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Fusion Protein:PLEK-IER3

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: PLEK-IER3
	FusionPDB ID: 66339
	FusionGDB2.0 ID: 66339
		Hgene	Tgene
	Gene symbol	PLEK	IER3
	Gene ID	5341	8870
	Gene name	pleckstrin	immediate early response 3
	Synonyms	P47	DIF-2\|DIF2\|GLY96\|IEX-1\|IEX-1L\|IEX1\|PRG1
	Cytomap	2p14	6p21.33
	Type of gene	protein-coding	protein-coding
	Description	pleckstrinplatelet 47 kDa protein	radiation-inducible immediate-early gene IEX-1PACAP-responsive gene 1 proteinanti-death proteindifferentiation-dependent gene 2 proteinexpressed in pancreatic carcinomagly96, mouse, homolog ofimmediate early protein GLY96immediate early response 3
	Modification date	20200313	20200313
	UniProtAcc	.	Q9Y5U9 Main function of 5'-partner protein: FUNCTION: Regulator of endoplasmic reticulum secretion that acts as a key determinant of brain size (PubMed:33122427). Required for secretion of extracellular matrix proteins (PubMed:33122427). Required for correct brain development by depositing sufficient extracellular matrix proteins for tissue integrity and the proliferation of neural progenitors (PubMed:33122427). Acts as a regulator of the unfolded protein response (UPR) (By similarity). {ECO:0000250\|UniProtKB:Q9CR20, ECO:0000269\|PubMed:33122427}.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000234313,	ENST00000383560, ENST00000400509, ENST00000416336, ENST00000416884, ENST00000429592, ENST00000435856, ENST00000436988, ENST00000439190, ENST00000446599, ENST00000450236, ENST00000259874, ENST00000376377,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	4 X 4 X 2=32	4 X 3 X 2=24
	# samples	4	4
	** MAII score	log2(4/32*10)=0.321928094887362 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0	log2(4/24*10)=0.736965594166206 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0
Fusion gene context	PubMed: PLEK [Title/Abstract] AND IER3 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: PLEK [Title/Abstract] AND IER3 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	PLEK(68592525)-IER3(30711973), # samples:1
Anticipated loss of major functional domain due to fusion event.	PLEK-IER3 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. PLEK-IER3 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. PLEK-IER3 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF. PLEK-IER3 seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor 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	PLEK	GO:0007229	integrin-mediated signaling pathway	10995449
Hgene	PLEK	GO:0010920	negative regulation of inositol phosphate biosynthetic process	7559487\|7782310
Hgene	PLEK	GO:0010925	positive regulation of inositol-polyphosphate 5-phosphatase activity	8999861
Hgene	PLEK	GO:0030030	cell projection organization	9060471
Hgene	PLEK	GO:0030836	positive regulation of actin filament depolymerization	10497244
Hgene	PLEK	GO:0030845	phospholipase C-inhibiting G protein-coupled receptor signaling pathway	7782310
Hgene	PLEK	GO:0030866	cortical actin cytoskeleton organization	10497244
Hgene	PLEK	GO:0031529	ruffle organization	10497244
Hgene	PLEK	GO:0031532	actin cytoskeleton reorganization	10497244
Hgene	PLEK	GO:0032233	positive regulation of actin filament bundle assembly	10497244
Hgene	PLEK	GO:0045744	negative regulation of G protein-coupled receptor signaling pathway	7782310
Hgene	PLEK	GO:0046488	phosphatidylinositol metabolic process	7559487
Hgene	PLEK	GO:0060305	regulation of cell diameter	10995449
Hgene	PLEK	GO:0070493	thrombin-activated receptor signaling pathway	7782310

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr2:68592525/chr6:30711973)
- 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 PLEK (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 IER3 (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)

ENST00000234313

PLEK

chr2

68592525

ENST00000376377

IER3

chr6

30711973

1219

221

143

481

112

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
ENST00000234313	ENST00000376377	PLEK	chr2	68592525	+	IER3	chr6	30711973	-	0.084218405	0.9157816

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 PLEK-IER3

+/-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
PLEK	chr2	68592525	IER3	chr6	30711973	221	26	EPKRIREGYLVKKVRRQLPVEEPNPA

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Potential FusionNeoAntigen Information of PLEK-IER3 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.

PLEK-IER3_68592525_30711973.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)
PLEK-IER3	chr2	68592525	chr6	30711973	221	HLA-B45:01	REGYLVKKV	0.997	0.5839	5	14
PLEK-IER3	chr2	68592525	chr6	30711973	221	HLA-A31:02	GYLVKKVRR	0.7521	0.6458	7	16
PLEK-IER3	chr2	68592525	chr6	30711973	221	HLA-B41:01	REGYLVKKV	0.4614	0.7032	5	14
PLEK-IER3	chr2	68592525	chr6	30711973	221	HLA-B51:07	EGYLVKKV	0.9976	0.7605	6	14
PLEK-IER3	chr2	68592525	chr6	30711973	221	HLA-B40:06	REGYLVKKV	0.9991	0.6136	5	14
PLEK-IER3	chr2	68592525	chr6	30711973	221	HLA-A31:01	GYLVKKVRR	0.9136	0.6208	7	16
PLEK-IER3	chr2	68592525	chr6	30711973	221	HLA-A30:01	KVRRQLPVE	0.9769	0.8407	12	21

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Potential FusionNeoAntigen Information of PLEK-IER3 in HLA II

PLEK-IER3_68592525_30711973.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)
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-0802	REGYLVKKVRRQLPV	5	20
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-0802	IREGYLVKKVRRQLP	4	19
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-0809	REGYLVKKVRRQLPV	5	20
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-0809	IREGYLVKKVRRQLP	4	19
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-0813	REGYLVKKVRRQLPV	5	20
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-0813	IREGYLVKKVRRQLP	4	19
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-0815	REGYLVKKVRRQLPV	5	20
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-0815	IREGYLVKKVRRQLP	4	19
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-0821	REGYLVKKVRRQLPV	5	20
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-0821	IREGYLVKKVRRQLP	4	19
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-0830	REGYLVKKVRRQLPV	5	20
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-0830	IREGYLVKKVRRQLP	4	19
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1102	EGYLVKKVRRQLPVE	6	21
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1103	EGYLVKKVRRQLPVE	6	21
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1111	REGYLVKKVRRQLPV	5	20
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1111	IREGYLVKKVRRQLP	4	19
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1116	EGYLVKKVRRQLPVE	6	21
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1121	EGYLVKKVRRQLPVE	6	21
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1121	REGYLVKKVRRQLPV	5	20
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1130	REGYLVKKVRRQLPV	5	20
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1130	IREGYLVKKVRRQLP	4	19
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1132	REGYLVKKVRRQLPV	5	20
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1136	EGYLVKKVRRQLPVE	6	21
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1145	REGYLVKKVRRQLPV	5	20
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1145	IREGYLVKKVRRQLP	4	19
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1148	EGYLVKKVRRQLPVE	6	21
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1155	EGYLVKKVRRQLPVE	6	21
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1155	REGYLVKKVRRQLPV	5	20
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1163	EGYLVKKVRRQLPVE	6	21
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1164	REGYLVKKVRRQLPV	5	20
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1164	IREGYLVKKVRRQLP	4	19
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1165	EGYLVKKVRRQLPVE	6	21
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1170	EGYLVKKVRRQLPVE	6	21
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1170	REGYLVKKVRRQLPV	5	20
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1172	REGYLVKKVRRQLPV	5	20
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1176	EGYLVKKVRRQLPVE	6	21
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1185	EGYLVKKVRRQLPVE	6	21
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1186	REGYLVKKVRRQLPV	5	20
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1186	IREGYLVKKVRRQLP	4	19
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1301	EGYLVKKVRRQLPVE	6	21
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1308	EGYLVKKVRRQLPVE	6	21
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1315	EGYLVKKVRRQLPVE	6	21
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1315	REGYLVKKVRRQLPV	5	20
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1316	REGYLVKKVRRQLPV	5	20
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1316	IREGYLVKKVRRQLP	4	19
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1319	EGYLVKKVRRQLPVE	6	21
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1319	REGYLVKKVRRQLPV	5	20
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1320	EGYLVKKVRRQLPVE	6	21
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1322	EGYLVKKVRRQLPVE	6	21
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1324	EGYLVKKVRRQLPVE	6	21
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1326	REGYLVKKVRRQLPV	5	20
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1326	IREGYLVKKVRRQLP	4	19
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1335	EGYLVKKVRRQLPVE	6	21
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1336	REGYLVKKVRRQLPV	5	20
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1343	EGYLVKKVRRQLPVE	6	21
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1347	REGYLVKKVRRQLPV	5	20
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1347	IREGYLVKKVRRQLP	4	19
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1351	EGYLVKKVRRQLPVE	6	21
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1352	EGYLVKKVRRQLPVE	6	21
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1353	EGYLVKKVRRQLPVE	6	21
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1353	REGYLVKKVRRQLPV	5	20
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1354	EGYLVKKVRRQLPVE	6	21
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1357	EGYLVKKVRRQLPVE	6	21
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1357	REGYLVKKVRRQLPV	5	20
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1359	EGYLVKKVRRQLPVE	6	21
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1361	EGYLVKKVRRQLPVE	6	21
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1363	REGYLVKKVRRQLPV	5	20
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1363	IREGYLVKKVRRQLP	4	19
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1364	EGYLVKKVRRQLPVE	6	21
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1367	REGYLVKKVRRQLPV	5	20
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1367	IREGYLVKKVRRQLP	4	19
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1368	EGYLVKKVRRQLPVE	6	21
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1369	EGYLVKKVRRQLPVE	6	21
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1370	EGYLVKKVRRQLPVE	6	21
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1372	EGYLVKKVRRQLPVE	6	21
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1375	EGYLVKKVRRQLPVE	6	21
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1376	EGYLVKKVRRQLPVE	6	21
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1378	EGYLVKKVRRQLPVE	6	21
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1379	EGYLVKKVRRQLPVE	6	21
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1380	EGYLVKKVRRQLPVE	6	21
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1383	EGYLVKKVRRQLPVE	6	21
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1384	EGYLVKKVRRQLPVE	6	21
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1387	EGYLVKKVRRQLPVE	6	21
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1391	EGYLVKKVRRQLPVE	6	21
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1392	EGYLVKKVRRQLPVE	6	21
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1398	EGYLVKKVRRQLPVE	6	21
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1403	REGYLVKKVRRQLPV	5	20
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1403	IREGYLVKKVRRQLP	4	19
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1416	EGYLVKKVRRQLPVE	6	21
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1427	REGYLVKKVRRQLPV	5	20
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1427	IREGYLVKKVRRQLP	4	19
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1427	RIREGYLVKKVRRQL	3	18
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1427	EGYLVKKVRRQLPVE	6	21
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1440	REGYLVKKVRRQLPV	5	20
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1440	IREGYLVKKVRRQLP	4	19
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1463	REGYLVKKVRRQLPV	5	20
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1463	IREGYLVKKVRRQLP	4	19
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1467	REGYLVKKVRRQLPV	5	20
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1467	IREGYLVKKVRRQLP	4	19
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1477	REGYLVKKVRRQLPV	5	20
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1477	IREGYLVKKVRRQLP	4	19
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1498	REGYLVKKVRRQLPV	5	20
PLEK-IER3	chr2	68592525	chr6	30711973	221	DRB1-1498	IREGYLVKKVRRQLP	4	19

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Fusion breakpoint peptide structures of PLEK-IER3

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
1766	EGYLVKKVRRQLPV	PLEK	IER3	chr2	68592525	chr6	30711973	221

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of PLEK-IER3

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	1766	EGYLVKKVRRQLPV	-7.15543	-7.26883
HLA-B14:02	3BVN	1766	EGYLVKKVRRQLPV	-4.77435	-5.80965
HLA-B52:01	3W39	1766	EGYLVKKVRRQLPV	-6.80875	-6.92215
HLA-B52:01	3W39	1766	EGYLVKKVRRQLPV	-4.20386	-5.23916
HLA-A11:01	4UQ2	1766	EGYLVKKVRRQLPV	-7.5194	-8.5547
HLA-A11:01	4UQ2	1766	EGYLVKKVRRQLPV	-6.9601	-7.0735
HLA-A24:02	5HGA	1766	EGYLVKKVRRQLPV	-7.52403	-7.63743
HLA-A24:02	5HGA	1766	EGYLVKKVRRQLPV	-5.82433	-6.85963
HLA-B27:05	6PYJ	1766	EGYLVKKVRRQLPV	-3.28285	-4.31815
HLA-B44:05	3DX8	1766	EGYLVKKVRRQLPV	-5.91172	-6.94702
HLA-B44:05	3DX8	1766	EGYLVKKVRRQLPV	-4.24346	-4.35686

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Vaccine Design for the FusionNeoAntigens of PLEK-IER3

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
PLEK-IER3	chr2	68592525	chr6	30711973	12	21	KVRRQLPVE	AAGGTCCGGCGCCAGCTGCCAGTCGAG
PLEK-IER3	chr2	68592525	chr6	30711973	5	14	REGYLVKKV	AGAGAGGGCTACCTTGTGAAGAAGGTC
PLEK-IER3	chr2	68592525	chr6	30711973	6	14	EGYLVKKV	GAGGGCTACCTTGTGAAGAAGGTC
PLEK-IER3	chr2	68592525	chr6	30711973	7	16	GYLVKKVRR	GGCTACCTTGTGAAGAAGGTCCGGCGC

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
PLEK-IER3	chr2	68592525	chr6	30711973	3	18	RIREGYLVKKVRRQL	CGGATCAGAGAGGGCTACCTTGTGAAGAAGGTCCGGCGCCAGCTG
PLEK-IER3	chr2	68592525	chr6	30711973	4	19	IREGYLVKKVRRQLP	ATCAGAGAGGGCTACCTTGTGAAGAAGGTCCGGCGCCAGCTGCCA
PLEK-IER3	chr2	68592525	chr6	30711973	5	20	REGYLVKKVRRQLPV	AGAGAGGGCTACCTTGTGAAGAAGGTCCGGCGCCAGCTGCCAGTC
PLEK-IER3	chr2	68592525	chr6	30711973	6	21	EGYLVKKVRRQLPVE	GAGGGCTACCTTGTGAAGAAGGTCCGGCGCCAGCTGCCAGTCGAG

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Information of the samples that have these potential fusion neoantigens of PLEK-IER3

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
Non-Cancer	PLEK-IER3	chr2	68592525	ENST00000234313	chr6	30711973	ENST00000376377	ERR315404

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Potential target of CAR-T therapy development for PLEK-IER3

Predicted 3D structure. We used RoseTTAFold.

Retention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, to provide the retention of the transmembrane domain, we only show the protein feature retention information of those transmembrane features

* Minus value of BPloci means that the break point is located before the CDS.

- In-frame and retained 'Transmembrane'.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

Tgene

IER3

chr2:68592525

chr6:30711973

ENST00000259874

83_99

157.0

Transmembrane

Helical%3B Signal-anchor for type II membrane protein

Tgene

IER3

chr2:68592525

chr6:30711973

ENST00000383560

83_99

157.0

Transmembrane

Helical%3B Signal-anchor for type II membrane protein

Tgene

IER3

chr2:68592525

chr6:30711973

ENST00000416884

83_99

157.0

Transmembrane

Helical%3B Signal-anchor for type II membrane protein

Tgene

IER3

chr2:68592525

chr6:30711973

ENST00000435856

83_99

157.0

Transmembrane

Helical%3B Signal-anchor for type II membrane protein

Tgene

IER3

chr2:68592525

chr6:30711973

ENST00000439190

83_99

157.0

Transmembrane

Helical%3B Signal-anchor for type II membrane protein

Tgene

IER3

chr2:68592525

chr6:30711973

ENST00000450236

83_99

157.0

Transmembrane

Helical%3B Signal-anchor for type II membrane protein

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 PLEK-IER3

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 PLEK-IER3

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)