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Fusion Protein:DNAJC14-SMARCC2

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: DNAJC14-SMARCC2
	FusionPDB ID: 23460
	FusionGDB2.0 ID: 23460
		Hgene	Tgene
	Gene symbol	DNAJC14	SMARCC2
	Gene ID	85406	6601
	Gene name	DnaJ heat shock protein family (Hsp40) member C14	SWI/SNF related, matrix associated, actin dependent regulator of chromatin subfamily c member 2
	Synonyms	DNAJ\|DRIP78\|HDJ3\|LIP6	BAF170\|CRACC2\|CSS8\|Rsc8
	Cytomap	12q13.2	12q13.2
	Type of gene	protein-coding	protein-coding
	Description	dnaJ homolog subfamily C member 14DnaJ (Hsp40) homolog, subfamily C, member 14LYST-interacting protein LIP6dnaJ protein homolog 3dopamine receptor interacting proteindopamine receptor-interacting protein of 78 kDahDj-3human DnaJ protein 3	SWI/SNF complex subunit SMARCC2SWI/SNF complex 170 kDa subunitSWI3-like proteinchromatin remodeling complex BAF170 subunitmammalian chromatin remodeling complex BRG1-associated factor 170
	Modification date	20200313	20200313
	UniProtAcc	Q6Y2X3 Main function of 5'-partner protein: FUNCTION: Regulates the export of target proteins, such as DRD1, from the endoplasmic reticulum to the cell surface. {ECO:0000250}.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000317269, ENST00000317287, ENST00000357606,	ENST00000550859, ENST00000267064, ENST00000347471, ENST00000394023, ENST00000550164,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	2 X 2 X 1=4	18 X 18 X 7=2268
	# samples	2	19
	** MAII score	log2(2/4*10)=2.32192809488736	log2(19/2268*10)=-3.57734931661128 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: DNAJC14 [Title/Abstract] AND SMARCC2 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: DNAJC14 [Title/Abstract] AND SMARCC2 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	DNAJC14(56216854)-SMARCC2(56568548), # samples:2
Anticipated loss of major functional domain due to fusion event.	DNAJC14-SMARCC2 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. DNAJC14-SMARCC2 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. DNAJC14-SMARCC2 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. DNAJC14-SMARCC2 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.

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

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

Partner	Gene	GO ID	GO term	PubMed ID
Tgene	SMARCC2	GO:0006337	nucleosome disassembly	8895581
Tgene	SMARCC2	GO:0006338	chromatin remodeling	10078207\|11018012\|11726552
Tgene	SMARCC2	GO:0045892	negative regulation of transcription, DNA-templated	12192000
Tgene	SMARCC2	GO:0045893	positive regulation of transcription, DNA-templated	11018012

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr12:56216854/chr12:56568548)
- 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 DNAJC14 (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 SMARCC2 (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)
ENST00000317269	DNAJC14	chr12	56216854	-	ENST00000394023	SMARCC2	chr12	56568548	-	4621	1838	204	3914	1236
ENST00000317269	DNAJC14	chr12	56216854	-	ENST00000550164	SMARCC2	chr12	56568548	-	4555	1838	204	4193	1329
ENST00000317269	DNAJC14	chr12	56216854	-	ENST00000347471	SMARCC2	chr12	56568548	-	4208	1838	204	3848	1214
ENST00000317269	DNAJC14	chr12	56216854	-	ENST00000267064	SMARCC2	chr12	56568548	-	4445	1838	204	4100	1298
ENST00000357606	DNAJC14	chr12	56216854	-	ENST00000394023	SMARCC2	chr12	56568548	-	4707	1924	290	4000	1236
ENST00000357606	DNAJC14	chr12	56216854	-	ENST00000550164	SMARCC2	chr12	56568548	-	4641	1924	290	4279	1329
ENST00000357606	DNAJC14	chr12	56216854	-	ENST00000347471	SMARCC2	chr12	56568548	-	4294	1924	290	3934	1214
ENST00000357606	DNAJC14	chr12	56216854	-	ENST00000267064	SMARCC2	chr12	56568548	-	4531	1924	290	4186	1298
ENST00000317287	DNAJC14	chr12	56216854	-	ENST00000394023	SMARCC2	chr12	56568548	-	4856	2073	439	4149	1236
ENST00000317287	DNAJC14	chr12	56216854	-	ENST00000550164	SMARCC2	chr12	56568548	-	4790	2073	439	4428	1329
ENST00000317287	DNAJC14	chr12	56216854	-	ENST00000347471	SMARCC2	chr12	56568548	-	4443	2073	439	4083	1214
ENST00000317287	DNAJC14	chr12	56216854	-	ENST00000267064	SMARCC2	chr12	56568548	-	4680	2073	439	4335	1298

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
ENST00000317269	ENST00000394023	DNAJC14	chr12	56216854	-	SMARCC2	chr12	56568548	-	0.002510755	0.9974892
ENST00000317269	ENST00000550164	DNAJC14	chr12	56216854	-	SMARCC2	chr12	56568548	-	0.002905461	0.9970945
ENST00000317269	ENST00000347471	DNAJC14	chr12	56216854	-	SMARCC2	chr12	56568548	-	0.002642118	0.9973579
ENST00000317269	ENST00000267064	DNAJC14	chr12	56216854	-	SMARCC2	chr12	56568548	-	0.004299782	0.99570024
ENST00000357606	ENST00000394023	DNAJC14	chr12	56216854	-	SMARCC2	chr12	56568548	-	0.002592495	0.9974075
ENST00000357606	ENST00000550164	DNAJC14	chr12	56216854	-	SMARCC2	chr12	56568548	-	0.002982669	0.9970174
ENST00000357606	ENST00000347471	DNAJC14	chr12	56216854	-	SMARCC2	chr12	56568548	-	0.002715357	0.99728465
ENST00000357606	ENST00000267064	DNAJC14	chr12	56216854	-	SMARCC2	chr12	56568548	-	0.004412641	0.99558735
ENST00000317287	ENST00000394023	DNAJC14	chr12	56216854	-	SMARCC2	chr12	56568548	-	0.002702586	0.99729747
ENST00000317287	ENST00000550164	DNAJC14	chr12	56216854	-	SMARCC2	chr12	56568548	-	0.003043886	0.9969561
ENST00000317287	ENST00000347471	DNAJC14	chr12	56216854	-	SMARCC2	chr12	56568548	-	0.002725948	0.9972741
ENST00000317287	ENST00000267064	DNAJC14	chr12	56216854	-	SMARCC2	chr12	56568548	-	0.004492895	0.9955071

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 DNAJC14-SMARCC2

+/-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
DNAJC14	chr12	56216854	SMARCC2	chr12	56568548	1838	544	MNTMMCSRCQGKHSYLAYRNFMIDTY
DNAJC14	chr12	56216854	SMARCC2	chr12	56568548	1924	544	MNTMMCSRCQGKHSYLAYRNFMIDTY
DNAJC14	chr12	56216854	SMARCC2	chr12	56568548	2073	544	MNTMMCSRCQGKHSYLAYRNFMIDTY

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Potential FusionNeoAntigen Information of DNAJC14-SMARCC2 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.

DNAJC14-SMARCC2_56216854_56568548.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)
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-B15:03	GKHSYLAY	0.8758	0.6678	10	18
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-B27:02	SRCQGKHSY	0.9986	0.5497	6	15
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-B27:05	SRCQGKHSY	0.9984	0.839	6	15
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-B57:01	HSYLAYRNF	0.9983	0.8908	12	21
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-B27:04	SRCQGKHSY	0.9982	0.6663	6	15
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-B58:02	HSYLAYRNF	0.9959	0.7841	12	21
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-B15:17	HSYLAYRNF	0.9946	0.8003	12	21
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-B57:03	HSYLAYRNF	0.9933	0.9568	12	21
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-B58:01	HSYLAYRNF	0.9908	0.6581	12	21
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-A32:13	HSYLAYRNF	0.7977	0.969	12	21
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-B15:03	SRCQGKHSY	0.3961	0.5778	6	15
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-B15:18	SRCQGKHSY	0.3587	0.5005	6	15
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-C07:95	SRCQGKHSY	0.9939	0.5583	6	15
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-B27:14	SRCQGKHSY	0.9929	0.7409	6	15
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-C07:27	SRCQGKHSY	0.9841	0.8901	6	15
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-B27:03	SRCQGKHSY	0.9819	0.8605	6	15
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-C07:05	SRCQGKHSY	0.9786	0.8779	6	15
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-C15:04	HSYLAYRNF	0.9484	0.7435	12	21
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-C07:19	SRCQGKHSY	0.8201	0.581	6	15
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-C07:80	SRCQGKHSY	0.8038	0.8168	6	15
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-C07:67	SRCQGKHSY	0.8038	0.8168	6	15
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-C07:10	SRCQGKHSY	0.8004	0.8399	6	15
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-C07:46	SRCQGKHSY	0.79	0.7218	6	15
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-C03:14	HSYLAYRNF	0.6868	0.947	12	21
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-C12:12	HSYLAYRNF	0.3572	0.9162	12	21
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-C12:04	HSYLAYRNF	0.2012	0.9932	12	21
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-C06:03	HSYLAYRNF	0.186	0.9936	12	21
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-C12:16	SRCQGKHSY	0.0572	0.9012	6	15
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-B39:12	SRCQGKHSYL	0.9784	0.8156	6	16
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-B15:68	GKHSYLAY	0.8244	0.6208	10	18
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-B57:10	HSYLAYRNF	0.9983	0.8908	12	21
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-B27:08	SRCQGKHSY	0.9982	0.6622	6	15
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-B27:10	SRCQGKHSY	0.9979	0.8154	6	15
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-B58:06	HSYLAYRNF	0.9961	0.5089	12	21
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-C07:01	SRCQGKHSY	0.9952	0.5423	6	15
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-B57:04	HSYLAYRNF	0.995	0.5671	12	21
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-A32:01	HSYLAYRNF	0.9792	0.9621	12	21
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-C15:09	HSYLAYRNF	0.9484	0.7435	12	21
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-B27:09	SRCQGKHSY	0.8919	0.7512	6	15
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-C03:02	HSYLAYRNF	0.8897	0.9314	12	21
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-C07:17	SRCQGKHSY	0.834	0.8893	6	15
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-C07:02	SRCQGKHSY	0.8038	0.8168	6	15
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-C16:04	HSYLAYRNF	0.7789	0.9824	12	21
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-C07:22	SRCQGKHSY	0.7734	0.5586	6	15
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-C16:01	HSYLAYRNF	0.577	0.9775	12	21
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-C06:08	SRCQGKHSY	0.5247	0.9781	6	15
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-C12:02	HSYLAYRNF	0.477	0.9545	12	21
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-C16:02	HSYLAYRNF	0.421	0.9915	12	21
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-C12:03	HSYLAYRNF	0.3758	0.9748	12	21
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-B48:02	SRCQGKHSY	0.3557	0.7707	6	15
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-B15:54	SRCQGKHSY	0.1257	0.6918	6	15
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-C06:06	SRCQGKHSY	0.0813	0.9815	6	15
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-C02:02	HSYLAYRNF	0.0253	0.9366	12	21
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-C02:10	HSYLAYRNF	0.0253	0.9366	12	21
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-C06:02	SRCQGKHSY	0.0133	0.9785	6	15
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-C06:17	SRCQGKHSY	0.0133	0.9785	6	15
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-B27:06	SRCQGKHSYL	0.9994	0.7215	6	16
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-B27:09	SRCQGKHSYL	0.9986	0.8549	6	16
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-B15:35	CQGKHSYLAY	0.9945	0.6308	8	18
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	HLA-C07:22	SRCQGKHSYL	0.9632	0.7148	6	16

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Potential FusionNeoAntigen Information of DNAJC14-SMARCC2 in HLA II

DNAJC14-SMARCC2_56216854_56568548.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)
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1502	KHSYLAYRNFMIDTY	11	26
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1502	GKHSYLAYRNFMIDT	10	25
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1502	QGKHSYLAYRNFMID	9	24
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1508	KHSYLAYRNFMIDTY	11	26
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1508	GKHSYLAYRNFMIDT	10	25
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1508	QGKHSYLAYRNFMID	9	24
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1511	KHSYLAYRNFMIDTY	11	26
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1511	GKHSYLAYRNFMIDT	10	25
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1511	QGKHSYLAYRNFMID	9	24
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1514	KHSYLAYRNFMIDTY	11	26
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1514	GKHSYLAYRNFMIDT	10	25
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1514	QGKHSYLAYRNFMID	9	24
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1515	KHSYLAYRNFMIDTY	11	26
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1515	GKHSYLAYRNFMIDT	10	25
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1515	QGKHSYLAYRNFMID	9	24
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1519	KHSYLAYRNFMIDTY	11	26
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1519	GKHSYLAYRNFMIDT	10	25
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1519	QGKHSYLAYRNFMID	9	24
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1526	KHSYLAYRNFMIDTY	11	26
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1526	GKHSYLAYRNFMIDT	10	25
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1526	QGKHSYLAYRNFMID	9	24
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1527	KHSYLAYRNFMIDTY	11	26
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1527	GKHSYLAYRNFMIDT	10	25
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1527	QGKHSYLAYRNFMID	9	24
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1529	GKHSYLAYRNFMIDT	10	25
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1529	KHSYLAYRNFMIDTY	11	26
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1529	QGKHSYLAYRNFMID	9	24
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1530	KHSYLAYRNFMIDTY	11	26
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1530	GKHSYLAYRNFMIDT	10	25
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1530	QGKHSYLAYRNFMID	9	24
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1531	KHSYLAYRNFMIDTY	11	26
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1531	GKHSYLAYRNFMIDT	10	25
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1531	QGKHSYLAYRNFMID	9	24
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1534	KHSYLAYRNFMIDTY	11	26
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1534	GKHSYLAYRNFMIDT	10	25
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1538	KHSYLAYRNFMIDTY	11	26
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1538	GKHSYLAYRNFMIDT	10	25
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1538	QGKHSYLAYRNFMID	9	24
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1539	KHSYLAYRNFMIDTY	11	26
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1539	GKHSYLAYRNFMIDT	10	25
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1539	QGKHSYLAYRNFMID	9	24
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1544	KHSYLAYRNFMIDTY	11	26
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1544	GKHSYLAYRNFMIDT	10	25
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1544	QGKHSYLAYRNFMID	9	24
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1547	KHSYLAYRNFMIDTY	11	26
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1547	GKHSYLAYRNFMIDT	10	25
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1547	QGKHSYLAYRNFMID	9	24
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1602	KHSYLAYRNFMIDTY	11	26
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1602	GKHSYLAYRNFMIDT	10	25
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1604	KHSYLAYRNFMIDTY	11	26
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1604	GKHSYLAYRNFMIDT	10	25
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1605	KHSYLAYRNFMIDTY	11	26
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1605	GKHSYLAYRNFMIDT	10	25
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1605	QGKHSYLAYRNFMID	9	24
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1607	KHSYLAYRNFMIDTY	11	26
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1607	GKHSYLAYRNFMIDT	10	25
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1607	QGKHSYLAYRNFMID	9	24
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1609	KHSYLAYRNFMIDTY	11	26
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1609	GKHSYLAYRNFMIDT	10	25
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1609	QGKHSYLAYRNFMID	9	24
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1610	KHSYLAYRNFMIDTY	11	26
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1610	GKHSYLAYRNFMIDT	10	25
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1610	QGKHSYLAYRNFMID	9	24
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1611	KHSYLAYRNFMIDTY	11	26
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1611	GKHSYLAYRNFMIDT	10	25
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1612	KHSYLAYRNFMIDTY	11	26
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1612	GKHSYLAYRNFMIDT	10	25
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1614	KHSYLAYRNFMIDTY	11	26
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1614	GKHSYLAYRNFMIDT	10	25
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1616	KHSYLAYRNFMIDTY	11	26
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB1-1616	GKHSYLAYRNFMIDT	10	25
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB5-0203	KHSYLAYRNFMIDTY	11	26
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	1838	DRB5-0203	GKHSYLAYRNFMIDT	10	25

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Fusion breakpoint peptide structures of DNAJC14-SMARCC2

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
8947	SRCQGKHSYLAYRN	DNAJC14	SMARCC2	chr12	56216854	chr12	56568548	1838

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of DNAJC14-SMARCC2

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	8947	SRCQGKHSYLAYRN	-7.15543	-7.26883
HLA-B14:02	3BVN	8947	SRCQGKHSYLAYRN	-4.77435	-5.80965
HLA-B52:01	3W39	8947	SRCQGKHSYLAYRN	-6.80875	-6.92215
HLA-B52:01	3W39	8947	SRCQGKHSYLAYRN	-4.20386	-5.23916
HLA-A11:01	4UQ2	8947	SRCQGKHSYLAYRN	-7.5194	-8.5547
HLA-A11:01	4UQ2	8947	SRCQGKHSYLAYRN	-6.9601	-7.0735
HLA-A24:02	5HGA	8947	SRCQGKHSYLAYRN	-7.52403	-7.63743
HLA-A24:02	5HGA	8947	SRCQGKHSYLAYRN	-5.82433	-6.85963
HLA-B27:05	6PYJ	8947	SRCQGKHSYLAYRN	-3.28285	-4.31815
HLA-B44:05	3DX8	8947	SRCQGKHSYLAYRN	-5.91172	-6.94702
HLA-B44:05	3DX8	8947	SRCQGKHSYLAYRN	-4.24346	-4.35686

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Vaccine Design for the FusionNeoAntigens of DNAJC14-SMARCC2

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
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	10	18	GKHSYLAY	AAAGCATAGCTACCTGGCCTATCG
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	12	21	HSYLAYRNF	TAGCTACCTGGCCTATCGAAACTTTAT
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	6	15	SRCQGKHSY	CCGATGCCAAGGAAAGCATAGCTACCT
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	6	16	SRCQGKHSYL	CCGATGCCAAGGAAAGCATAGCTACCTGGC
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	8	18	CQGKHSYLAY	CCAAGGAAAGCATAGCTACCTGGCCTATCG

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
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	10	25	GKHSYLAYRNFMIDT	AAAGCATAGCTACCTGGCCTATCGAAACTTTATGATTGACACTTA
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	11	26	KHSYLAYRNFMIDTY	GCATAGCTACCTGGCCTATCGAAACTTTATGATTGACACTTACCG
DNAJC14-SMARCC2	chr12	56216854	chr12	56568548	9	24	QGKHSYLAYRNFMID	AGGAAAGCATAGCTACCTGGCCTATCGAAACTTTATGATTGACAC

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Information of the samples that have these potential fusion neoantigens of DNAJC14-SMARCC2

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	DNAJC14-SMARCC2	chr12	56216854	ENST00000317269	chr12	56568548	ENST00000267064	TCGA-BR-8060-01A

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Potential target of CAR-T therapy development for DNAJC14-SMARCC2

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

Hgene

DNAJC14

chr12:56216854

chr12:56568548

ENST00000317269

250_270

544

703.0

Transmembrane

Helical

Hgene

DNAJC14

chr12:56216854

chr12:56568548

ENST00000317269

300_320

544

703.0

Transmembrane

Helical

Hgene

DNAJC14

chr12:56216854

chr12:56568548

ENST00000317269

326_346

544

703.0

Transmembrane

Helical

Hgene

DNAJC14

chr12:56216854

chr12:56568548

ENST00000317287

250_270

544

703.0

Transmembrane

Helical

Hgene

DNAJC14

chr12:56216854

chr12:56568548

ENST00000317287

300_320

544

703.0

Transmembrane

Helical

Hgene

DNAJC14

chr12:56216854

chr12:56568548

ENST00000317287

326_346

544

703.0

Transmembrane

Helical

Hgene

DNAJC14

chr12:56216854

chr12:56568548

ENST00000357606

250_270

544

703.0

Transmembrane

Helical

Hgene

DNAJC14

chr12:56216854

chr12:56568548

ENST00000357606

300_320

544

703.0

Transmembrane

Helical

Hgene

DNAJC14

chr12:56216854

chr12:56568548

ENST00000357606

326_346

544

703.0

Transmembrane

Helical

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

Hgene

Hchr

Hbp

Henst

Tgene

Tchr

Tbp

Tenst

DeepLoc result

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Related Drugs to DNAJC14-SMARCC2

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 DNAJC14-SMARCC2

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)