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Fusion Protein:SP3-SCRN3

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: SP3-SCRN3
	FusionPDB ID: 85402
	FusionGDB2.0 ID: 85402
		Hgene	Tgene
	Gene symbol	SP3	SCRN3
	Gene ID	6670	79634
	Gene name	Sp3 transcription factor	secernin 3
	Synonyms	SPR2	SES3
	Cytomap	2q31.1	2q31.1
	Type of gene	protein-coding	protein-coding
	Description	transcription factor Sp3GC-binding transcription factor Sp3specificity protein 3	secernin-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}.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000310015, ENST00000418194, ENST00000455789, ENST00000483084,	ENST00000548921, ENST00000272732, ENST00000409673,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	12 X 8 X 9=864	4 X 4 X 4=64
	# samples	18	5
	** MAII score	log2(18/864*10)=-2.26303440583379 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(5/64*10)=-0.356143810225275 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: SP3 [Title/Abstract] AND SCRN3 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: SP3 [Title/Abstract] AND SCRN3 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	SP3(174819601)-SCRN3(175287613), # samples:2
Anticipated loss of major functional domain due to fusion event.	SP3-SCRN3 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-SCRN3 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-SCRN3 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-SCRN3 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-SCRN3 seems lost the major protein functional domain in Hgene partner, which is a transcription factor 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
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/chr2:174819601/chr2:175287613)
- 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 SCRN3 (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)
ENST00000310015	SP3	chr2	174819600	-	ENST00000409673	SCRN3	chr2	175287612	+	3213	2170	510	2690	726
ENST00000310015	SP3	chr2	174819600	-	ENST00000272732	SCRN3	chr2	175287612	+	4371	2170	510	2690	726
ENST00000418194	SP3	chr2	174819600	-	ENST00000409673	SCRN3	chr2	175287612	+	2862	1819	360	2339	659
ENST00000418194	SP3	chr2	174819600	-	ENST00000272732	SCRN3	chr2	175287612	+	4020	1819	360	2339	659
ENST00000310015	SP3	chr2	174819601	-	ENST00000409673	SCRN3	chr2	175287613	+	3213	2170	510	2690	726
ENST00000310015	SP3	chr2	174819601	-	ENST00000272732	SCRN3	chr2	175287613	+	4371	2170	510	2690	726
ENST00000418194	SP3	chr2	174819601	-	ENST00000409673	SCRN3	chr2	175287613	+	2862	1819	360	2339	659
ENST00000418194	SP3	chr2	174819601	-	ENST00000272732	SCRN3	chr2	175287613	+	4020	1819	360	2339	659

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	ENST00000409673	SP3	chr2	174819600	-	SCRN3	chr2	175287612	+	0.000846476	0.9991535
ENST00000310015	ENST00000272732	SP3	chr2	174819600	-	SCRN3	chr2	175287612	+	0.000444509	0.9995555
ENST00000418194	ENST00000409673	SP3	chr2	174819600	-	SCRN3	chr2	175287612	+	0.000509189	0.99949074
ENST00000418194	ENST00000272732	SP3	chr2	174819600	-	SCRN3	chr2	175287612	+	0.000391334	0.9996087
ENST00000310015	ENST00000409673	SP3	chr2	174819601	-	SCRN3	chr2	175287613	+	0.000846476	0.9991535
ENST00000310015	ENST00000272732	SP3	chr2	174819601	-	SCRN3	chr2	175287613	+	0.000444509	0.9995555
ENST00000418194	ENST00000409673	SP3	chr2	174819601	-	SCRN3	chr2	175287613	+	0.000509189	0.99949074
ENST00000418194	ENST00000272732	SP3	chr2	174819601	-	SCRN3	chr2	175287613	+	0.000391334	0.9996087

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 SP3-SCRN3

+/-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	174819600	SCRN3	chr2	175287612	1819	486	IQLHPGENADSPAGNITFETMMEILR
SP3	chr2	174819600	SCRN3	chr2	175287612	2170	64	VAAAAAAQDTQPSPLALLAATCSKIG
SP3	chr2	174819601	SCRN3	chr2	175287613	1819	486	IQLHPGENADSPAGNITFETMMEILR
SP3	chr2	174819601	SCRN3	chr2	175287613	2170	64	VAAAAAAQDTQPSPLALLAATCSKIG

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Potential FusionNeoAntigen Information of SP3-SCRN3 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-SCRN3_174819600_175287612.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-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B48:01	TQPSPLAL	0.9947	0.8133	9	17
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B15:10	TQPSPLAL	0.9713	0.7384	9	17
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B15:37	TQPSPLAL	0.9682	0.7414	9	17
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B39:13	TQPSPLAL	0.951	0.9908	9	17
SP3-SCRN3	chr2	174819600	chr2	175287612	1819	HLA-B35:01	SPAGNITF	0.9474	0.6872	10	18
SP3-SCRN3	chr2	174819600	chr2	175287612	1819	HLA-B35:08	SPAGNITF	0.9448	0.7061	10	18
SP3-SCRN3	chr2	174819600	chr2	175287612	1819	HLA-B35:03	SPAGNITF	0.9079	0.7138	10	18
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B81:01	QPSPLALL	0.8845	0.5059	10	18
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B35:03	QPSPLALL	0.8411	0.9251	10	18
SP3-SCRN3	chr2	174819600	chr2	175287612	1819	HLA-B35:02	SPAGNITF	0.6693	0.7841	10	18
SP3-SCRN3	chr2	174819600	chr2	175287612	1819	HLA-B35:04	SPAGNITF	0.6693	0.7841	10	18
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B35:02	QPSPLALL	0.6145	0.9797	10	18
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B35:04	QPSPLALL	0.6145	0.9797	10	18
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B48:01	AQDTQPSPL	0.9957	0.8394	6	15
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B14:02	DTQPSPLAL	0.9864	0.9251	8	17
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B14:01	DTQPSPLAL	0.9864	0.9251	8	17
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B39:01	AQDTQPSPL	0.9585	0.9647	6	15
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B48:01	TQPSPLALL	0.9549	0.8282	9	18
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B56:01	SPLALLAAT	0.9257	0.7033	12	21
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B39:13	AQDTQPSPL	0.919	0.9873	6	15
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B56:01	QPSPLALLA	0.883	0.5411	10	19
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B35:03	DTQPSPLAL	0.873	0.931	8	17
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B15:10	AQDTQPSPL	0.8309	0.7449	6	15
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B13:01	AQDTQPSPL	0.7821	0.9775	6	15
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B39:13	TQPSPLALL	0.7422	0.9951	9	18
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B35:02	DTQPSPLAL	0.7122	0.9824	8	17
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B35:04	DTQPSPLAL	0.7122	0.9824	8	17
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-A24:14	TQPSPLALL	0.6529	0.6879	9	18
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B35:02	QPSPLALLA	0.6379	0.9509	10	19
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B35:04	QPSPLALLA	0.6379	0.9509	10	19
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B13:01	TQPSPLALL	0.4916	0.9911	9	18
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B82:01	QPSPLALLA	0.4245	0.5651	10	19
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B52:01	TQPSPLALL	0.4205	0.9957	9	18
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B07:10	AQDTQPSPL	0.3676	0.632	6	15
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B55:01	QPSPLALLAA	0.9169	0.5136	10	20
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B56:01	QPSPLALLAA	0.9019	0.6834	10	20
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B56:01	TQPSPLALLA	0.7106	0.6846	9	19
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B48:01	AQDTQPSPLAL	0.9995	0.9018	6	17
SP3-SCRN3	chr2	174819600	chr2	175287612	1819	HLA-B35:08	NADSPAGNITF	0.9983	0.7397	7	18
SP3-SCRN3	chr2	174819600	chr2	175287612	1819	HLA-B35:01	SPAGNITFETM	0.9964	0.7325	10	21
SP3-SCRN3	chr2	174819600	chr2	175287612	1819	HLA-B35:08	SPAGNITFETM	0.9915	0.8128	10	21
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B39:13	AQDTQPSPLAL	0.9908	0.9924	6	17
SP3-SCRN3	chr2	174819600	chr2	175287612	1819	HLA-B35:03	SPAGNITFETM	0.9854	0.7823	10	21
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B13:01	AQDTQPSPLAL	0.9821	0.9891	6	17
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B07:10	AQDTQPSPLAL	0.9337	0.6767	6	17
SP3-SCRN3	chr2	174819600	chr2	175287612	1819	HLA-B35:02	SPAGNITFETM	0.9234	0.8785	10	21
SP3-SCRN3	chr2	174819600	chr2	175287612	1819	HLA-B35:04	SPAGNITFETM	0.9234	0.8785	10	21
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-C01:30	TQPSPLAL	0.9983	0.9649	9	17
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-C01:17	TQPSPLAL	0.9974	0.9693	9	17
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B54:01	SPLALLAA	0.9935	0.7315	12	20
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B39:09	TQPSPLAL	0.99	0.9189	9	17
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-C07:13	TQPSPLAL	0.9832	0.9765	9	17
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B39:08	TQPSPLAL	0.9762	0.975	9	17
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B14:03	TQPSPLAL	0.9648	0.9121	9	17
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B07:12	QPSPLALL	0.9603	0.6508	10	18
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B48:03	TQPSPLAL	0.9399	0.7446	9	17
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B42:02	QPSPLALL	0.9336	0.8324	10	18
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B42:01	QPSPLALL	0.9277	0.8255	10	18
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B39:05	TQPSPLAL	0.9229	0.9719	9	17
SP3-SCRN3	chr2	174819600	chr2	175287612	1819	HLA-B35:12	SPAGNITF	0.6693	0.7841	10	18
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B39:10	QPSPLALL	0.6582	0.9877	10	18
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B35:12	QPSPLALL	0.6145	0.9797	10	18
SP3-SCRN3	chr2	174819600	chr2	175287612	1819	HLA-B39:10	SPAGNITF	0.4668	0.7769	10	18
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-C05:09	AQDTQPSPL	0.9999	0.9844	6	15
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-C04:07	AQDTQPSPL	0.9999	0.9635	6	15
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-C04:10	AQDTQPSPL	0.9999	0.9583	6	15
SP3-SCRN3	chr2	174819600	chr2	175287612	1819	HLA-C05:09	NADSPAGNI	0.9998	0.8125	7	16
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-C08:15	AQDTQPSPL	0.9998	0.9863	6	15
SP3-SCRN3	chr2	174819600	chr2	175287612	1819	HLA-C08:15	NADSPAGNI	0.9995	0.8275	7	16
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B54:01	SPLALLAAT	0.9834	0.8818	12	21
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-C03:08	DTQPSPLAL	0.9827	0.9195	8	17
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B48:03	AQDTQPSPL	0.9819	0.7098	6	15
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-C08:13	AQDTQPSPL	0.9722	0.9863	6	15
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-C08:04	AQDTQPSPL	0.9722	0.9863	6	15
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-C04:14	AQDTQPSPL	0.9709	0.9704	6	15
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-C01:17	TQPSPLALL	0.9667	0.9722	9	18
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-C01:30	TQPSPLALL	0.963	0.9683	9	18
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B54:01	QPSPLALLA	0.9565	0.8725	10	19
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B39:09	AQDTQPSPL	0.9557	0.8925	6	15
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-C08:03	AQDTQPSPL	0.9475	0.9928	6	15
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-C01:30	DTQPSPLAL	0.9366	0.9695	8	17
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-A02:05	TQPSPLALL	0.9145	0.582	9	18
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B39:08	AQDTQPSPL	0.9079	0.9506	6	15
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B51:07	DTQPSPLAL	0.9034	0.988	8	17
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B14:03	DTQPSPLAL	0.8995	0.9102	8	17
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B39:05	AQDTQPSPL	0.8758	0.9622	6	15
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B39:09	TQPSPLALL	0.8708	0.9437	9	18
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B39:08	TQPSPLALL	0.8496	0.983	9	18
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-C07:13	TQPSPLALL	0.8063	0.9741	9	18
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B78:01	QPSPLALLA	0.7835	0.7918	10	19
SP3-SCRN3	chr2	174819600	chr2	175287612	1819	HLA-C08:04	NADSPAGNI	0.7775	0.881	7	16
SP3-SCRN3	chr2	174819600	chr2	175287612	1819	HLA-C08:13	NADSPAGNI	0.7775	0.881	7	16
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-C07:29	TQPSPLALL	0.735	0.9739	9	18
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B35:12	DTQPSPLAL	0.7122	0.9824	8	17
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B14:03	AQDTQPSPL	0.6687	0.8912	6	15
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B48:03	TQPSPLALL	0.6393	0.7422	9	18
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B35:12	QPSPLALLA	0.6379	0.9509	10	19
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-A02:07	TQPSPLALL	0.6224	0.6902	9	18
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B56:04	QPSPLALLA	0.5938	0.6202	10	19
SP3-SCRN3	chr2	174819600	chr2	175287612	1819	HLA-C01:30	DSPAGNITF	0.4765	0.9295	9	18
SP3-SCRN3	chr2	174819600	chr2	175287612	1819	HLA-C08:03	NADSPAGNI	0.3294	0.9048	7	16
SP3-SCRN3	chr2	174819600	chr2	175287612	1819	HLA-C01:17	DSPAGNITF	0.2743	0.8999	9	18
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B39:10	QPSPLALLA	0.2314	0.9782	10	19
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-C08:15	AAQDTQPSPL	0.9993	0.9859	5	15
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B54:01	QPSPLALLAA	0.9764	0.8815	10	20
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B54:01	TQPSPLALLA	0.836	0.8936	9	19
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B56:04	QPSPLALLAA	0.6712	0.6567	10	20
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-C08:15	AQDTQPSPLAL	1	0.9914	6	17
SP3-SCRN3	chr2	174819600	chr2	175287612	1819	HLA-C08:15	NADSPAGNITF	1	0.8787	7	18
SP3-SCRN3	chr2	174819600	chr2	175287612	1819	HLA-C05:09	NADSPAGNITF	1	0.8591	7	18
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-C05:09	AQDTQPSPLAL	1	0.9858	6	17
SP3-SCRN3	chr2	174819600	chr2	175287612	1819	HLA-B07:12	SPAGNITFETM	0.9982	0.5042	10	21
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B48:03	AQDTQPSPLAL	0.9965	0.8807	6	17
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B39:08	AQDTQPSPLAL	0.9956	0.977	6	17
SP3-SCRN3	chr2	174819600	chr2	175287612	1819	HLA-C08:03	NADSPAGNITF	0.9869	0.9359	7	18
SP3-SCRN3	chr2	174819600	chr2	175287612	1819	HLA-B35:12	SPAGNITFETM	0.9234	0.8785	10	21
SP3-SCRN3	chr2	174819600	chr2	175287612	1819	HLA-B39:10	SPAGNITFETM	0.8784	0.9034	10	21
SP3-SCRN3	chr2	174819600	chr2	175287612	1819	HLA-B42:01	SPAGNITFETM	0.8216	0.6981	10	21
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-C01:03	TQPSPLAL	0.9992	0.9741	9	17
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-C01:02	TQPSPLAL	0.9986	0.9674	9	17
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B78:02	SPLALLAA	0.9938	0.7622	12	20
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B39:02	TQPSPLAL	0.9894	0.991	9	17
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B39:11	TQPSPLAL	0.9721	0.9382	9	17
SP3-SCRN3	chr2	174819600	chr2	175287612	1819	HLA-B35:23	SPAGNITF	0.9558	0.6953	10	18
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B07:26	QPSPLALL	0.9504	0.5022	10	18
SP3-SCRN3	chr2	174819600	chr2	175287612	1819	HLA-B35:77	SPAGNITF	0.9474	0.6872	10	18
SP3-SCRN3	chr2	174819600	chr2	175287612	1819	HLA-B35:11	SPAGNITF	0.9417	0.7434	10	18
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B40:12	TQPSPLAL	0.9399	0.7446	9	17
SP3-SCRN3	chr2	174819600	chr2	175287612	1819	HLA-B35:17	SPAGNITF	0.9241	0.5316	10	18
SP3-SCRN3	chr2	174819600	chr2	175287612	1819	HLA-B35:30	SPAGNITF	0.9241	0.5316	10	18
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B15:09	TQPSPLAL	0.8709	0.9433	9	17
SP3-SCRN3	chr2	174819600	chr2	175287612	1819	HLA-B35:24	SPAGNITF	0.8616	0.727	10	18
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B55:04	QPSPLALL	0.848	0.5296	10	18
SP3-SCRN3	chr2	174819600	chr2	175287612	1819	HLA-B35:43	SPAGNITF	0.7831	0.6511	10	18
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B67:01	QPSPLALL	0.749	0.9721	10	18
SP3-SCRN3	chr2	174819600	chr2	175287612	1819	HLA-B35:09	SPAGNITF	0.6693	0.7841	10	18
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B35:09	QPSPLALL	0.6145	0.9797	10	18
SP3-SCRN3	chr2	174819600	chr2	175287612	1819	HLA-B67:01	SPAGNITF	0.4792	0.5791	10	18
SP3-SCRN3	chr2	174819600	chr2	175287612	1819	HLA-B18:07	SPAGNITF	0.4656	0.7787	10	18
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-C04:01	AQDTQPSPL	0.9999	0.9635	6	15
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-C18:01	AQDTQPSPL	0.9999	0.959	6	15
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-C04:03	AQDTQPSPL	0.9999	0.9713	6	15
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-C05:01	AQDTQPSPL	0.9999	0.9844	6	15
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-C08:02	AQDTQPSPL	0.9998	0.9863	6	15
SP3-SCRN3	chr2	174819600	chr2	175287612	1819	HLA-C05:01	NADSPAGNI	0.9998	0.8125	7	16
SP3-SCRN3	chr2	174819600	chr2	175287612	1819	HLA-C04:03	NADSPAGNI	0.9998	0.6738	7	16
SP3-SCRN3	chr2	174819600	chr2	175287612	1819	HLA-C08:02	NADSPAGNI	0.9995	0.8275	7	16
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-A25:01	DTQPSPLAL	0.9959	0.9272	8	17
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-C01:03	TQPSPLALL	0.9854	0.9756	9	18
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-A68:02	DTQPSPLAL	0.9824	0.5699	8	17
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B40:12	AQDTQPSPL	0.9819	0.7098	6	15
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-C01:02	TQPSPLALL	0.9814	0.9708	9	18
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B39:02	AQDTQPSPL	0.9719	0.987	6	15
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B15:73	TQPSPLALL	0.9682	0.9918	9	18
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B39:31	AQDTQPSPL	0.9622	0.9641	6	15
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-C08:01	AQDTQPSPL	0.9475	0.9928	6	15
SP3-SCRN3	chr2	174819600	chr2	175287612	1819	HLA-A25:01	DSPAGNITF	0.9458	0.8461	9	18
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B15:30	TQPSPLALL	0.9453	0.9901	9	18
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B51:06	DTQPSPLAL	0.9254	0.6575	8	17
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B40:49	AQDTQPSPL	0.9199	0.704	6	15
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B55:02	SPLALLAAT	0.9195	0.7228	12	21
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B39:02	TQPSPLALL	0.8736	0.9949	9	18
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B39:11	AQDTQPSPL	0.8659	0.8916	6	15
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B56:05	QPSPLALLA	0.8611	0.656	10	19
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B40:21	AQDTQPSPL	0.8477	0.8155	6	15
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-A69:01	DTQPSPLAL	0.8407	0.7109	8	17
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-C03:06	DTQPSPLAL	0.8319	0.992	8	17
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B55:02	QPSPLALLA	0.8145	0.6591	10	19
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B15:73	AQDTQPSPL	0.814	0.9917	6	15
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B51:29	DTQPSPLAL	0.7795	0.5193	8	17
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B78:02	QPSPLALLA	0.7736	0.8879	10	19
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B59:01	QPSPLALLA	0.7599	0.7129	10	19
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B15:30	AQDTQPSPL	0.7183	0.989	6	15
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B35:22	DTQPSPLAL	0.7138	0.8068	8	17
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B35:09	DTQPSPLAL	0.7122	0.9824	8	17
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B15:09	AQDTQPSPL	0.7024	0.961	6	15
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-A02:14	TQPSPLALL	0.696	0.7298	9	18
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B56:05	SPLALLAAT	0.6792	0.6641	12	21
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B40:12	TQPSPLALL	0.6393	0.7422	9	18
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B35:09	QPSPLALLA	0.6379	0.9509	10	19
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B55:04	QPSPLALLA	0.6323	0.6968	10	19
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B56:02	QPSPLALLA	0.5938	0.6202	10	19
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B15:09	TQPSPLALL	0.5099	0.9447	9	18
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B08:12	DTQPSPLAL	0.4879	0.8111	8	17
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B40:21	TQPSPLALL	0.4543	0.8535	9	18
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B40:49	TQPSPLALL	0.4534	0.6785	9	18
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B07:13	AQDTQPSPL	0.431	0.8857	6	15
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B82:02	QPSPLALLA	0.4245	0.5651	10	19
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B67:01	QPSPLALLA	0.3846	0.9697	10	19
SP3-SCRN3	chr2	174819600	chr2	175287612	1819	HLA-C08:01	NADSPAGNI	0.3294	0.9048	7	16
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-C08:02	AAQDTQPSPL	0.9993	0.9859	5	15
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-A68:02	DTQPSPLALL	0.9784	0.6149	8	18
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B55:02	QPSPLALLAA	0.9281	0.7446	10	20
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-A69:01	DTQPSPLALL	0.8324	0.68	8	18
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B56:05	QPSPLALLAA	0.7802	0.7191	10	20
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B55:02	TQPSPLALLA	0.7684	0.7148	9	19
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B56:02	QPSPLALLAA	0.6712	0.6567	10	20
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-C05:01	AQDTQPSPLAL	1	0.9858	6	17
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-C04:03	AQDTQPSPLAL	1	0.9863	6	17
SP3-SCRN3	chr2	174819600	chr2	175287612	1819	HLA-C05:01	NADSPAGNITF	1	0.8591	7	18
SP3-SCRN3	chr2	174819600	chr2	175287612	1819	HLA-C08:02	NADSPAGNITF	1	0.8787	7	18
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-C08:02	AQDTQPSPLAL	1	0.9914	6	17
SP3-SCRN3	chr2	174819600	chr2	175287612	1819	HLA-C04:03	NADSPAGNITF	1	0.7115	7	18
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B39:02	AQDTQPSPLAL	0.9971	0.9919	6	17
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B40:12	AQDTQPSPLAL	0.9965	0.8807	6	17
SP3-SCRN3	chr2	174819600	chr2	175287612	1819	HLA-B35:77	SPAGNITFETM	0.9964	0.7325	10	21
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B15:73	AQDTQPSPLAL	0.9958	0.9944	6	17
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B15:30	AQDTQPSPLAL	0.9953	0.993	6	17
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B40:49	AQDTQPSPLAL	0.9949	0.8752	6	17
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B40:21	AQDTQPSPLAL	0.9916	0.9258	6	17
SP3-SCRN3	chr2	174819600	chr2	175287612	1819	HLA-C08:01	NADSPAGNITF	0.9869	0.9359	7	18
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B39:11	AQDTQPSPLAL	0.9843	0.9559	6	17
SP3-SCRN3	chr2	174819600	chr2	175287612	1819	HLA-B35:43	SPAGNITFETM	0.9827	0.6877	10	21
SP3-SCRN3	chr2	174819600	chr2	175287612	1819	HLA-B35:13	SPAGNITFETM	0.9787	0.793	10	21
SP3-SCRN3	chr2	174819600	chr2	175287612	2170	HLA-B48:05	AQDTQPSPLAL	0.9456	0.6027	6	17
SP3-SCRN3	chr2	174819600	chr2	175287612	1819	HLA-B35:09	SPAGNITFETM	0.9234	0.8785	10	21
SP3-SCRN3	chr2	174819600	chr2	175287612	1819	HLA-B67:01	SPAGNITFETM	0.8891	0.776	10	21

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Potential FusionNeoAntigen Information of SP3-SCRN3 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)

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Fusion breakpoint peptide structures of SP3-SCRN3

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
511	AQDTQPSPLALLAA	SP3	SCRN3	chr2	174819600	chr2	175287612	2170

File name	BPseq	Hgene	Tgene	Hchr	Hbp	Tchr	Tbp	AAlen
1967	ENADSPAGNITFET	SP3	SCRN3	chr2	174819600	chr2	175287612	1819

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of SP3-SCRN3

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	511	AQDTQPSPLALLAA	-5.68508	-5.79848
HLA-B14:02	3BVN	511	AQDTQPSPLALLAA	-4.48181	-5.51711
HLA-B52:01	3W39	511	AQDTQPSPLALLAA	-6.58333	-6.69673
HLA-B52:01	3W39	511	AQDTQPSPLALLAA	-5.63259	-6.66789
HLA-A11:01	4UQ2	511	AQDTQPSPLALLAA	-10.3303	-10.4437
HLA-A11:01	4UQ2	511	AQDTQPSPLALLAA	-6.29447	-7.32977
HLA-A24:02	5HGA	511	AQDTQPSPLALLAA	-7.77035	-7.88375
HLA-A24:02	5HGA	511	AQDTQPSPLALLAA	-5.35627	-6.39157
HLA-B27:05	6PYJ	511	AQDTQPSPLALLAA	-3.97515	-5.01045
HLA-B44:05	3DX8	511	AQDTQPSPLALLAA	-5.81963	-5.93303
HLA-B44:05	3DX8	511	AQDTQPSPLALLAA	-4.86027	-5.89557
HLA-A02:01	6TDR	511	AQDTQPSPLALLAA	-5.17978	-6.21508
HLA-A02:01	6TDR	511	AQDTQPSPLALLAA	-5.36237	-5.47577
HLA-B14:02	3BVN	1967	ENADSPAGNITFET	-7.15543	-7.26883
HLA-B14:02	3BVN	1967	ENADSPAGNITFET	-4.77435	-5.80965
HLA-B52:01	3W39	1967	ENADSPAGNITFET	-6.80875	-6.92215
HLA-B52:01	3W39	1967	ENADSPAGNITFET	-4.20386	-5.23916
HLA-A11:01	4UQ2	1967	ENADSPAGNITFET	-7.5194	-8.5547
HLA-A11:01	4UQ2	1967	ENADSPAGNITFET	-6.9601	-7.0735
HLA-A24:02	5HGA	1967	ENADSPAGNITFET	-7.52403	-7.63743
HLA-A24:02	5HGA	1967	ENADSPAGNITFET	-5.82433	-6.85963
HLA-B27:05	6PYJ	1967	ENADSPAGNITFET	-3.28285	-4.31815
HLA-B44:05	3DX8	1967	ENADSPAGNITFET	-5.91172	-6.94702
HLA-B44:05	3DX8	1967	ENADSPAGNITFET	-4.24346	-4.35686

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Vaccine Design for the FusionNeoAntigens of SP3-SCRN3

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-SCRN3	chr2	174819600	chr2	175287612	10	18	QPSPLALL	GTCCTGCAGGAAATATAACTTTTG
SP3-SCRN3	chr2	174819600	chr2	175287612	10	18	SPAGNITF	GTCCTGCAGGAAATATAACTTTTG
SP3-SCRN3	chr2	174819600	chr2	175287612	10	19	QPSPLALLA	GTCCTGCAGGAAATATAACTTTTGAAA
SP3-SCRN3	chr2	174819600	chr2	175287612	10	20	QPSPLALLAA	GTCCTGCAGGAAATATAACTTTTGAAACAA
SP3-SCRN3	chr2	174819600	chr2	175287612	10	21	SPAGNITFETM	GTCCTGCAGGAAATATAACTTTTGAAACAATGA
SP3-SCRN3	chr2	174819600	chr2	175287612	12	20	SPLALLAA	CAGGAAATATAACTTTTGAAACAA
SP3-SCRN3	chr2	174819600	chr2	175287612	12	21	SPLALLAAT	CAGGAAATATAACTTTTGAAACAATGA
SP3-SCRN3	chr2	174819600	chr2	175287612	5	15	AAQDTQPSPL	GAGAGAATGCTGACAGTCCTGCAGGAAATA
SP3-SCRN3	chr2	174819600	chr2	175287612	6	15	AQDTQPSPL	AGAATGCTGACAGTCCTGCAGGAAATA
SP3-SCRN3	chr2	174819600	chr2	175287612	6	17	AQDTQPSPLAL	AGAATGCTGACAGTCCTGCAGGAAATATAACTT
SP3-SCRN3	chr2	174819600	chr2	175287612	7	16	NADSPAGNI	ATGCTGACAGTCCTGCAGGAAATATAA
SP3-SCRN3	chr2	174819600	chr2	175287612	7	18	NADSPAGNITF	ATGCTGACAGTCCTGCAGGAAATATAACTTTTG
SP3-SCRN3	chr2	174819600	chr2	175287612	8	17	DTQPSPLAL	CTGACAGTCCTGCAGGAAATATAACTT
SP3-SCRN3	chr2	174819600	chr2	175287612	8	18	DTQPSPLALL	CTGACAGTCCTGCAGGAAATATAACTTTTG
SP3-SCRN3	chr2	174819600	chr2	175287612	9	17	TQPSPLAL	ACAGTCCTGCAGGAAATATAACTT
SP3-SCRN3	chr2	174819600	chr2	175287612	9	18	DSPAGNITF	ACAGTCCTGCAGGAAATATAACTTTTG
SP3-SCRN3	chr2	174819600	chr2	175287612	9	18	TQPSPLALL	ACAGTCCTGCAGGAAATATAACTTTTG
SP3-SCRN3	chr2	174819600	chr2	175287612	9	19	TQPSPLALLA	ACAGTCCTGCAGGAAATATAACTTTTGAAA

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

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Information of the samples that have these potential fusion neoantigens of SP3-SCRN3

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
STAD	SP3-SCRN3	chr2	174819600	ENST00000310015	chr2	175287612	ENST00000272732	TCGA-BR-A4PD
STAD	SP3-SCRN3	chr2	174819600	ENST00000418194	chr2	175287612	ENST00000272732	TCGA-BR-A4PD

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Potential target of CAR-T therapy development for SP3-SCRN3

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 SP3-SCRN3

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 SP3-SCRN3

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)