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Fusion Protein:SRCAP-RPS4Y1

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: SRCAP-RPS4Y1
	FusionPDB ID: 86243
	FusionGDB2.0 ID: 86243
		Hgene	Tgene
	Gene symbol	SRCAP	RPS4Y1
	Gene ID	10847	6192
	Gene name	Snf2 related CREBBP activator protein	ribosomal protein S4 Y-linked 1
	Synonyms	DOMO1\|EAF1\|FLHS\|SWR1	RPS4Y\|S4
	Cytomap	16p11.2	Yp11.2
	Type of gene	protein-coding	protein-coding
	Description	helicase SRCAPSnf2-related CBP activator proteinSwi2/Snf2-related ATPase homolog, domino homolog 1domino homolog 2	40S ribosomal protein S4, Y isoform 140S ribosomal protein S4, Yribosomal protein S4, Y-linkedribosomal protein S4Ysmall ribosomal subunit protein eS4
	Modification date	20200313	20200313
	UniProtAcc	.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000262518, ENST00000344771, ENST00000395059,	ENST00000477725, ENST00000250784,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	10 X 10 X 6=600	12 X 13 X 3=468
	# samples	13	13
	** MAII score	log2(13/600*10)=-2.20645087746743 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(13/468*10)=-1.84799690655495 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: SRCAP [Title/Abstract] AND RPS4Y1 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: SRCAP [Title/Abstract] AND RPS4Y1 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	SRCAP(30727800)-RPS4Y1(2722641), # samples:3
Anticipated loss of major functional domain due to fusion event.	SRCAP-RPS4Y1 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. SRCAP-RPS4Y1 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. SRCAP-RPS4Y1 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. SRCAP-RPS4Y1 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

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr16:30727800/chrY:2722641)
- 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 SRCAP (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 RPS4Y1 (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)

ENST00000344771

SRCAP

chr16

30727800

ENST00000250784

RPS4Y1

chrY

2722641

4008

3202

208

3633

1141

ENST00000395059

SRCAP

chr16

30727800

ENST00000250784

RPS4Y1

chrY

2722641

4008

3202

208

3633

1141

ENST00000262518

SRCAP

chr16

30727800

ENST00000250784

RPS4Y1

chrY

2722641

4008

3202

208

3633

1141

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
ENST00000344771	ENST00000250784	SRCAP	chr16	30727800	+	RPS4Y1	chrY	2722641	+	0.005138444	0.99486154
ENST00000395059	ENST00000250784	SRCAP	chr16	30727800	+	RPS4Y1	chrY	2722641	+	0.005138444	0.99486154
ENST00000262518	ENST00000250784	SRCAP	chr16	30727800	+	RPS4Y1	chrY	2722641	+	0.005138444	0.99486154

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 SRCAP-RPS4Y1

+/-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
SRCAP	chr16	30727800	RPS4Y1	chrY	2722641	3202	996	TASLVLRATDVHPLQYKLCKVRKITV

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Potential FusionNeoAntigen Information of SRCAP-RPS4Y1 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.

SRCAP-RPS4Y1_30727800_2722641.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)
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B39:01	VHPLQYKL	0.9866	0.6593	10	18
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B38:01	VHPLQYKL	0.9504	0.7845	10	18
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B38:02	VHPLQYKL	0.9433	0.8084	10	18
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B27:07	LRATDVHPL	0.9995	0.5893	5	14
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B39:01	LRATDVHPL	0.9976	0.8346	5	14
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B39:06	LRATDVHPL	0.9956	0.7304	5	14
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B14:01	LRATDVHPL	0.9939	0.8424	5	14
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B14:02	LRATDVHPL	0.9939	0.8424	5	14
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B38:01	LRATDVHPL	0.9936	0.9113	5	14
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B38:02	LRATDVHPL	0.9934	0.904	5	14
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B14:01	DVHPLQYKL	0.9741	0.5398	9	18
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B14:02	DVHPLQYKL	0.9741	0.5398	9	18
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B15:25	ATDVHPLQY	0.9625	0.8741	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B15:10	LRATDVHPL	0.9532	0.6155	5	14
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B35:08	ATDVHPLQY	0.9256	0.8394	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B15:37	LRATDVHPL	0.8916	0.6262	5	14
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B15:02	ATDVHPLQY	0.8884	0.8958	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B15:17	ATDVHPLQY	0.868	0.8943	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B35:03	DVHPLQYKL	0.7942	0.7211	9	18
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B15:18	LRATDVHPL	0.7346	0.8174	5	14
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B58:01	ATDVHPLQY	0.7219	0.8789	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B15:16	ATDVHPLQY	0.6978	0.7784	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B35:04	DVHPLQYKL	0.5913	0.7074	9	18
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B35:02	DVHPLQYKL	0.5913	0.7074	9	18
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B58:02	ATDVHPLQY	0.5738	0.8908	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B08:01	DVHPLQYKL	0.2249	0.5117	9	18
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-A32:13	ATDVHPLQY	0.1741	0.92	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B15:25	RATDVHPLQY	0.9997	0.9041	6	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B57:01	RATDVHPLQY	0.9996	0.976	6	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B15:17	RATDVHPLQY	0.9989	0.9117	6	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B15:01	RATDVHPLQY	0.9988	0.8736	6	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B58:02	RATDVHPLQY	0.9985	0.9299	6	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B58:01	RATDVHPLQY	0.9962	0.9434	6	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B15:16	RATDVHPLQY	0.9962	0.831	6	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-A30:08	ATDVHPLQYK	0.9542	0.6046	7	17
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B27:04	LRATDVHPLQY	0.9999	0.6918	5	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-A30:08	RATDVHPLQYK	0.998	0.6076	6	17
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C03:19	RATDVHPL	0.9997	0.9925	6	14
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B39:12	VHPLQYKL	0.991	0.6674	10	18
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C07:29	VHPLQYKL	0.985	0.8404	10	18
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C07:13	VHPLQYKL	0.9812	0.7199	10	18
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B14:03	VHPLQYKL	0.921	0.6563	10	18
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B39:05	VHPLQYKL	0.902	0.6391	10	18
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B39:09	LRATDVHPL	0.9978	0.7092	5	14
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C07:05	LRATDVHPL	0.9973	0.9536	5	14
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B39:12	LRATDVHPL	0.9969	0.8378	5	14
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C05:09	ATDVHPLQY	0.9964	0.943	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C04:10	ATDVHPLQY	0.9961	0.7546	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C04:07	ATDVHPLQY	0.9957	0.7996	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C07:27	LRATDVHPL	0.9953	0.9475	5	14
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C07:95	LRATDVHPL	0.995	0.6303	5	14
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C07:13	LRATDVHPL	0.9907	0.9372	5	14
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C07:29	LRATDVHPL	0.9889	0.8931	5	14
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B39:05	LRATDVHPL	0.9882	0.8053	5	14
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C08:15	ATDVHPLQY	0.9435	0.9639	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C07:80	LRATDVHPL	0.9268	0.942	5	14
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C07:67	LRATDVHPL	0.9268	0.942	5	14
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C07:46	LRATDVHPL	0.922	0.8464	5	14
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B51:07	DVHPLQYKL	0.9129	0.5442	9	18
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C07:10	LRATDVHPL	0.8917	0.9572	5	14
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C07:19	LRATDVHPL	0.8876	0.7225	5	14
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B15:05	ATDVHPLQY	0.8571	0.7935	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C15:04	ATDVHPLQY	0.8011	0.8707	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B15:31	ATDVHPLQY	0.7831	0.8121	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C07:10	ATDVHPLQY	0.7482	0.8816	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C07:67	ATDVHPLQY	0.7353	0.8535	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C07:80	ATDVHPLQY	0.7353	0.8535	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B14:03	DVHPLQYKL	0.7201	0.694	9	18
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C07:46	ATDVHPLQY	0.7163	0.7279	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C15:06	ATDVHPLQY	0.7053	0.8845	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C07:27	ATDVHPLQY	0.6984	0.8918	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C04:06	ATDVHPLQY	0.6759	0.86	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B35:12	DVHPLQYKL	0.5913	0.7074	9	18
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B14:03	LRATDVHPL	0.5223	0.8609	5	14
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C04:14	ATDVHPLQY	0.4607	0.7959	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C07:05	ATDVHPLQY	0.4566	0.8928	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C03:14	ATDVHPLQY	0.4467	0.9301	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C12:04	ATDVHPLQY	0.1596	0.9796	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C08:13	ATDVHPLQY	0.1291	0.94	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C08:04	ATDVHPLQY	0.1291	0.94	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C06:03	ATDVHPLQY	0.1229	0.9723	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C12:16	LRATDVHPL	0.1189	0.9669	5	14
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C12:16	ATDVHPLQY	0.0912	0.928	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C08:03	ATDVHPLQY	0.0479	0.9605	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C12:12	ATDVHPLQY	0.009	0.8237	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C15:04	RATDVHPLQY	0.9964	0.9043	6	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B15:07	RATDVHPLQY	0.995	0.7172	6	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B15:05	RATDVHPLQY	0.9894	0.8544	6	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C12:04	RATDVHPLQY	0.9668	0.9895	6	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C06:03	RATDVHPLQY	0.9667	0.988	6	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C03:14	RATDVHPLQY	0.934	0.9595	6	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C12:12	RATDVHPLQY	0.8768	0.9033	6	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C05:09	ATDVHPLQYKL	1	0.9099	7	18
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C07:19	LRATDVHPLQY	0.9996	0.6927	5	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C07:46	LRATDVHPLQY	0.9989	0.8477	5	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B27:03	LRATDVHPLQY	0.9989	0.6886	5	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C16:01	RATDVHPL	0.9968	0.9716	6	14
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B07:13	RATDVHPL	0.9709	0.8892	6	14
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B38:05	VHPLQYKL	0.9504	0.7845	10	18
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B39:11	VHPLQYKL	0.847	0.6916	10	18
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B27:06	LRATDVHPL	0.9995	0.7978	5	14
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B27:09	LRATDVHPL	0.9993	0.8781	5	14
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B27:08	LRATDVHPL	0.9991	0.7992	5	14
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B39:31	LRATDVHPL	0.9976	0.8356	5	14
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-A25:01	DVHPLQYKL	0.9968	0.8494	9	18
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C04:03	ATDVHPLQY	0.9968	0.8543	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C05:01	ATDVHPLQY	0.9964	0.943	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C04:01	ATDVHPLQY	0.9957	0.7996	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C07:01	LRATDVHPL	0.995	0.625	5	14
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C18:01	ATDVHPLQY	0.9943	0.8208	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B38:05	LRATDVHPL	0.9936	0.9113	5	14
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B15:39	ATDVHPLQY	0.9531	0.7777	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C08:02	ATDVHPLQY	0.9435	0.9639	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C06:08	LRATDVHPL	0.9431	0.9938	5	14
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C07:02	LRATDVHPL	0.9268	0.942	5	14
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B57:04	ATDVHPLQY	0.9207	0.7867	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C07:04	LRATDVHPL	0.9161	0.8919	5	14
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B15:20	ATDVHPLQY	0.8672	0.8579	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B15:09	LRATDVHPL	0.8647	0.811	5	14
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B35:28	ATDVHPLQY	0.8206	0.8724	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C07:22	LRATDVHPL	0.8055	0.6592	5	14
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C15:09	ATDVHPLQY	0.8011	0.8707	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C06:06	ATDVHPLQY	0.7816	0.9883	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B35:20	ATDVHPLQY	0.7783	0.8855	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C07:17	ATDVHPLQY	0.7414	0.9057	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C07:02	ATDVHPLQY	0.7353	0.8535	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C03:02	ATDVHPLQY	0.7332	0.9435	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C07:22	ATDVHPLQY	0.7323	0.5321	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B39:11	LRATDVHPL	0.7038	0.7868	5	14
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C15:05	ATDVHPLQY	0.7007	0.9093	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C15:02	ATDVHPLQY	0.6879	0.8923	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B58:06	ATDVHPLQY	0.595	0.8763	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B35:09	DVHPLQYKL	0.5913	0.7074	9	18
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B57:02	ATDVHPLQY	0.5855	0.9194	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C04:04	ATDVHPLQY	0.5826	0.7964	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B15:13	ATDVHPLQY	0.5725	0.6984	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B08:12	DVHPLQYKL	0.4382	0.6223	9	18
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C16:02	ATDVHPLQY	0.4304	0.9873	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C16:01	ATDVHPLQY	0.3027	0.9692	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B08:18	DVHPLQYKL	0.2249	0.5117	9	18
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C16:04	ATDVHPLQY	0.2018	0.9476	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C06:02	LRATDVHPL	0.1329	0.9922	5	14
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C06:17	LRATDVHPL	0.1329	0.9922	5	14
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C08:01	ATDVHPLQY	0.0479	0.9605	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C12:02	ATDVHPLQY	0.0296	0.9338	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C02:10	ATDVHPLQY	0.0213	0.9571	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C02:02	ATDVHPLQY	0.0213	0.9571	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C12:03	ATDVHPLQY	0.0201	0.9479	7	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B15:39	RATDVHPLQY	0.9997	0.8163	6	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B57:10	RATDVHPLQY	0.9996	0.976	6	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B57:04	RATDVHPLQY	0.9996	0.7792	6	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B15:125	RATDVHPLQY	0.9988	0.8736	6	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B15:34	RATDVHPLQY	0.9988	0.8736	6	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B15:33	RATDVHPLQY	0.9988	0.8736	6	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B15:135	RATDVHPLQY	0.9986	0.8897	6	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B58:06	RATDVHPLQY	0.9986	0.8801	6	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B15:12	RATDVHPLQY	0.9978	0.7472	6	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B15:50	RATDVHPLQY	0.9977	0.8748	6	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C15:09	RATDVHPLQY	0.9964	0.9043	6	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B15:35	RATDVHPLQY	0.9948	0.8907	6	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B15:20	RATDVHPLQY	0.9894	0.9104	6	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C16:02	RATDVHPLQY	0.9893	0.9919	6	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B35:28	RATDVHPLQY	0.9877	0.9216	6	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C02:02	RATDVHPLQY	0.9781	0.9685	6	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C02:10	RATDVHPLQY	0.9781	0.9685	6	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-B57:02	RATDVHPLQY	0.9771	0.9179	6	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C03:02	RATDVHPLQY	0.9604	0.9631	6	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C16:01	RATDVHPLQY	0.9387	0.9778	6	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C12:02	RATDVHPLQY	0.9241	0.9535	6	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C16:04	RATDVHPLQY	0.8871	0.9689	6	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C12:03	RATDVHPLQY	0.8834	0.9719	6	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C05:01	ATDVHPLQYKL	1	0.9099	7	18
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C07:01	LRATDVHPLQY	0.9996	0.5889	5	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-C07:22	LRATDVHPLQY	0.9983	0.6676	5	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	HLA-A30:01	RATDVHPLQYK	0.998	0.7768	6	17

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Potential FusionNeoAntigen Information of SRCAP-RPS4Y1 in HLA II

SRCAP-RPS4Y1_30727800_2722641.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)
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	DRB1-0701	SLVLRATDVHPLQYK	2	17
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	DRB1-0701	ASLVLRATDVHPLQY	1	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	DRB1-0703	SLVLRATDVHPLQYK	2	17
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	DRB1-0703	ASLVLRATDVHPLQY	1	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	DRB1-0705	SLVLRATDVHPLQYK	2	17
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	DRB1-0705	ASLVLRATDVHPLQY	1	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	DRB1-0706	SLVLRATDVHPLQYK	2	17
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	DRB1-0707	SLVLRATDVHPLQYK	2	17
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	DRB1-0707	ASLVLRATDVHPLQY	1	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	DRB1-0708	SLVLRATDVHPLQYK	2	17
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	DRB1-0708	ASLVLRATDVHPLQY	1	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	DRB1-0709	SLVLRATDVHPLQYK	2	17
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	DRB1-0712	SLVLRATDVHPLQYK	2	17
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	DRB1-0712	ASLVLRATDVHPLQY	1	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	DRB1-0713	SLVLRATDVHPLQYK	2	17
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	DRB1-0713	ASLVLRATDVHPLQY	1	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	DRB1-0714	SLVLRATDVHPLQYK	2	17
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	DRB1-0714	ASLVLRATDVHPLQY	1	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	DRB1-0715	SLVLRATDVHPLQYK	2	17
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	DRB1-0715	ASLVLRATDVHPLQY	1	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	DRB1-0716	SLVLRATDVHPLQYK	2	17
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	DRB1-0716	ASLVLRATDVHPLQY	1	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	DRB1-0717	SLVLRATDVHPLQYK	2	17
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	DRB1-0717	ASLVLRATDVHPLQY	1	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	DRB1-0719	SLVLRATDVHPLQYK	2	17
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	DRB1-0719	ASLVLRATDVHPLQY	1	16
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	3202	DRB1-0906	SLVLRATDVHPLQYK	2	17

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Fusion breakpoint peptide structures of SRCAP-RPS4Y1

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
7712	RATDVHPLQYKLCK	SRCAP	RPS4Y1	chr16	30727800	chrY	2722641	3202

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of SRCAP-RPS4Y1

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	7712	RATDVHPLQYKLCK	-5.45575	-5.46295
HLA-B52:01	3W39	7712	RATDVHPLQYKLCK	-5.51835	-5.52555
HLA-A24:02	5HGA	7712	RATDVHPLQYKLCK	-7.37668	-7.38388
HLA-B44:05	3DX8	7712	RATDVHPLQYKLCK	-4.22448	-4.23168

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Vaccine Design for the FusionNeoAntigens of SRCAP-RPS4Y1

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
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	10	18	VHPLQYKL	CCCCTCCAGTACAAGTTGTGCAAA
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	5	14	LRATDVHPL	GCCACGGATGTCCATCCCCTCCAGTAC
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	5	16	LRATDVHPLQY	GCCACGGATGTCCATCCCCTCCAGTACAAGTTG
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	6	14	RATDVHPL	ACGGATGTCCATCCCCTCCAGTAC
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	6	16	RATDVHPLQY	ACGGATGTCCATCCCCTCCAGTACAAGTTG
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	6	17	RATDVHPLQYK	ACGGATGTCCATCCCCTCCAGTACAAGTTGTGC
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	7	16	ATDVHPLQY	GATGTCCATCCCCTCCAGTACAAGTTG
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	7	17	ATDVHPLQYK	GATGTCCATCCCCTCCAGTACAAGTTGTGC
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	7	18	ATDVHPLQYKL	GATGTCCATCCCCTCCAGTACAAGTTGTGCAAA
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	9	18	DVHPLQYKL	CATCCCCTCCAGTACAAGTTGTGCAAA

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
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	1	16	ASLVLRATDVHPLQY	CTGGTGCTAAGGGCCACGGATGTCCATCCCCTCCAGTACAAGTTG
SRCAP-RPS4Y1	chr16	30727800	chrY	2722641	2	17	SLVLRATDVHPLQYK	GTGCTAAGGGCCACGGATGTCCATCCCCTCCAGTACAAGTTGTGC

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Information of the samples that have these potential fusion neoantigens of SRCAP-RPS4Y1

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
GBM	SRCAP-RPS4Y1	chr16	30727800	ENST00000262518	chrY	2722641	ENST00000250784	TCGA-06-0132-01A

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Potential target of CAR-T therapy development for SRCAP-RPS4Y1

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 SRCAP-RPS4Y1

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 SRCAP-RPS4Y1

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)