Home

Download

Statistics

Examples

Help

Contact

Fusion Protein:SP3-CYBRD1

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: SP3-CYBRD1
	FusionPDB ID: 85396
	FusionGDB2.0 ID: 85396
		Hgene	Tgene
	Gene symbol	SP3	CYBRD1
	Gene ID	6670	79901
	Gene name	Sp3 transcription factor	cytochrome b reductase 1
	Synonyms	SPR2	CYB561A2\|DCYTB\|FRRS3
	Cytomap	2q31.1	2q31.1
	Type of gene	protein-coding	protein-coding
	Description	transcription factor Sp3GC-binding transcription factor Sp3specificity protein 3	cytochrome b reductase 1cytochrome b561 family, member A2duodenal cytochrome bferric-chelate reductase 3
	Modification date	20200313	20200313
	UniProtAcc	Q02447 Main function of 5'-partner protein: FUNCTION: Transcriptional factor that can act as an activator or repressor depending on isoform and/or post-translational modifications. Binds to GT and GC boxes promoter elements. Competes with SP1 for the GC-box promoters. Weak activator of transcription but can activate a number of genes involved in different processes such as cell-cycle regulation, hormone-induction and house-keeping. {ECO:0000269\|PubMed:10391891, ECO:0000269\|PubMed:11812829, ECO:0000269\|PubMed:12419227, ECO:0000269\|PubMed:12837748, ECO:0000269\|PubMed:15247228, ECO:0000269\|PubMed:15494207, ECO:0000269\|PubMed:15554904, ECO:0000269\|PubMed:16781829, ECO:0000269\|PubMed:17548428, ECO:0000269\|PubMed:18187045, ECO:0000269\|PubMed:18617891, ECO:0000269\|PubMed:9278495}.	Q53TN4 Main function of 5'-partner protein: FUNCTION: Plasma membrane reductase that uses cytoplasmic ascorbate as an electron donor to reduce extracellular Fe(3+) into Fe(2+) (PubMed:30272000). Probably functions in dietary iron absorption at the brush border of duodenal enterocytes by producing Fe(2+), the divalent form of iron that can be transported into enterocytes (PubMed:30272000). It is also able to reduce extracellular monodehydro-L-ascorbate and may be involved in extracellular ascorbate regeneration by erythrocytes in blood (PubMed:17068337). May also act as a ferrireductase in airway epithelial cells (Probable). {ECO:0000269\|PubMed:17068337, ECO:0000269\|PubMed:30272000, ECO:0000305\|PubMed:16510471}.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000310015, ENST00000418194, ENST00000455789, ENST00000483084,	ENST00000321348, ENST00000375252, ENST00000468308, ENST00000409484,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	12 X 8 X 9=864	8 X 9 X 4=288
	# samples	18	10
	** MAII score	log2(18/864*10)=-2.26303440583379 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(10/288*10)=-1.52606881166759 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: SP3 [Title/Abstract] AND CYBRD1 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: SP3 [Title/Abstract] AND CYBRD1 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	SP3(174828489)-CYBRD1(172409856), # samples:3
Anticipated loss of major functional domain due to fusion event.	SP3-CYBRD1 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. SP3-CYBRD1 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. SP3-CYBRD1 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. SP3-CYBRD1 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	SP3	GO:0006355	regulation of transcription, DNA-templated	12560508
Hgene	SP3	GO:0045893	positive regulation of transcription, DNA-templated	12771217

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr2:174828489/chr2:172409856)
- 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 SP3 (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 CYBRD1 (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)
ENST00000310015	SP3	chr2	174828489	-	ENST00000409484	CYBRD1	chr2	172409856	+	2049	810	510	1268	252
ENST00000418194	SP3	chr2	174828489	-	ENST00000409484	CYBRD1	chr2	172409856	+	1698	459	360	917	185
ENST00000310015	SP3	chr2	174828488	-	ENST00000409484	CYBRD1	chr2	172409855	+	2049	810	510	1268	252
ENST00000418194	SP3	chr2	174828488	-	ENST00000409484	CYBRD1	chr2	172409855	+	1698	459	360	917	185

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
ENST00000310015	ENST00000409484	SP3	chr2	174828489	-	CYBRD1	chr2	172409856	+	0.007713054	0.9922869
ENST00000418194	ENST00000409484	SP3	chr2	174828489	-	CYBRD1	chr2	172409856	+	0.007843118	0.99215686
ENST00000310015	ENST00000409484	SP3	chr2	174828488	-	CYBRD1	chr2	172409855	+	0.007713054	0.9922869
ENST00000418194	ENST00000409484	SP3	chr2	174828488	-	CYBRD1	chr2	172409855	+	0.007843118	0.99215686

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 SP3-CYBRD1

+/-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
SP3	chr2	174828488	CYBRD1	chr2	172409855	459	33	AAAAAGAPAAAGALLSGFSVFLLPWA
SP3	chr2	174828488	CYBRD1	chr2	172409855	810	63	AVAAAAAAQDTQPSPLALLAATCSKI
SP3	chr2	174828489	CYBRD1	chr2	172409856	459	33	AAAAAGAPAAAGALLSGFSVFLLPWA
SP3	chr2	174828489	CYBRD1	chr2	172409856	810	63	AVAAAAAAQDTQPSPLALLAATCSKI

Top

Potential FusionNeoAntigen Information of SP3-CYBRD1 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.

SP3-CYBRD1_174828488_172409855.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)
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B07:02	APAAAGAL	0.9994	0.5488	6	14
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B81:01	APAAAGAL	0.5272	0.6842	6	14
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B82:01	APAAAGAL	0.4256	0.6964	6	14
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B07:10	APAAAGALL	0.9991	0.589	6	15
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B07:02	APAAAGALL	0.9991	0.5203	6	15
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B15:01	ALLSGFSVF	0.9978	0.9736	12	21
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B15:25	ALLSGFSVF	0.9634	0.9748	12	21
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B15:02	ALLSGFSVF	0.9561	0.9759	12	21
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B35:03	APAAAGALL	0.9544	0.8826	6	15
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B35:08	APAAAGALL	0.9177	0.8221	6	15
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-A32:13	ALLSGFSVF	0.9059	0.9763	12	21
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B46:01	ALLSGFSVF	0.8835	0.7089	12	21
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B35:02	APAAAGALL	0.827	0.9663	6	15
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B35:04	APAAAGALL	0.827	0.9663	6	15
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B15:03	ALLSGFSVF	0.8059	0.9097	12	21
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B81:01	APAAAGALL	0.1744	0.6796	6	15
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B13:01	ALLSGFSVF	0.1429	0.9583	12	21
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B82:01	APAAAGALL	0.0856	0.676	6	15
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B46:01	AAAGALLSGF	0.9989	0.777	8	18
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-A02:22	ALLSGFSVFL	0.9976	0.8148	12	22
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-A02:11	ALLSGFSVFL	0.9953	0.8035	12	22
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-A02:24	ALLSGFSVFL	0.995	0.7644	12	22
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-A02:67	ALLSGFSVFL	0.995	0.7644	12	22
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-A02:30	ALLSGFSVFL	0.995	0.7644	12	22
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-A02:60	ALLSGFSVFL	0.995	0.7637	12	22
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-A02:27	ALLSGFSVFL	0.9941	0.8611	12	22
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-A02:16	ALLSGFSVFL	0.9938	0.7349	12	22
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-A02:04	ALLSGFSVFL	0.9893	0.7334	12	22
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-A02:17	ALLSGFSVFL	0.9863	0.682	12	22
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B07:05	GAPAAAGALL	0.9376	0.6117	5	15
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-A02:29	ALLSGFSVFL	0.9162	0.7701	12	22
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-A02:35	ALLSGFSVFL	0.9146	0.7937	12	22
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-A02:20	ALLSGFSVFL	0.8986	0.7719	12	22
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-A02:60	ALLSGFSVFLL	0.9926	0.7274	12	23
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-A02:24	ALLSGFSVFLL	0.9925	0.7084	12	23
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-A02:67	ALLSGFSVFLL	0.9925	0.7084	12	23
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-A02:30	ALLSGFSVFLL	0.9925	0.7084	12	23
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B07:02	AGAPAAAGALL	0.9916	0.6867	4	15
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B07:05	AGAPAAAGALL	0.9889	0.6011	4	15
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-A02:16	ALLSGFSVFLL	0.9888	0.6572	12	23
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-A02:04	ALLSGFSVFLL	0.9856	0.7684	12	23
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-A02:17	ALLSGFSVFLL	0.9819	0.731	12	23
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B81:01	AGAPAAAGALL	0.9697	0.7492	4	15
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B82:01	AGAPAAAGALL	0.8816	0.7851	4	15
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-A02:29	ALLSGFSVFLL	0.8525	0.7154	12	23
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B07:12	APAAAGAL	0.9981	0.6384	6	14
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B07:04	APAAAGAL	0.9582	0.5804	6	14
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B42:02	APAAAGAL	0.8298	0.7307	6	14
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B42:01	APAAAGAL	0.8153	0.723	6	14
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B56:04	APAAAGAL	0.7708	0.68	6	14
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B39:10	APAAAGAL	0.7254	0.9819	6	14
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B07:12	APAAAGALL	0.9965	0.6071	6	15
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B15:07	ALLSGFSVF	0.9945	0.9222	12	21
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B15:04	ALLSGFSVF	0.9684	0.9718	12	21
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B56:04	APAAAGALL	0.8586	0.6281	6	15
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B07:04	APAAAGALL	0.8432	0.5563	6	15
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B15:31	ALLSGFSVF	0.8343	0.9606	12	21
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B35:12	APAAAGALL	0.827	0.9663	6	15
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B15:05	ALLSGFSVF	0.8177	0.9559	12	21
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B39:10	APAAAGALL	0.7193	0.9743	6	15
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-C01:17	GAPAAAGAL	0.5045	0.9522	5	14
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-C01:30	GAPAAAGAL	0.3293	0.9505	5	14
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B42:02	APAAAGALL	0.3069	0.675	6	15
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B42:01	APAAAGALL	0.3064	0.6691	6	15
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-A02:02	ALLSGFSVFL	0.9977	0.7322	12	22
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-A02:01	ALLSGFSVFL	0.995	0.7644	12	22
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-C01:17	AGAPAAAGAL	0.9945	0.9493	4	14
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B07:12	GAPAAAGALL	0.959	0.7034	5	15
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B07:12	AGAPAAAGALL	0.9947	0.73	4	15
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-A02:01	ALLSGFSVFLL	0.9925	0.7084	12	23
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B07:09	APAAAGAL	0.9994	0.5614	6	14
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B07:22	APAAAGAL	0.9994	0.5488	6	14
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B55:04	APAAAGAL	0.9142	0.6845	6	14
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B07:26	APAAAGAL	0.8856	0.5991	6	14
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B56:02	APAAAGAL	0.7708	0.68	6	14
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B67:01	APAAAGAL	0.6911	0.9876	6	14
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B82:02	APAAAGAL	0.4256	0.6964	6	14
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B07:22	APAAAGALL	0.9991	0.5203	6	15
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B07:09	APAAAGALL	0.9989	0.5147	6	15
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B15:27	ALLSGFSVF	0.9978	0.9289	12	21
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B15:33	ALLSGFSVF	0.9978	0.9736	12	21
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B15:34	ALLSGFSVF	0.9978	0.9736	12	21
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B15:125	ALLSGFSVF	0.9978	0.9736	12	21
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B15:135	ALLSGFSVF	0.9977	0.976	12	21
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B15:24	ALLSGFSVF	0.9967	0.9835	12	21
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B15:50	ALLSGFSVF	0.9966	0.9879	12	21
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B15:35	ALLSGFSVF	0.9954	0.9598	12	21
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B15:53	ALLSGFSVF	0.9951	0.9693	12	21
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B15:12	ALLSGFSVF	0.9813	0.958	12	21
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B15:54	ALLSGFSVF	0.973	0.9632	12	21
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B15:39	ALLSGFSVF	0.9611	0.9335	12	21
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-A32:01	ALLSGFSVF	0.9604	0.9852	12	21
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B35:13	APAAAGALL	0.942	0.8857	6	15
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B15:73	ALLSGFSVF	0.8928	0.8827	12	21
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B56:02	APAAAGALL	0.8586	0.6281	6	15
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B15:68	ALLSGFSVF	0.8576	0.8771	12	21
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B35:22	APAAAGALL	0.8492	0.5952	6	15
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B15:20	ALLSGFSVF	0.8362	0.9679	12	21
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B35:09	APAAAGALL	0.827	0.9663	6	15
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B15:30	ALLSGFSVF	0.8259	0.8606	12	21
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B35:28	ALLSGFSVF	0.7959	0.9674	12	21
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B55:04	APAAAGALL	0.7829	0.616	6	15
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B67:01	APAAAGALL	0.7244	0.9782	6	15
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B51:05	APAAAGALL	0.6322	0.501	6	15
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B07:26	APAAAGALL	0.5116	0.516	6	15
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-C01:02	GAPAAAGAL	0.4963	0.9515	5	14
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B56:05	APAAAGALL	0.4265	0.6986	6	15
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-C01:03	GAPAAAGAL	0.381	0.9626	5	14
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B51:06	APAAAGALL	0.3428	0.6336	6	15
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B82:02	APAAAGALL	0.0856	0.676	6	15
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-C01:02	AGAPAAAGAL	0.9958	0.9485	4	14
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B07:22	AGAPAAAGALL	0.9916	0.6867	4	15
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B67:01	AGAPAAAGALL	0.9534	0.9642	4	15
SP3-CYBRD1	chr2	174828488	chr2	172409855	459	HLA-B82:02	AGAPAAAGALL	0.8816	0.7851	4	15

Top

Potential FusionNeoAntigen Information of SP3-CYBRD1 in HLA II

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)

Top

Fusion breakpoint peptide structures of SP3-CYBRD1

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
473	APAAAGALLSGFSV	SP3	CYBRD1	chr2	174828488	chr2	172409855	459

Top

Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of SP3-CYBRD1

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	473	APAAAGALLSGFSV	-6.66111	-6.77451
HLA-B14:02	3BVN	473	APAAAGALLSGFSV	-6.49216	-7.52746
HLA-B52:01	3W39	473	APAAAGALLSGFSV	-5.57342	-5.68682
HLA-B52:01	3W39	473	APAAAGALLSGFSV	-3.59959	-4.63489
HLA-A11:01	4UQ2	473	APAAAGALLSGFSV	-3.54213	-3.65553
HLA-A24:02	5HGA	473	APAAAGALLSGFSV	-7.6647	-7.7781
HLA-A24:02	5HGA	473	APAAAGALLSGFSV	-4.05482	-5.09012
HLA-B44:05	3DX8	473	APAAAGALLSGFSV	-5.24587	-5.35927
HLA-B44:05	3DX8	473	APAAAGALLSGFSV	-4.91507	-5.95037
HLA-A02:01	6TDR	473	APAAAGALLSGFSV	-3.67735	-4.71265

Top

Vaccine Design for the FusionNeoAntigens of SP3-CYBRD1

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
SP3-CYBRD1	chr2	174828488	chr2	172409855	12	21	ALLSGFSVF	GCGCTTCTTTCAGGTTTTTCAGTCTTT
SP3-CYBRD1	chr2	174828488	chr2	172409855	12	22	ALLSGFSVFL	GCGCTTCTTTCAGGTTTTTCAGTCTTTCTG
SP3-CYBRD1	chr2	174828488	chr2	172409855	12	23	ALLSGFSVFLL	GCGCTTCTTTCAGGTTTTTCAGTCTTTCTGCTT
SP3-CYBRD1	chr2	174828488	chr2	172409855	4	14	AGAPAAAGAL	GCCGGGGCCCCCGCCGCCGCCGGAGCGCTT
SP3-CYBRD1	chr2	174828488	chr2	172409855	4	15	AGAPAAAGALL	GCCGGGGCCCCCGCCGCCGCCGGAGCGCTTCTT
SP3-CYBRD1	chr2	174828488	chr2	172409855	5	14	GAPAAAGAL	GGGGCCCCCGCCGCCGCCGGAGCGCTT
SP3-CYBRD1	chr2	174828488	chr2	172409855	5	15	GAPAAAGALL	GGGGCCCCCGCCGCCGCCGGAGCGCTTCTT
SP3-CYBRD1	chr2	174828488	chr2	172409855	6	14	APAAAGAL	GCCCCCGCCGCCGCCGGAGCGCTT
SP3-CYBRD1	chr2	174828488	chr2	172409855	6	15	APAAAGALL	GCCCCCGCCGCCGCCGGAGCGCTTCTT
SP3-CYBRD1	chr2	174828488	chr2	172409855	8	18	AAAGALLSGF	GCCGCCGCCGGAGCGCTTCTTTCAGGTTTT

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

Top

Information of the samples that have these potential fusion neoantigens of SP3-CYBRD1

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
SARC	SP3-CYBRD1	chr2	174828488	ENST00000418194	chr2	172409855	ENST00000409484	TCGA-DX-A1KY

Top

Potential target of CAR-T therapy development for SP3-CYBRD1

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

CYBRD1

chr2:174828488

chr2:172409855

ENST00000321348

158_178

287.0

Transmembrane

Helical%3B Name%3D5

Tgene

CYBRD1

chr2:174828488

chr2:172409855

ENST00000321348

199_219

287.0

Transmembrane

Helical%3B Name%3D6

Tgene

CYBRD1

chr2:174828488

chr2:172409855

ENST00000375252

123_143

158.0

Transmembrane

Helical%3B Name%3D4

Tgene

CYBRD1

chr2:174828488

chr2:172409855

ENST00000375252

158_178

158.0

Transmembrane

Helical%3B Name%3D5

Tgene

CYBRD1

chr2:174828488

chr2:172409855

ENST00000375252

199_219

158.0

Transmembrane

Helical%3B Name%3D6

Tgene

CYBRD1

chr2:174828488

chr2:172409855

ENST00000375252

85_105

158.0

Transmembrane

Helical%3B Name%3D3

Tgene

CYBRD1

chr2:174828488

chr2:172409855

ENST00000409484

123_143

229.0

Transmembrane

Helical%3B Name%3D4

Tgene

CYBRD1

chr2:174828488

chr2:172409855

ENST00000409484

158_178

229.0

Transmembrane

Helical%3B Name%3D5

Tgene

CYBRD1

chr2:174828488

chr2:172409855

ENST00000409484

199_219

229.0

Transmembrane

Helical%3B Name%3D6

Tgene

CYBRD1

chr2:174828488

chr2:172409855

ENST00000409484

85_105

229.0

Transmembrane

Helical%3B Name%3D3

Tgene

CYBRD1

chr2:174828489

chr2:172409856

ENST00000321348

158_178

287.0

Transmembrane

Helical%3B Name%3D5

Tgene

CYBRD1

chr2:174828489

chr2:172409856

ENST00000321348

199_219

287.0

Transmembrane

Helical%3B Name%3D6

Tgene

CYBRD1

chr2:174828489

chr2:172409856

ENST00000375252

123_143

158.0

Transmembrane

Helical%3B Name%3D4

Tgene

CYBRD1

chr2:174828489

chr2:172409856

ENST00000375252

158_178

158.0

Transmembrane

Helical%3B Name%3D5

Tgene

CYBRD1

chr2:174828489

chr2:172409856

ENST00000375252

199_219

158.0

Transmembrane

Helical%3B Name%3D6

Tgene

CYBRD1

chr2:174828489

chr2:172409856

ENST00000375252

85_105

158.0

Transmembrane

Helical%3B Name%3D3

Tgene

CYBRD1

chr2:174828489

chr2:172409856

ENST00000409484

123_143

229.0

Transmembrane

Helical%3B Name%3D4

Tgene

CYBRD1

chr2:174828489

chr2:172409856

ENST00000409484

158_178

229.0

Transmembrane

Helical%3B Name%3D5

Tgene

CYBRD1

chr2:174828489

chr2:172409856

ENST00000409484

199_219

229.0

Transmembrane

Helical%3B Name%3D6

Tgene

CYBRD1

chr2:174828489

chr2:172409856

ENST00000409484

85_105

229.0

Transmembrane

Helical%3B Name%3D3

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 SP3-CYBRD1

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

Hgene

Tgene

Drug

Source

PMID

Top

Related Diseases to SP3-CYBRD1

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)