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Fusion Protein:UAP1-LMX1A

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: UAP1-LMX1A
	FusionPDB ID: 95787
	FusionGDB2.0 ID: 95787
		Hgene	Tgene
	Gene symbol	UAP1	LMX1A
	Gene ID	6675	4009
	Gene name	UDP-N-acetylglucosamine pyrophosphorylase 1	LIM homeobox transcription factor 1 alpha
	Synonyms	AGX\|AGX1\|AGX2\|SPAG2	DFNA7\|LMX1\|LMX1.1
	Cytomap	1q23.3	1q23.3
	Type of gene	protein-coding	protein-coding
	Description	UDP-N-acetylhexosamine pyrophosphorylaseUDP-N-acetylglucosamine diphosphorylase 1UDP-N-acetylhexosamine pyrophosphorylase 1antigen Xsperm associated antigen 2testis tissue sperm-binding protein Li 37a	LIM homeobox transcription factor 1-alphaLIM/homeobox protein 1.1
	Modification date	20200313	20200322
	UniProtAcc	.	Q8TE12 Main function of 5'-partner protein: FUNCTION: Acts as a transcriptional activator by binding to an A/T-rich sequence, the FLAT element, in the insulin gene promoter. Required for development of the roof plate and, in turn, for specification of dorsal cell fates in the CNS and developing vertebrae (By similarity). {ECO:0000250}.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000271469, ENST00000367924, ENST00000367925, ENST00000367926, ENST00000476240,	ENST00000489443, ENST00000294816, ENST00000342310, ENST00000367893,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	12 X 6 X 7=504	3 X 2 X 2=12
	# samples	13	3
	** MAII score	log2(13/504*10)=-1.95491211047146 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(3/12*10)=1.32192809488736 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0
Fusion gene context	PubMed: UAP1 [Title/Abstract] AND LMX1A [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: UAP1 [Title/Abstract] AND LMX1A [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	UAP1(162560301)-LMX1A(165218877), # samples:2
Anticipated loss of major functional domain due to fusion event.	UAP1-LMX1A 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. UAP1-LMX1A 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. UAP1-LMX1A 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. UAP1-LMX1A 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/chr1:162560301/chr1:165218877)
- 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 UAP1 (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 LMX1A (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)
ENST00000271469	UAP1	chr1	162560301	+	ENST00000342310	LMX1A	chr1	165218877	-	4559	1660	302	2545	747
ENST00000271469	UAP1	chr1	162560301	+	ENST00000294816	LMX1A	chr1	165218877	-	4553	1660	302	2545	747
ENST00000271469	UAP1	chr1	162560301	+	ENST00000367893	LMX1A	chr1	165218877	-	2552	1660	302	2545	747
ENST00000367926	UAP1	chr1	162560301	+	ENST00000342310	LMX1A	chr1	165218877	-	4559	1660	302	2545	747
ENST00000367926	UAP1	chr1	162560301	+	ENST00000294816	LMX1A	chr1	165218877	-	4553	1660	302	2545	747
ENST00000367926	UAP1	chr1	162560301	+	ENST00000367893	LMX1A	chr1	165218877	-	2552	1660	302	2545	747
ENST00000367924	UAP1	chr1	162560301	+	ENST00000342310	LMX1A	chr1	165218877	-	4289	1390	32	2275	747
ENST00000367924	UAP1	chr1	162560301	+	ENST00000294816	LMX1A	chr1	165218877	-	4283	1390	32	2275	747
ENST00000367924	UAP1	chr1	162560301	+	ENST00000367893	LMX1A	chr1	165218877	-	2282	1390	32	2275	747
ENST00000367925	UAP1	chr1	162560301	+	ENST00000342310	LMX1A	chr1	165218877	-	4289	1390	32	2275	747
ENST00000367925	UAP1	chr1	162560301	+	ENST00000294816	LMX1A	chr1	165218877	-	4283	1390	32	2275	747
ENST00000367925	UAP1	chr1	162560301	+	ENST00000367893	LMX1A	chr1	165218877	-	2282	1390	32	2275	747

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
ENST00000271469	ENST00000342310	UAP1	chr1	162560301	+	LMX1A	chr1	165218877	-	0.000594624	0.9994054
ENST00000271469	ENST00000294816	UAP1	chr1	162560301	+	LMX1A	chr1	165218877	-	0.000599323	0.99940073
ENST00000271469	ENST00000367893	UAP1	chr1	162560301	+	LMX1A	chr1	165218877	-	0.003075986	0.996924
ENST00000367926	ENST00000342310	UAP1	chr1	162560301	+	LMX1A	chr1	165218877	-	0.000594624	0.9994054
ENST00000367926	ENST00000294816	UAP1	chr1	162560301	+	LMX1A	chr1	165218877	-	0.000599323	0.99940073
ENST00000367926	ENST00000367893	UAP1	chr1	162560301	+	LMX1A	chr1	165218877	-	0.003075986	0.996924
ENST00000367924	ENST00000342310	UAP1	chr1	162560301	+	LMX1A	chr1	165218877	-	0.000616692	0.99938333
ENST00000367924	ENST00000294816	UAP1	chr1	162560301	+	LMX1A	chr1	165218877	-	0.000621894	0.9993781
ENST00000367924	ENST00000367893	UAP1	chr1	162560301	+	LMX1A	chr1	165218877	-	0.003701224	0.99629885
ENST00000367925	ENST00000342310	UAP1	chr1	162560301	+	LMX1A	chr1	165218877	-	0.000616692	0.99938333
ENST00000367925	ENST00000294816	UAP1	chr1	162560301	+	LMX1A	chr1	165218877	-	0.000621894	0.9993781
ENST00000367925	ENST00000367893	UAP1	chr1	162560301	+	LMX1A	chr1	165218877	-	0.003701224	0.99629885

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 UAP1-LMX1A

+/-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
UAP1	chr1	162560301	LMX1A	chr1	165218877	1390	452	FIDENGSRLPAIPRLFAVKCGGCFEA
UAP1	chr1	162560301	LMX1A	chr1	165218877	1660	452	FIDENGSRLPAIPRLFAVKCGGCFEA

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Potential FusionNeoAntigen Information of UAP1-LMX1A 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.

UAP1-LMX1A_162560301_165218877.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)
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-A02:17	RLPAIPRL	0.9805	0.5389	7	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B27:02	SRLPAIPRL	0.9999	0.7403	6	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B27:05	SRLPAIPRL	0.9999	0.9287	6	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B27:04	SRLPAIPRL	0.9999	0.7729	6	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B39:24	SRLPAIPRL	0.9995	0.6006	6	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B39:06	SRLPAIPRL	0.999	0.6785	6	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B39:01	SRLPAIPRL	0.9983	0.8711	6	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B14:01	SRLPAIPRL	0.998	0.7965	6	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B14:02	SRLPAIPRL	0.998	0.7965	6	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B38:01	SRLPAIPRL	0.9963	0.9389	6	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-A31:08	RLPAIPRLF	0.9954	0.5629	7	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B38:02	SRLPAIPRL	0.9953	0.9435	6	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-A30:08	GSRLPAIPR	0.9918	0.8205	5	14
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-A32:13	RLPAIPRLF	0.9905	0.9526	7	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-A74:11	GSRLPAIPR	0.9857	0.7677	5	14
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-A74:09	GSRLPAIPR	0.9857	0.7677	5	14
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-A74:03	GSRLPAIPR	0.9857	0.7677	5	14
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B15:01	RLPAIPRLF	0.9726	0.936	7	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-A31:02	GSRLPAIPR	0.9542	0.777	5	14
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-A31:06	GSRLPAIPR	0.9134	0.5758	5	14
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B58:02	RLPAIPRLF	0.8584	0.9622	7	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-A24:14	RLPAIPRLF	0.8405	0.5396	7	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B15:10	SRLPAIPRL	0.8098	0.8107	6	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B47:01	SRLPAIPRL	0.6566	0.7393	6	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B15:18	SRLPAIPRL	0.5841	0.8775	6	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B15:37	SRLPAIPRL	0.5359	0.832	6	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B13:01	RLPAIPRLF	0.0715	0.9691	7	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B07:10	SRLPAIPRL	0.0134	0.5359	6	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B27:05	SRLPAIPRLF	1	0.9021	6	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B27:02	SRLPAIPRLF	1	0.6098	6	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B27:04	SRLPAIPRLF	1	0.7516	6	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B27:02	GSRLPAIPRL	0.9858	0.728	5	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B27:05	GSRLPAIPRL	0.9858	0.9315	5	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B27:04	GSRLPAIPRL	0.9856	0.7884	5	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B27:07	GSRLPAIPRL	0.9695	0.5947	5	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B27:02	GSRLPAIPRLF	0.9998	0.6524	5	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-A02:11	RLPAIPRLFAV	0.9799	0.6016	7	18
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-A02:60	RLPAIPRLFAV	0.9776	0.592	7	18
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-A02:04	RLPAIPRLFAV	0.9703	0.7618	7	18
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-A02:20	RLPAIPRLFAV	0.8916	0.5899	7	18
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B42:02	LPAIPRLF	0.9967	0.5221	8	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B42:01	LPAIPRLF	0.9914	0.5135	8	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-A02:07	RLPAIPRL	0.9816	0.8211	7	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C01:17	RLPAIPRL	0.9682	0.9736	7	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C01:30	RLPAIPRL	0.8956	0.9787	7	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B27:14	SRLPAIPRL	0.9999	0.8293	6	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C07:95	SRLPAIPRL	0.9996	0.7902	6	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C07:05	SRLPAIPRL	0.9996	0.9493	6	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C07:27	SRLPAIPRL	0.9994	0.9738	6	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B39:09	SRLPAIPRL	0.9991	0.7064	6	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B27:03	SRLPAIPRL	0.9988	0.9342	6	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C07:13	SRLPAIPRL	0.9984	0.9526	6	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C07:29	SRLPAIPRL	0.9978	0.973	6	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B39:12	SRLPAIPRL	0.9976	0.8791	6	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B39:05	SRLPAIPRL	0.9958	0.8671	6	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-A31:01	GSRLPAIPR	0.989	0.7432	5	14
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B73:01	SRLPAIPRL	0.986	0.6977	6	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B15:07	RLPAIPRLF	0.9658	0.809	7	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C07:46	SRLPAIPRL	0.9637	0.8897	6	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B42:02	LPAIPRLFA	0.9455	0.5483	8	17
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C07:19	RLPAIPRLF	0.9204	0.7724	7	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B42:01	LPAIPRLFA	0.918	0.5419	8	17
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B15:04	RLPAIPRLF	0.8981	0.9313	7	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C07:67	RLPAIPRLF	0.8813	0.948	7	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C07:80	RLPAIPRLF	0.8813	0.948	7	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C07:10	RLPAIPRLF	0.8712	0.9527	7	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C07:19	SRLPAIPRL	0.8686	0.8052	6	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C07:80	SRLPAIPRL	0.858	0.928	6	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C07:67	SRLPAIPRL	0.858	0.928	6	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C07:29	RLPAIPRLF	0.8566	0.9648	7	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C07:10	SRLPAIPRL	0.8364	0.9012	6	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C07:13	RLPAIPRLF	0.7872	0.9031	7	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C04:14	SRLPAIPRL	0.4532	0.9331	6	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B14:03	SRLPAIPRL	0.3895	0.8429	6	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C12:16	SRLPAIPRL	0.0976	0.9387	6	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C01:17	RLPAIPRLF	0.089	0.97	7	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C01:30	RLPAIPRLF	0.0691	0.9782	7	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B27:14	SRLPAIPRLF	1	0.794	6	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C07:95	SRLPAIPRLF	0.9998	0.7739	6	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C07:05	SRLPAIPRLF	0.9997	0.9381	6	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B27:03	SRLPAIPRLF	0.9996	0.9135	6	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C07:27	SRLPAIPRLF	0.9993	0.9707	6	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C07:29	SRLPAIPRLF	0.9983	0.961	6	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C07:19	SRLPAIPRLF	0.9978	0.778	6	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C07:46	SRLPAIPRLF	0.9976	0.8717	6	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C07:10	SRLPAIPRLF	0.9963	0.888	6	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C07:80	SRLPAIPRLF	0.9961	0.9152	6	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C07:67	SRLPAIPRLF	0.9961	0.9152	6	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B42:02	LPAIPRLFAV	0.9896	0.6993	8	18
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B27:14	GSRLPAIPRL	0.9878	0.8606	5	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B42:01	LPAIPRLFAV	0.9864	0.6915	8	18
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C12:16	SRLPAIPRLF	0.9701	0.9357	6	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B27:03	GSRLPAIPRL	0.8508	0.9386	5	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B27:14	SRLPAIPRLFA	0.9999	0.7286	6	17
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B73:01	SRLPAIPRLFA	0.9982	0.7553	6	17
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-A02:07	RLPAIPRLFAV	0.9775	0.6664	7	18
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B35:17	LPAIPRLF	0.9981	0.6039	8	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B35:30	LPAIPRLF	0.9981	0.6039	8	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B35:24	LPAIPRLF	0.9979	0.828	8	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B35:11	LPAIPRLF	0.9959	0.8577	8	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C01:03	RLPAIPRL	0.9819	0.9019	7	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C01:02	RLPAIPRL	0.9704	0.9728	7	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B18:07	LPAIPRLF	0.9454	0.9075	8	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B27:08	SRLPAIPRL	0.9999	0.8191	6	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B27:10	SRLPAIPRL	0.9999	0.8755	6	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B27:09	SRLPAIPRL	0.9999	0.9314	6	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B27:06	SRLPAIPRL	0.9999	0.7625	6	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C07:01	SRLPAIPRL	0.9997	0.7982	6	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B39:31	SRLPAIPRL	0.9984	0.8722	6	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B39:02	SRLPAIPRL	0.998	0.9013	6	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B38:05	SRLPAIPRL	0.9963	0.9389	6	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-A32:01	RLPAIPRLF	0.9952	0.9816	7	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-A30:01	GSRLPAIPR	0.9926	0.908	5	14
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C07:17	SRLPAIPRL	0.9926	0.9426	6	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-A74:01	GSRLPAIPR	0.9857	0.7677	5	14
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C06:08	SRLPAIPRL	0.9819	0.983	6	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B15:135	RLPAIPRLF	0.9776	0.9389	7	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C07:04	SRLPAIPRL	0.9766	0.9566	6	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B15:50	RLPAIPRLF	0.9761	0.9676	7	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B15:27	RLPAIPRLF	0.9739	0.9371	7	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B15:125	RLPAIPRLF	0.9726	0.936	7	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B15:33	RLPAIPRLF	0.9726	0.936	7	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B15:34	RLPAIPRLF	0.9726	0.936	7	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B15:39	RLPAIPRLF	0.9679	0.8615	7	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B15:24	RLPAIPRLF	0.9625	0.9155	7	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B15:35	RLPAIPRLF	0.9619	0.9248	7	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C07:22	SRLPAIPRL	0.9474	0.7813	6	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B58:06	RLPAIPRLF	0.9337	0.8645	7	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C07:02	RLPAIPRLF	0.8813	0.948	7	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C07:02	SRLPAIPRL	0.858	0.928	6	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B15:09	SRLPAIPRL	0.6896	0.7197	6	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C03:67	SRLPAIPRL	0.6462	0.9854	6	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B39:11	SRLPAIPRL	0.6299	0.8009	6	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C04:04	SRLPAIPRL	0.5255	0.8814	6	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C06:02	RLPAIPRLF	0.4896	0.9964	7	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C06:17	RLPAIPRLF	0.4896	0.9964	7	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C06:06	SRLPAIPRL	0.4428	0.9908	6	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B67:01	LPAIPRLFA	0.4343	0.7735	8	17
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C06:08	RLPAIPRLF	0.4255	0.9949	7	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C06:06	RLPAIPRLF	0.3941	0.9936	7	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C18:01	SRLPAIPRL	0.3004	0.9297	6	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C04:04	RLPAIPRLF	0.2824	0.8159	7	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C06:02	SRLPAIPRL	0.1078	0.9859	6	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C06:17	SRLPAIPRL	0.1078	0.9859	6	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C01:02	RLPAIPRLF	0.0694	0.9691	7	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C01:03	RLPAIPRLF	0.0412	0.9073	7	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B27:10	SRLPAIPRLF	1	0.8729	6	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B27:08	SRLPAIPRLF	1	0.7766	6	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B27:06	SRLPAIPRLF	0.9999	0.7375	6	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B27:09	SRLPAIPRLF	0.9998	0.8986	6	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C07:01	SRLPAIPRLF	0.9998	0.7507	6	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C07:22	SRLPAIPRLF	0.9993	0.7769	6	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C06:08	SRLPAIPRLF	0.998	0.9804	6	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C07:02	SRLPAIPRLF	0.9961	0.9152	6	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B27:10	GSRLPAIPRL	0.985	0.8657	5	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B78:02	LPAIPRLFAV	0.9841	0.5341	8	18
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C06:06	SRLPAIPRLF	0.9838	0.9866	6	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B27:08	GSRLPAIPRL	0.9797	0.8648	5	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B27:06	GSRLPAIPRL	0.9731	0.7746	5	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B27:09	GSRLPAIPRL	0.9603	0.9186	5	15
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C06:02	SRLPAIPRLF	0.9572	0.9843	6	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-C06:17	SRLPAIPRLF	0.9572	0.9843	6	16
UAP1-LMX1A	chr1	162560301	chr1	165218877	1660	HLA-B27:09	NGSRLPAIPRL	0.9972	0.7559	4	15

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Potential FusionNeoAntigen Information of UAP1-LMX1A in HLA II

Potential FusionNeoAntigen Information
* We used NetMHCIIpan v4.1 (%rank<0.5).

Fusion gene

Hchr

Hbp

Tgene

Tchr

Tbp

HLA II

FusionNeoAntigen peptide

Neoantigen start (at BP 13)

Neoantigen end (at BP 13)

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Fusion breakpoint peptide structures of UAP1-LMX1A

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
8965	SRLPAIPRLFAVKC	UAP1	LMX1A	chr1	162560301	chr1	165218877	1660

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of UAP1-LMX1A

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	8965	SRLPAIPRLFAVKC	-7.15543	-7.26883
HLA-B14:02	3BVN	8965	SRLPAIPRLFAVKC	-4.77435	-5.80965
HLA-B52:01	3W39	8965	SRLPAIPRLFAVKC	-6.80875	-6.92215
HLA-B52:01	3W39	8965	SRLPAIPRLFAVKC	-4.20386	-5.23916
HLA-A11:01	4UQ2	8965	SRLPAIPRLFAVKC	-7.5194	-8.5547
HLA-A11:01	4UQ2	8965	SRLPAIPRLFAVKC	-6.9601	-7.0735
HLA-A24:02	5HGA	8965	SRLPAIPRLFAVKC	-7.52403	-7.63743
HLA-A24:02	5HGA	8965	SRLPAIPRLFAVKC	-5.82433	-6.85963
HLA-B27:05	6PYJ	8965	SRLPAIPRLFAVKC	-3.28285	-4.31815
HLA-B44:05	3DX8	8965	SRLPAIPRLFAVKC	-5.91172	-6.94702
HLA-B44:05	3DX8	8965	SRLPAIPRLFAVKC	-4.24346	-4.35686

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Vaccine Design for the FusionNeoAntigens of UAP1-LMX1A

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
UAP1-LMX1A	chr1	162560301	chr1	165218877	4	15	NGSRLPAIPRL	TGGCTCTCGCCTTCCAGCAATTCCCCGGCTGTT
UAP1-LMX1A	chr1	162560301	chr1	165218877	5	14	GSRLPAIPR	CTCTCGCCTTCCAGCAATTCCCCGGCT
UAP1-LMX1A	chr1	162560301	chr1	165218877	5	15	GSRLPAIPRL	CTCTCGCCTTCCAGCAATTCCCCGGCTGTT
UAP1-LMX1A	chr1	162560301	chr1	165218877	5	16	GSRLPAIPRLF	CTCTCGCCTTCCAGCAATTCCCCGGCTGTTTGC
UAP1-LMX1A	chr1	162560301	chr1	165218877	6	15	SRLPAIPRL	TCGCCTTCCAGCAATTCCCCGGCTGTT
UAP1-LMX1A	chr1	162560301	chr1	165218877	6	16	SRLPAIPRLF	TCGCCTTCCAGCAATTCCCCGGCTGTTTGC
UAP1-LMX1A	chr1	162560301	chr1	165218877	6	17	SRLPAIPRLFA	TCGCCTTCCAGCAATTCCCCGGCTGTTTGCTGT
UAP1-LMX1A	chr1	162560301	chr1	165218877	7	15	RLPAIPRL	CCTTCCAGCAATTCCCCGGCTGTT
UAP1-LMX1A	chr1	162560301	chr1	165218877	7	16	RLPAIPRLF	CCTTCCAGCAATTCCCCGGCTGTTTGC
UAP1-LMX1A	chr1	162560301	chr1	165218877	7	18	RLPAIPRLFAV	CCTTCCAGCAATTCCCCGGCTGTTTGCTGTTAA
UAP1-LMX1A	chr1	162560301	chr1	165218877	8	16	LPAIPRLF	TCCAGCAATTCCCCGGCTGTTTGC
UAP1-LMX1A	chr1	162560301	chr1	165218877	8	17	LPAIPRLFA	TCCAGCAATTCCCCGGCTGTTTGCTGT
UAP1-LMX1A	chr1	162560301	chr1	165218877	8	18	LPAIPRLFAV	TCCAGCAATTCCCCGGCTGTTTGCTGTTAA

mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.

Fusion gene

Hchr

Hbp

Tchr

Tbp

Start in +/-13AA

End in +/-13AA

FusionNeoAntigen peptide

FusionNEoAntigen RNA sequence

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Information of the samples that have these potential fusion neoantigens of UAP1-LMX1A

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
BRCA	UAP1-LMX1A	chr1	162560301	ENST00000271469	chr1	165218877	ENST00000294816	TCGA-A2-A0T7-01A

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Potential target of CAR-T therapy development for UAP1-LMX1A

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 UAP1-LMX1A

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 UAP1-LMX1A

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)