.9814	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C06:03	IAKIQQLQI	0.9582	0.9959	7	16
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C12:04	IAKIQQLQI	0.9572	0.9974	7	16
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C07:05	KIIAKIQQL	0.941	0.9781	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C07:13	KIIAKIQQL	0.937	0.922	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C07:29	KIIAKIQQL	0.9357	0.9721	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C07:10	KIIAKIQQL	0.9305	0.9698	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C03:14	KIIAKIQQL	0.9205	0.9889	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C07:19	KIIAKIQQL	0.8984	0.8058	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C07:27	KIIAKIQQL	0.885	0.9762	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C02:06	KIIAKIQQL	0.874	0.9487	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C12:12	IAKIQQLQI	0.8658	0.9545	7	16
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C07:95	KIIAKIQQL	0.82	0.8387	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C02:06	IAKIQQLQI	0.7928	0.9794	7	16
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C01:17	KIIAKIQQL	0.7406	0.9525	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C01:30	KIIAKIQQL	0.3082	0.9503	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C12:16	AKIQQLQIL	0.0919	0.9804	8	17
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C15:09	KIIAKIQQL	0.9998	0.9476	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C15:05	KIIAKIQQL	0.9997	0.9536	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C15:02	KIIAKIQQL	0.9997	0.9406	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C03:03	KIIAKIQQL	0.999	0.9845	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C03:04	KIIAKIQQL	0.999	0.9845	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C16:02	KIIAKIQQL	0.9989	0.994	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C12:03	KIIAKIQQL	0.9987	0.9913	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C03:17	KIIAKIQQL	0.9985	0.8883	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-A32:01	KIIAKIQQL	0.9982	0.9696	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C03:67	KIIAKIQQL	0.9979	0.9692	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C03:05	KIIAKIQQL	0.9974	0.9095	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C06:17	KIIAKIQQL	0.9969	0.9975	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C06:02	KIIAKIQQL	0.9969	0.9975	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C15:02	IAKIQQLQI	0.9962	0.8967	7	16
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C06:06	KIIAKIQQL	0.9959	0.9932	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C15:05	IAKIQQLQI	0.9957	0.914	7	16
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C04:04	KIIAKIQQL	0.9952	0.9259	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C16:04	KIIAKIQQL	0.9951	0.9878	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C07:04	KIIAKIQQL	0.9944	0.966	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C12:02	KIIAKIQQL	0.9882	0.9849	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-B15:35	KIIAKIQQL	0.9877	0.8036	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-A02:03	KIIAKIQQL	0.9859	0.6806	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-A02:14	KIIAKIQQL	0.9853	0.7078	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-A02:06	KIIAKIQQL	0.9846	0.7935	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-B39:02	AKIQQLQIL	0.9805	0.9605	8	17
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-A30:01	KIIAKIQQL	0.9778	0.9071	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C07:22	KIIAKIQQL	0.9771	0.807	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-B15:73	KIIAKIQQL	0.976	0.8501	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C03:17	IAKIQQLQI	0.9704	0.9723	7	16
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-A02:14	KIQQLQILV	0.9507	0.6288	9	18
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-A02:06	KIQQLQILV	0.9504	0.6604	9	18
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-B15:30	KIIAKIQQL	0.9261	0.7923	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C07:01	KIIAKIQQL	0.8745	0.8104	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C16:04	IAKIQQLQI	0.8738	0.9904	7	16
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C12:03	IAKIQQLQI	0.8696	0.9913	7	16
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C16:02	IAKIQQLQI	0.8516	0.9933	7	16
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C06:08	KIIAKIQQL	0.839	0.9824	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C02:02	KIIAKIQQL	0.8364	0.9604	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C02:10	KIIAKIQQL	0.8364	0.9604	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C01:03	KIIAKIQQL	0.7571	0.9605	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C01:02	KIIAKIQQL	0.7318	0.9515	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-B07:13	KIIAKIQQL	0.7078	0.712	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C06:08	AKIQQLQIL	0.7037	0.9946	8	17
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C16:01	IAKIQQLQI	0.6957	0.9833	7	16
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-C17:01	KIIAKIQQL	0.6177	0.8616	5	14
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-B48:02	AKIQQLQIL	0.5315	0.8828	8	17
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-B15:68	AKIQQLQIL	0.1638	0.6258	8	17
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	HLA-B15:54	AKIQQLQIL	0.1034	0.8127	8	17

Top

Potential FusionNeoAntigen Information of C21orf59-BACE2 in HLA II

C21orf59-BACE2_33975471_42598193.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)
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	DRB1-0804	NEKTKIIAKIQQLQI	1	16
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	DRB1-0828	NEKTKIIAKIQQLQI	1	16
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	DRB1-0828	EKTKIIAKIQQLQIL	2	17
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	DRB1-0828	KTKIIAKIQQLQILV	3	18
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	DRB1-1125	NEKTKIIAKIQQLQI	1	16
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	DRB1-1167	NEKTKIIAKIQQLQI	1	16
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	DRB1-1167	EKTKIIAKIQQLQIL	2	17
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	DRB1-1167	KTKIIAKIQQLQILV	3	18
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	DRB1-1201	TKIIAKIQQLQILVD	4	19
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	DRB1-1203	TKIIAKIQQLQILVD	4	19
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	DRB1-1205	TKIIAKIQQLQILVD	4	19
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	DRB1-1206	TKIIAKIQQLQILVD	4	19
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	DRB1-1207	TKIIAKIQQLQILVD	4	19
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	DRB1-1210	TKIIAKIQQLQILVD	4	19
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	DRB1-1214	TKIIAKIQQLQILVD	4	19
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	DRB1-1217	TKIIAKIQQLQILVD	4	19
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	DRB1-1318	NEKTKIIAKIQQLQI	1	16
C21orf59-BACE2	chr21	33975471	chr21	42598193	1289	DRB1-1415	NEKTKIIAKIQQLQI	1	16

Top

Fusion breakpoint peptide structures of C21orf59-BACE2

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
3724	IIAKIQQLQILVDT	C21orf59	BACE2	chr21	33975471	chr21	42598193	1289

Top

Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of C21orf59-BACE2

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	3724	IIAKIQQLQILVDT	-7.15543	-7.26883
HLA-B14:02	3BVN	3724	IIAKIQQLQILVDT	-4.77435	-5.80965
HLA-B52:01	3W39	3724	IIAKIQQLQILVDT	-6.80875	-6.92215
HLA-B52:01	3W39	3724	IIAKIQQLQILVDT	-4.20386	-5.23916
HLA-A11:01	4UQ2	3724	IIAKIQQLQILVDT	-7.5194	-8.5547
HLA-A11:01	4UQ2	3724	IIAKIQQLQILVDT	-6.9601	-7.0735
HLA-A24:02	5HGA	3724	IIAKIQQLQILVDT	-7.52403	-7.63743
HLA-A24:02	5HGA	3724	IIAKIQQLQILVDT	-5.82433	-6.85963
HLA-B27:05	6PYJ	3724	IIAKIQQLQILVDT	-3.28285	-4.31815
HLA-B44:05	3DX8	3724	IIAKIQQLQILVDT	-5.91172	-6.94702
HLA-B44:05	3DX8	3724	IIAKIQQLQILVDT	-4.24346	-4.35686

Top

Vaccine Design for the FusionNeoAntigens of C21orf59-BACE2

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
C21orf59-BACE2	chr21	33975471	chr21	42598193	10	18	IQQLQILV	ATTCAGCAACTACAGATTCTCGTT
C21orf59-BACE2	chr21	33975471	chr21	42598193	5	14	KIIAKIQQL	AAAATTATCGCCAAGATTCAGCAACTA
C21orf59-BACE2	chr21	33975471	chr21	42598193	7	16	IAKIQQLQI	ATCGCCAAGATTCAGCAACTACAGATT
C21orf59-BACE2	chr21	33975471	chr21	42598193	8	17	AKIQQLQIL	GCCAAGATTCAGCAACTACAGATTCTC
C21orf59-BACE2	chr21	33975471	chr21	42598193	9	18	KIQQLQILV	AAGATTCAGCAACTACAGATTCTCGTT

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
C21orf59-BACE2	chr21	33975471	chr21	42598193	1	16	NEKTKIIAKIQQLQI	AATGAAAAAACCAAAATTATCGCCAAGATTCAGCAACTACAGATT
C21orf59-BACE2	chr21	33975471	chr21	42598193	2	17	EKTKIIAKIQQLQIL	GAAAAAACCAAAATTATCGCCAAGATTCAGCAACTACAGATTCTC
C21orf59-BACE2	chr21	33975471	chr21	42598193	3	18	KTKIIAKIQQLQILV	AAAACCAAAATTATCGCCAAGATTCAGCAACTACAGATTCTCGTT
C21orf59-BACE2	chr21	33975471	chr21	42598193	4	19	TKIIAKIQQLQILVD	ACCAAAATTATCGCCAAGATTCAGCAACTACAGATTCTCGTTGAC

Top

Information of the samples that have these potential fusion neoantigens of C21orf59-BACE2

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	C21orf59-BACE2	chr21	33975471	ENST00000290155	chr21	42598193	ENST00000328735	TCGA-4Z-AA87-01A

Top

Potential target of CAR-T therapy development for C21orf59-BACE2

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

BACE2

chr21:33975471

chr21:42598193

ENST00000328735

474_494

397.0

Transmembrane

Helical

Tgene

BACE2

chr21:33975471

chr21:42598193

ENST00000330333

474_494

519.0

Transmembrane

Helical

Tgene

BACE2

chr21:33975471

chr21:42598193

ENST00000347667

474_494

469.0

Transmembrane

Helical

Subcellular localization prediction of the transmembrane domain retained fusion proteins
* We used DeepLoc 1.0. The order of the X-axis of the barplot is as follows: Entry_ID, Localization, Type, Nucleus, Cytoplasm, Extracellular, Mitochondrion, Cell_membrane, Endoplasmic_reticulum, Plastid, Golgi.apparatus, Lysosome.Vacuole, Peroxisome. Y-axis is the output score of DeepLoc. Clicking the image will open a new tab with a large image.

Hgene

Hchr

Hbp

Henst

Tgene

Tchr

Tbp

Tenst

DeepLoc result

Top

Related Drugs to C21orf59-BACE2

Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)

Hgene

Tgene

Drug

Source

PMID

Top

Related Diseases to C21orf59-BACE2

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)