Home

Download

Statistics

Examples

Help

Contact

Fusion Protein:XPR1-LHX4

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: XPR1-LHX4
	FusionPDB ID: 99736
	FusionGDB2.0 ID: 99736
		Hgene	Tgene
	Gene symbol	XPR1	LHX4
	Gene ID	9213	89884
	Gene name	xenotropic and polytropic retrovirus receptor 1	LIM homeobox 4
	Synonyms	IBGC6\|SLC53A1\|SYG1\|X3	CPHD4
	Cytomap	1q25.3	1q25.2
	Type of gene	protein-coding	protein-coding
	Description	xenotropic and polytropic retrovirus receptor 1X-receptorprotein SYG1 homologsolute carrier family 53 (phosphate exporter), member 1xenotropic and polytropic murine leukemia virus receptor X3	LIM/homeobox protein Lhx4LIM homeobox protein 4
	Modification date	20200313	20200313
	UniProtAcc	.	Q969G2 Main function of 5'-partner protein: FUNCTION: May play a critical role in the development of respiratory control mechanisms and in the normal growth and maturation of the lung. Binds preferentially to methylated DNA (PubMed:28473536). {ECO:0000250, ECO:0000269\|PubMed:28473536}.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000367589, ENST00000367590, ENST00000467345,	ENST00000263726,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	24 X 7 X 12=2016	3 X 3 X 5=45
	# samples	27	7
	** MAII score	log2(27/2016*10)=-2.90046432644909 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(7/45*10)=0.637429920615292 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0
Fusion gene context	PubMed: XPR1 [Title/Abstract] AND LHX4 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: XPR1 [Title/Abstract] AND LHX4 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	XPR1(180805852)-LHX4(180217420), # samples:2
Anticipated loss of major functional domain due to fusion event.	XPR1-LHX4 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. XPR1-LHX4 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. XPR1-LHX4 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. XPR1-LHX4 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	LHX4	GO:0045944	positive regulation of transcription by RNA polymerase II	15998782

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr1:180805852/chr1:180217420)
- 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 XPR1 (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 LHX4 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Top

Fusion Amino Acid Sequences

Fusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.

Henst

Tenst

Hgene

Hchr

Hbp

Hstrand

Tgene

Tchr

Tbp

Tstrand

Seq length
(transcript)

BP loci
(transcript)

Predicted start
(transcript)

Predicted stop
(transcript)

Seq length
(amino acids)

ENST00000367590

XPR1

chr1

180651547

ENST00000263726

LHX4

chr1

180217419

7082

319

198

1415

405

ENST00000367589

XPR1

chr1

180651547

ENST00000263726

LHX4

chr1

180217419

7054

291

170

1387

405

ENST00000367590

XPR1

chr1

180651547

ENST00000263726

LHX4

chr1

180217420

7082

319

198

1415

405

ENST00000367589

XPR1

chr1

180651547

ENST00000263726

LHX4

chr1

180217420

7054

291

170

1387

405

ENST00000367590

XPR1

chr1

180805852

ENST00000263726

LHX4

chr1

180217420

8462

1699

198

2795

865

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
ENST00000367590	ENST00000263726	XPR1	chr1	180651547	+	LHX4	chr1	180217419	+	0.00388699	0.99611294
ENST00000367589	ENST00000263726	XPR1	chr1	180651547	+	LHX4	chr1	180217419	+	0.003870135	0.9961299
ENST00000367590	ENST00000263726	XPR1	chr1	180651547	+	LHX4	chr1	180217420	+	0.00388699	0.99611294
ENST00000367589	ENST00000263726	XPR1	chr1	180651547	+	LHX4	chr1	180217420	+	0.003870135	0.9961299
ENST00000367590	ENST00000263726	XPR1	chr1	180805852	+	LHX4	chr1	180217420	+	0.001355121	0.9986449

Predicted full-length fusion amino acid sequences. For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among all the predicted ones.

Get the fusion protein sequences from here.

Fusion protein sequence information is available in the fasta format.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

Top

Fusion Protein Breakpoint Sequences for XPR1-LHX4

+/-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
XPR1	chr1	180651547	LHX4	chr1	180217419	291	40	MLYSAQDQAPSVEEIPQCAGCNQHIL
XPR1	chr1	180651547	LHX4	chr1	180217419	319	40	MLYSAQDQAPSVEEIPQCAGCNQHIL
XPR1	chr1	180651547	LHX4	chr1	180217420	291	40	MLYSAQDQAPSVEEIPQCAGCNQHIL
XPR1	chr1	180651547	LHX4	chr1	180217420	319	40	MLYSAQDQAPSVEEIPQCAGCNQHIL
XPR1	chr1	180805852	LHX4	chr1	180217420	1699	500	FMVTFAALYSTHKEIPQCAGCNQHIL

Top

Potential FusionNeoAntigen Information of XPR1-LHX4 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.

XPR1-LHX4_180651547_180217419.msa
XPR1-LHX4_180805852_180217420.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)
XPR1-LHX4	chr1	180651547	chr1	180217419	291	HLA-B14:02	DQAPSVEEI	0.9943	0.7601	6	15
XPR1-LHX4	chr1	180651547	chr1	180217419	291	HLA-B14:01	DQAPSVEEI	0.9943	0.7601	6	15
XPR1-LHX4	chr1	180651547	chr1	180217419	291	HLA-B52:01	DQAPSVEEI	0.9138	0.9641	6	15
XPR1-LHX4	chr1	180651547	chr1	180217419	291	HLA-B15:37	DQAPSVEEI	0.9026	0.5569	6	15
XPR1-LHX4	chr1	180651547	chr1	180217419	291	HLA-B39:01	DQAPSVEEI	0.8674	0.8738	6	15
XPR1-LHX4	chr1	180651547	chr1	180217419	291	HLA-B13:02	DQAPSVEEI	0.8504	0.7878	6	15
XPR1-LHX4	chr1	180651547	chr1	180217419	291	HLA-B39:13	DQAPSVEEI	0.8043	0.8878	6	15
XPR1-LHX4	chr1	180651547	chr1	180217419	291	HLA-B13:01	DQAPSVEEI	0.7763	0.943	6	15
XPR1-LHX4	chr1	180651547	chr1	180217419	291	HLA-B38:01	DQAPSVEEI	0.7434	0.9375	6	15
XPR1-LHX4	chr1	180651547	chr1	180217419	291	HLA-B38:02	DQAPSVEEI	0.7284	0.9431	6	15
XPR1-LHX4	chr1	180651547	chr1	180217419	291	HLA-B15:10	DQAPSVEEI	0.6471	0.5074	6	15
XPR1-LHX4	chr1	180651547	chr1	180217419	291	HLA-B13:02	QDQAPSVEEI	0.5483	0.8202	5	15
XPR1-LHX4	chr1	180651547	chr1	180217419	291	HLA-B13:01	QDQAPSVEEI	0.4283	0.9654	5	15
XPR1-LHX4	chr1	180651547	chr1	180217419	291	HLA-B13:02	AQDQAPSVEEI	0.9875	0.8557	4	15
XPR1-LHX4	chr1	180651547	chr1	180217419	291	HLA-B13:01	AQDQAPSVEEI	0.9628	0.9728	4	15
XPR1-LHX4	chr1	180651547	chr1	180217419	291	HLA-B39:09	DQAPSVEEI	0.9105	0.6519	6	15
XPR1-LHX4	chr1	180651547	chr1	180217419	291	HLA-B51:07	DQAPSVEEI	0.8978	0.9308	6	15
XPR1-LHX4	chr1	180651547	chr1	180217419	291	HLA-B39:08	DQAPSVEEI	0.8148	0.8691	6	15
XPR1-LHX4	chr1	180651547	chr1	180217419	291	HLA-B14:03	DQAPSVEEI	0.793	0.7509	6	15
XPR1-LHX4	chr1	180651547	chr1	180217419	291	HLA-B39:05	DQAPSVEEI	0.7305	0.8629	6	15
XPR1-LHX4	chr1	180651547	chr1	180217419	291	HLA-B48:03	DQAPSVEEI	0.6312	0.5036	6	15
XPR1-LHX4	chr1	180651547	chr1	180217419	291	HLA-C01:03	QAPSVEEI	0.996	0.9379	7	15
XPR1-LHX4	chr1	180651547	chr1	180217419	291	HLA-B39:31	DQAPSVEEI	0.9223	0.8728	6	15
XPR1-LHX4	chr1	180651547	chr1	180217419	291	HLA-B39:02	DQAPSVEEI	0.8842	0.8815	6	15
XPR1-LHX4	chr1	180651547	chr1	180217419	291	HLA-B39:11	DQAPSVEEI	0.7847	0.8152	6	15
XPR1-LHX4	chr1	180651547	chr1	180217419	291	HLA-B18:04	DQAPSVEEI	0.7527	0.8398	6	15
XPR1-LHX4	chr1	180651547	chr1	180217419	291	HLA-B38:05	DQAPSVEEI	0.7434	0.9375	6	15
XPR1-LHX4	chr1	180651547	chr1	180217419	291	HLA-B40:12	DQAPSVEEI	0.6312	0.5036	6	15
XPR1-LHX4	chr1	180651547	chr1	180217419	291	HLA-B15:09	DQAPSVEEI	0.4924	0.8145	6	15
XPR1-LHX4	chr1	180805852	chr1	180217420	1699	HLA-B39:06	THKEIPQC	0.9979	0.739	10	18
XPR1-LHX4	chr1	180805852	chr1	180217420	1699	HLA-B39:06	THKEIPQCA	0.9926	0.8164	10	19
XPR1-LHX4	chr1	180805852	chr1	180217420	1699	HLA-B39:24	THKEIPQCA	0.992	0.7046	10	19
XPR1-LHX4	chr1	180805852	chr1	180217420	1699	HLA-B39:01	THKEIPQCA	0.9785	0.9444	10	19
XPR1-LHX4	chr1	180805852	chr1	180217420	1699	HLA-A02:13	ALYSTHKEI	0.9722	0.6236	6	15
XPR1-LHX4	chr1	180805852	chr1	180217420	1699	HLA-A02:27	ALYSTHKEI	0.9566	0.5727	6	15
XPR1-LHX4	chr1	180805852	chr1	180217420	1699	HLA-B14:02	THKEIPQCA	0.9419	0.8868	10	19
XPR1-LHX4	chr1	180805852	chr1	180217420	1699	HLA-B14:01	THKEIPQCA	0.9419	0.8868	10	19
XPR1-LHX4	chr1	180805852	chr1	180217420	1699	HLA-A02:11	ALYSTHKEI	0.9385	0.6733	6	15
XPR1-LHX4	chr1	180805852	chr1	180217420	1699	HLA-A02:38	ALYSTHKEI	0.9324	0.5861	6	15
XPR1-LHX4	chr1	180805852	chr1	180217420	1699	HLA-A02:35	ALYSTHKEI	0.8051	0.6654	6	15
XPR1-LHX4	chr1	180805852	chr1	180217420	1699	HLA-B15:10	THKEIPQCA	0.6177	0.7969	10	19
XPR1-LHX4	chr1	180805852	chr1	180217420	1699	HLA-B15:37	THKEIPQCA	0.4676	0.7987	10	19
XPR1-LHX4	chr1	180805852	chr1	180217420	1699	HLA-B13:01	ALYSTHKEI	0.0342	0.9586	6	15
XPR1-LHX4	chr1	180805852	chr1	180217420	1699	HLA-B13:02	ALYSTHKEI	0.028	0.6267	6	15
XPR1-LHX4	chr1	180805852	chr1	180217420	1699	HLA-B50:01	KEIPQCAGC	0.0249	0.7191	12	21
XPR1-LHX4	chr1	180805852	chr1	180217420	1699	HLA-B52:01	ALYSTHKEI	0.0176	0.9575	6	15
XPR1-LHX4	chr1	180805852	chr1	180217420	1699	HLA-B08:09	THKEIPQCA	0.0119	0.6315	10	19
XPR1-LHX4	chr1	180805852	chr1	180217420	1699	HLA-B39:06	STHKEIPQCA	0.4358	0.7675	9	19
XPR1-LHX4	chr1	180805852	chr1	180217420	1699	HLA-B39:06	YSTHKEIPQCA	0.8287	0.7592	8	19
XPR1-LHX4	chr1	180805852	chr1	180217420	1699	HLA-B39:09	THKEIPQCA	0.9784	0.8467	10	19
XPR1-LHX4	chr1	180805852	chr1	180217420	1699	HLA-B39:12	THKEIPQCA	0.9783	0.947	10	19
XPR1-LHX4	chr1	180805852	chr1	180217420	1699	HLA-B39:05	THKEIPQCA	0.9455	0.9383	10	19
XPR1-LHX4	chr1	180805852	chr1	180217420	1699	HLA-B15:04	ALYSTHKEI	0.853	0.9206	6	15
XPR1-LHX4	chr1	180805852	chr1	180217420	1699	HLA-B14:03	THKEIPQCA	0.3157	0.8895	10	19
XPR1-LHX4	chr1	180805852	chr1	180217420	1699	HLA-B73:01	THKEIPQCA	0.2858	0.8045	10	19
XPR1-LHX4	chr1	180805852	chr1	180217420	1699	HLA-A02:03	ALYSTHKEI	0.9864	0.6445	6	15
XPR1-LHX4	chr1	180805852	chr1	180217420	1699	HLA-B39:31	THKEIPQCA	0.975	0.9437	10	19
XPR1-LHX4	chr1	180805852	chr1	180217420	1699	HLA-B15:09	THKEIPQCA	0.7505	0.8919	10	19
XPR1-LHX4	chr1	180805852	chr1	180217420	1699	HLA-B39:11	THKEIPQCA	0.6049	0.7599	10	19
XPR1-LHX4	chr1	180805852	chr1	180217420	1699	HLA-B50:04	KEIPQCAGC	0.0249	0.7191	12	21
XPR1-LHX4	chr1	180805852	chr1	180217420	1699	HLA-B50:05	KEIPQCAGC	0.0249	0.7191	12	21

Top

Potential FusionNeoAntigen Information of XPR1-LHX4 in HLA II

XPR1-LHX4_180805852_180217420.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)
XPR1-LHX4	chr1	180805852	chr1	180217420	1699	DRB5-0101	MVTFAALYSTHKEIP	1	16
XPR1-LHX4	chr1	180805852	chr1	180217420	1699	DRB5-0101	FMVTFAALYSTHKEI	0	15
XPR1-LHX4	chr1	180805852	chr1	180217420	1699	DRB5-0101	VTFAALYSTHKEIPQ	2	17
XPR1-LHX4	chr1	180805852	chr1	180217420	1699	DRB5-0102	MVTFAALYSTHKEIP	1	16
XPR1-LHX4	chr1	180805852	chr1	180217420	1699	DRB5-0102	FMVTFAALYSTHKEI	0	15
XPR1-LHX4	chr1	180805852	chr1	180217420	1699	DRB5-0103	MVTFAALYSTHKEIP	1	16
XPR1-LHX4	chr1	180805852	chr1	180217420	1699	DRB5-0104	MVTFAALYSTHKEIP	1	16
XPR1-LHX4	chr1	180805852	chr1	180217420	1699	DRB5-0105	MVTFAALYSTHKEIP	1	16
XPR1-LHX4	chr1	180805852	chr1	180217420	1699	DRB5-0105	FMVTFAALYSTHKEI	0	15
XPR1-LHX4	chr1	180805852	chr1	180217420	1699	DRB5-0105	VTFAALYSTHKEIPQ	2	17
XPR1-LHX4	chr1	180805852	chr1	180217420	1699	DRB5-0108N	MVTFAALYSTHKEIP	1	16
XPR1-LHX4	chr1	180805852	chr1	180217420	1699	DRB5-0108N	FMVTFAALYSTHKEI	0	15
XPR1-LHX4	chr1	180805852	chr1	180217420	1699	DRB5-0113	MVTFAALYSTHKEIP	1	16
XPR1-LHX4	chr1	180805852	chr1	180217420	1699	DRB5-0113	FMVTFAALYSTHKEI	0	15
XPR1-LHX4	chr1	180805852	chr1	180217420	1699	DRB5-0113	VTFAALYSTHKEIPQ	2	17
XPR1-LHX4	chr1	180805852	chr1	180217420	1699	DRB5-0114	MVTFAALYSTHKEIP	1	16
XPR1-LHX4	chr1	180805852	chr1	180217420	1699	DRB5-0114	FMVTFAALYSTHKEI	0	15
XPR1-LHX4	chr1	180805852	chr1	180217420	1699	DRB5-0114	VTFAALYSTHKEIPQ	2	17

Top

Fusion breakpoint peptide structures of XPR1-LHX4

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
424	ALYSTHKEIPQCAG	XPR1	LHX4	chr1	180805852	chr1	180217420	1699

File name	BPseq	Hgene	Tgene	Hchr	Hbp	Tchr	Tbp	AAlen
1340	DQAPSVEEIPQCAG	XPR1	LHX4	chr1	180651547	chr1	180217419	291

Top

Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of XPR1-LHX4

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	424	ALYSTHKEIPQCAG	-6.69561	-6.80901
HLA-B14:02	3BVN	424	ALYSTHKEIPQCAG	-4.57314	-5.60844
HLA-B52:01	3W39	424	ALYSTHKEIPQCAG	-8.26982	-8.38322
HLA-B52:01	3W39	424	ALYSTHKEIPQCAG	-4.20619	-5.24149
HLA-A11:01	4UQ2	424	ALYSTHKEIPQCAG	-6.38936	-6.50276
HLA-A11:01	4UQ2	424	ALYSTHKEIPQCAG	-5.4102	-6.4455
HLA-A24:02	5HGA	424	ALYSTHKEIPQCAG	-7.10684	-7.22024
HLA-A24:02	5HGA	424	ALYSTHKEIPQCAG	-5.37582	-6.41112
HLA-B44:05	3DX8	424	ALYSTHKEIPQCAG	-5.61918	-5.73258
HLA-B44:05	3DX8	424	ALYSTHKEIPQCAG	-4.56468	-5.59998
HLA-B14:02	3BVN	1340	DQAPSVEEIPQCAG	-5.93943	-6.05283
HLA-B14:02	3BVN	1340	DQAPSVEEIPQCAG	-4.10869	-5.14399
HLA-B52:01	3W39	1340	DQAPSVEEIPQCAG	-7.1889	-7.3023
HLA-B52:01	3W39	1340	DQAPSVEEIPQCAG	-5.67749	-6.71279
HLA-A24:02	5HGA	1340	DQAPSVEEIPQCAG	-8.1699	-8.2833
HLA-A24:02	5HGA	1340	DQAPSVEEIPQCAG	-4.72047	-5.75577
HLA-B44:05	3DX8	1340	DQAPSVEEIPQCAG	-5.70652	-5.81992
HLA-B44:05	3DX8	1340	DQAPSVEEIPQCAG	-5.03111	-6.06641

Top

Vaccine Design for the FusionNeoAntigens of XPR1-LHX4

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
XPR1-LHX4	chr1	180651547	chr1	180217419	4	15	AQDQAPSVEEI	CTCAGGACCAGGCACCTTCTGTGGAAGAGATTC
XPR1-LHX4	chr1	180651547	chr1	180217419	5	15	QDQAPSVEEI	AGGACCAGGCACCTTCTGTGGAAGAGATTC
XPR1-LHX4	chr1	180651547	chr1	180217419	6	15	DQAPSVEEI	ACCAGGCACCTTCTGTGGAAGAGATTC
XPR1-LHX4	chr1	180651547	chr1	180217419	7	15	QAPSVEEI	AGGCACCTTCTGTGGAAGAGATTC
XPR1-LHX4	chr1	180805852	chr1	180217420	10	18	THKEIPQC	CTCACAAAGAGATTCCCCAGTGCG
XPR1-LHX4	chr1	180805852	chr1	180217420	10	19	THKEIPQCA	CTCACAAAGAGATTCCCCAGTGCGCTG
XPR1-LHX4	chr1	180805852	chr1	180217420	12	21	KEIPQCAGC	AAGAGATTCCCCAGTGCGCTGGCTGCA
XPR1-LHX4	chr1	180805852	chr1	180217420	6	15	ALYSTHKEI	CCCTTTACAGCACTCACAAAGAGATTC
XPR1-LHX4	chr1	180805852	chr1	180217420	8	19	YSTHKEIPQCA	ACAGCACTCACAAAGAGATTCCCCAGTGCGCTG
XPR1-LHX4	chr1	180805852	chr1	180217420	9	19	STHKEIPQCA	GCACTCACAAAGAGATTCCCCAGTGCGCTG

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
XPR1-LHX4	chr1	180805852	chr1	180217420	0	15	FMVTFAALYSTHKEI	TCATGGTGACGTTTGCAGCCCTTTACAGCACTCACAAAGAGATTC
XPR1-LHX4	chr1	180805852	chr1	180217420	1	16	MVTFAALYSTHKEIP	TGGTGACGTTTGCAGCCCTTTACAGCACTCACAAAGAGATTCCCC
XPR1-LHX4	chr1	180805852	chr1	180217420	2	17	VTFAALYSTHKEIPQ	TGACGTTTGCAGCCCTTTACAGCACTCACAAAGAGATTCCCCAGT

Top

Information of the samples that have these potential fusion neoantigens of XPR1-LHX4

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
OV	XPR1-LHX4	chr1	180651547	ENST00000367589	chr1	180217419	ENST00000263726	TCGA-13-1506
UCEC	XPR1-LHX4	chr1	180805852	ENST00000367590	chr1	180217420	ENST00000263726	TCGA-D1-A3DG-01A

Top

Potential target of CAR-T therapy development for XPR1-LHX4

Predicted 3D structure. We used RoseTTAFold.

528_XPR1-LHX4_c7cb0_pred.pdb

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

XPR1

chr1:180805852

chr1:180217420

ENST00000367590

237_257

500

697.0

Transmembrane

Helical

Hgene

XPR1

chr1:180805852

chr1:180217420

ENST00000367590

265_285

500

697.0

Transmembrane

Helical

Hgene

XPR1

chr1:180805852

chr1:180217420

ENST00000367590

319_339

500

697.0

Transmembrane

Helical

Hgene

XPR1

chr1:180805852

chr1:180217420

ENST00000367590

346_368

500

697.0

Transmembrane

Helical

Hgene

XPR1

chr1:180805852

chr1:180217420

ENST00000367590

377_397

500

697.0

Transmembrane

Helical

Hgene

XPR1

chr1:180805852

chr1:180217420

ENST00000367590

403_423

500

697.0

Transmembrane

Helical

Hgene

XPR1

chr1:180805852

chr1:180217420

ENST00000367590

474_496

500

697.0

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
XPR1	chr1	180651547	ENST00000367589	LHX4	chr1	180217419	ENST00000263726
XPR1	chr1	180805852	ENST00000367590	LHX4	chr1	180217420	ENST00000263726

Top

Related Drugs to XPR1-LHX4

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

Hgene

Tgene

Drug

Source

PMID

Top

Related Diseases to XPR1-LHX4

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)