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Fusion Protein:AMD1-FIG4

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: AMD1-FIG4
	FusionPDB ID: 4194
	FusionGDB2.0 ID: 4194
		Hgene	Tgene
	Gene symbol	AMD1	FIG4
	Gene ID	262	9896
	Gene name	adenosylmethionine decarboxylase 1	FIG4 phosphoinositide 5-phosphatase
	Synonyms	ADOMETDC\|AMD\|SAMDC	ALS11\|BTOP\|CMT4J\|KIAA0274\|SAC3\|YVS\|dJ249I4.1
	Cytomap	6q21	6q21
	Type of gene	protein-coding	protein-coding
	Description	S-adenosylmethionine decarboxylase proenzymeS-adenosylmethionine decarboxylase 1	polyphosphoinositide phosphataseFIG4 homolog, SAC domain containing lipid phosphataseFIG4 homolog, SAC1 domain containing lipid phosphataseFIG4 homolog, SAC1 lipid phosphatase domain containingSAC domain-containing protein 3Sac domain-containing inos
	Modification date	20200313	20200328
	UniProtAcc	P17707 Main function of 5'-partner protein: FUNCTION: Essential for biosynthesis of the polyamines spermidine and spermine. Promotes maintenance and self-renewal of embryonic stem cells, by maintaining spermine levels. {ECO:0000250\|UniProtKB:P0DMN7}.	Q92562 Main function of 5'-partner protein: FUNCTION: The PI(3,5)P2 regulatory complex regulates both the synthesis and turnover of phosphatidylinositol 3,5-bisphosphate (PtdIns(3,5)P2). In vitro, hydrolyzes all three D5-phosphorylated polyphosphoinositide substrates in the order PtdIns(4,5)P2 > PtdIns(3,5)P2 > PtdIns(3,4,5)P3. Plays a role in the biogenesis of endosome carrier vesicles (ECV) / multivesicular bodies (MVB) transport intermediates from early endosomes. {ECO:0000269\|PubMed:17556371}.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000368877, ENST00000368885, ENST00000451850, ENST00000368882, ENST00000368876,	ENST00000368941, ENST00000230124, ENST00000441478,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	15 X 13 X 4=780	6 X 10 X 5=300
	# samples	15	7
	** MAII score	log2(15/780*10)=-2.37851162325373 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(7/300*10)=-2.09953567355091 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: AMD1 [Title/Abstract] AND FIG4 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: AMD1 [Title/Abstract] AND FIG4 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	AMD1(111196418)-FIG4(110146291), # samples:2
Anticipated loss of major functional domain due to fusion event.	AMD1-FIG4 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. AMD1-FIG4 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. AMD1-FIG4 seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF. AMD1-FIG4 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF. AMD1-FIG4 seems lost the major protein functional domain in Tgene partner, which is a cell metabolism gene 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

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr6:111196418/chr6:110146291)
- 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 AMD1 (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 FIG4 (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)
ENST00000368885	AMD1	chr6	111196418	+	ENST00000230124	FIG4	chr6	110146291	+	787	446	294	623	109
ENST00000451850	AMD1	chr6	111196418	+	ENST00000230124	FIG4	chr6	110146291	+	773	432	280	609	109
ENST00000368877	AMD1	chr6	111196418	+	ENST00000230124	FIG4	chr6	110146291	+	772	431	279	608	109
ENST00000368885	AMD1	chr6	111196417	+	ENST00000230124	FIG4	chr6	110146290	+	787	446	294	623	109
ENST00000451850	AMD1	chr6	111196417	+	ENST00000230124	FIG4	chr6	110146290	+	773	432	280	609	109
ENST00000368877	AMD1	chr6	111196417	+	ENST00000230124	FIG4	chr6	110146290	+	772	431	279	608	109

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
ENST00000368885	ENST00000230124	AMD1	chr6	111196418	+	FIG4	chr6	110146291	+	0.072592795	0.9274072
ENST00000451850	ENST00000230124	AMD1	chr6	111196418	+	FIG4	chr6	110146291	+	0.07411107	0.9258889
ENST00000368877	ENST00000230124	AMD1	chr6	111196418	+	FIG4	chr6	110146291	+	0.074721694	0.92527825
ENST00000368885	ENST00000230124	AMD1	chr6	111196417	+	FIG4	chr6	110146290	+	0.072592795	0.9274072
ENST00000451850	ENST00000230124	AMD1	chr6	111196417	+	FIG4	chr6	110146290	+	0.07411107	0.9258889
ENST00000368877	ENST00000230124	AMD1	chr6	111196417	+	FIG4	chr6	110146290	+	0.074721694	0.92527825

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 AMD1-FIG4

+/-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
AMD1	chr6	111196417	FIG4	chr6	110146290	431	50	DANQGSGDLRTIPRTPISAFSQDNIY
AMD1	chr6	111196417	FIG4	chr6	110146290	432	50	DANQGSGDLRTIPRTPISAFSQDNIY
AMD1	chr6	111196417	FIG4	chr6	110146290	446	50	DANQGSGDLRTIPRTPISAFSQDNIY
AMD1	chr6	111196418	FIG4	chr6	110146291	431	50	DANQGSGDLRTIPRTPISAFSQDNIY
AMD1	chr6	111196418	FIG4	chr6	110146291	432	50	DANQGSGDLRTIPRTPISAFSQDNIY
AMD1	chr6	111196418	FIG4	chr6	110146291	446	50	DANQGSGDLRTIPRTPISAFSQDNIY

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Potential FusionNeoAntigen Information of AMD1-FIG4 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.

AMD1-FIG4_111196417_110146290.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)
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B08:09	IPRTPISA	0.9961	0.7372	11	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B07:02	PRTPISAF	0.729	0.585	12	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B35:01	IPRTPISAF	0.9895	0.8369	11	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-A30:08	RTIPRTPIS	0.981	0.7855	9	18
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B35:08	IPRTPISAF	0.9808	0.8458	11	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B35:05	IPRTPISAF	0.9569	0.5591	11	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B15:02	IPRTPISAF	0.9528	0.866	11	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B35:03	IPRTPISAF	0.9341	0.8678	11	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B08:01	IPRTPISAF	0.919	0.6982	11	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B08:09	IPRTPISAF	0.8461	0.715	11	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B15:18	IPRTPISAF	0.7284	0.6701	11	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B35:04	IPRTPISAF	0.5691	0.9258	11	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B35:02	IPRTPISAF	0.5691	0.9258	11	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B46:01	TIPRTPISAF	0.9974	0.577	10	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-A30:08	RTIPRTPISA	0.9924	0.9231	9	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B07:02	TIPRTPISAF	0.9645	0.6433	10	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B07:05	TIPRTPISAF	0.9598	0.5303	10	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B35:05	TIPRTPISAF	0.9553	0.7977	10	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B35:01	TIPRTPISAF	0.9492	0.924	10	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B81:01	TIPRTPISAF	0.7514	0.5756	10	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B82:01	TIPRTPISAF	0.6889	0.5532	10	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B57:01	RTIPRTPISAF	0.9999	0.991	9	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B58:02	RTIPRTPISAF	0.9997	0.9765	9	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B15:01	RTIPRTPISAF	0.9995	0.9571	9	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B15:17	RTIPRTPISAF	0.9995	0.9681	9	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B15:25	RTIPRTPISAF	0.9993	0.9648	9	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B15:16	RTIPRTPISAF	0.9991	0.8948	9	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B58:01	RTIPRTPISAF	0.999	0.9757	9	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B57:03	RTIPRTPISAF	0.999	0.9946	9	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-A31:08	RTIPRTPISAF	0.9986	0.7256	9	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B46:01	RTIPRTPISAF	0.9961	0.6977	9	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B07:02	RTIPRTPISAF	0.9895	0.7054	9	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-A32:13	RTIPRTPISAF	0.9876	0.9848	9	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B07:05	RTIPRTPISAF	0.9848	0.6128	9	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B81:01	RTIPRTPISAF	0.9785	0.7294	9	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-A30:08	RTIPRTPISAF	0.9511	0.9184	9	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B07:04	PRTPISAF	0.9789	0.5433	12	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B15:31	IPRTPISAF	0.9885	0.8117	11	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B15:21	IPRTPISAF	0.9551	0.8473	11	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B42:02	IPRTPISAF	0.925	0.7021	11	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B42:01	IPRTPISAF	0.9031	0.6935	11	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B07:12	IPRTPISAF	0.8939	0.594	11	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B51:07	IPRTPISAF	0.5944	0.5915	11	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B35:12	IPRTPISAF	0.5691	0.9258	11	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B39:10	IPRTPISAF	0.2439	0.9281	11	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-C04:14	IPRTPISAF	0.0046	0.7465	11	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B07:04	TIPRTPISAF	0.9747	0.6205	10	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B07:12	TIPRTPISAF	0.9603	0.7784	10	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-C01:17	TIPRTPISAF	0.9482	0.974	10	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B42:02	TIPRTPISAF	0.9353	0.8694	10	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-C01:30	TIPRTPISAF	0.9347	0.9771	10	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B42:01	TIPRTPISAF	0.9143	0.8637	10	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B15:07	RTIPRTPISAF	0.9997	0.9138	9	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-C15:04	RTIPRTPISAF	0.9985	0.9671	9	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B07:04	RTIPRTPISAF	0.9905	0.6981	9	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B07:12	RTIPRTPISAF	0.9877	0.8335	9	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B42:02	RTIPRTPISAF	0.9733	0.871	9	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B42:01	RTIPRTPISAF	0.9694	0.865	9	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-C15:02	RTIPRTPI	0.9986	0.8901	9	17
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B07:09	PRTPISAF	0.7543	0.5666	12	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B07:22	PRTPISAF	0.729	0.585	12	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B35:77	IPRTPISAF	0.9895	0.8369	11	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B35:23	IPRTPISAF	0.9886	0.8244	11	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B35:20	IPRTPISAF	0.985	0.8891	11	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B35:24	IPRTPISAF	0.9831	0.8771	11	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-A30:01	RTIPRTPIS	0.9807	0.9153	9	18
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B35:17	IPRTPISAF	0.9625	0.7281	11	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B35:30	IPRTPISAF	0.9625	0.7281	11	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B35:11	IPRTPISAF	0.9534	0.8364	11	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B35:13	IPRTPISAF	0.9313	0.8752	11	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B08:18	IPRTPISAF	0.919	0.6982	11	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B15:13	IPRTPISAF	0.8239	0.5168	11	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B18:04	IPRTPISAF	0.7396	0.902	11	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-C03:67	IPRTPISAF	0.7168	0.968	11	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B35:09	IPRTPISAF	0.5691	0.9258	11	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B08:12	IPRTPISAF	0.5519	0.8461	11	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B35:43	IPRTPISAF	0.3996	0.8189	11	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B18:07	IPRTPISAF	0.3916	0.8597	11	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B15:08	IPRTPISAF	0.3778	0.8156	11	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B15:11	IPRTPISAF	0.362	0.8165	11	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B67:01	IPRTPISAF	0.3263	0.6965	11	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B18:03	IPRTPISAF	0.3207	0.883	11	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B18:08	IPRTPISAF	0.2599	0.8786	11	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-C04:04	IPRTPISAF	0.0032	0.7922	11	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B15:08	TIPRTPISAF	0.9961	0.895	10	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B15:11	TIPRTPISAF	0.996	0.8919	10	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B35:43	TIPRTPISAF	0.9951	0.8954	10	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B35:11	TIPRTPISAF	0.9947	0.9275	10	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-A30:01	RTIPRTPISA	0.9926	0.9771	9	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B07:22	TIPRTPISAF	0.9645	0.6433	10	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B35:17	TIPRTPISAF	0.9595	0.8841	10	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B35:30	TIPRTPISAF	0.9595	0.8841	10	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B07:09	TIPRTPISAF	0.9505	0.6329	10	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B35:77	TIPRTPISAF	0.9492	0.924	10	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-C01:02	TIPRTPISAF	0.9402	0.9742	10	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B07:26	TIPRTPISAF	0.8966	0.6227	10	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B55:04	TIPRTPISAF	0.8455	0.6524	10	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-A25:01	TIPRTPISAF	0.8101	0.9663	10	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B82:02	TIPRTPISAF	0.6889	0.5532	10	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B67:01	TIPRTPISAF	0.5253	0.9778	10	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B57:04	RTIPRTPISAF	0.9999	0.9449	9	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B57:10	RTIPRTPISAF	0.9999	0.991	9	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B58:06	RTIPRTPISAF	0.9998	0.9437	9	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B15:35	RTIPRTPISAF	0.9997	0.9682	9	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B15:135	RTIPRTPISAF	0.9995	0.9683	9	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B15:125	RTIPRTPISAF	0.9995	0.9571	9	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B15:33	RTIPRTPISAF	0.9995	0.9571	9	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B15:27	RTIPRTPISAF	0.9995	0.9664	9	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B15:34	RTIPRTPISAF	0.9995	0.9571	9	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B15:24	RTIPRTPISAF	0.9995	0.9748	9	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B57:02	RTIPRTPISAF	0.9994	0.9853	9	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B15:39	RTIPRTPISAF	0.9993	0.9275	9	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B15:50	RTIPRTPISAF	0.9993	0.9727	9	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-C15:09	RTIPRTPISAF	0.9985	0.9671	9	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-C02:10	RTIPRTPISAF	0.9981	0.9885	9	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-C02:02	RTIPRTPISAF	0.9981	0.9885	9	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-A32:01	RTIPRTPISAF	0.9976	0.9906	9	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B07:26	RTIPRTPISAF	0.9922	0.637	9	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B07:09	RTIPRTPISAF	0.9902	0.7131	9	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B07:22	RTIPRTPISAF	0.9895	0.7054	9	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-A30:04	RTIPRTPISAF	0.9794	0.6151	9	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	HLA-B55:04	RTIPRTPISAF	0.9748	0.7779	9	20

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Potential FusionNeoAntigen Information of AMD1-FIG4 in HLA II

AMD1-FIG4_111196417_110146290.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)
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1113	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1113	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1117	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1117	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1117	QGSGDLRTIPRTPIS	3	18
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1117	GDLRTIPRTPISAFS	6	21
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1134	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1134	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1152	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1152	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1152	QGSGDLRTIPRTPIS	3	18
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1152	GDLRTIPRTPISAFS	6	21
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1189	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1189	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1189	QGSGDLRTIPRTPIS	3	18
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1192	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1192	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1208	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1208	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1220	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1220	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1304	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-13100	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-13100	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1331	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1331	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1332	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1332	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1343	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1343	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1344	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1344	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1346	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1346	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1348	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1348	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1354	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1354	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1354	QGSGDLRTIPRTPIS	3	18
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1375	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1375	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1376	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1376	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1377	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1377	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1377	QGSGDLRTIPRTPIS	3	18
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1381	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1393	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1401	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1401	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1401	QGSGDLRTIPRTPIS	3	18
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1401	GDLRTIPRTPISAFS	6	21
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1404	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1404	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1404	QGSGDLRTIPRTPIS	3	18
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1404	GDLRTIPRTPISAFS	6	21
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1405	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1405	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1405	QGSGDLRTIPRTPIS	3	18
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1405	GDLRTIPRTPISAFS	6	21
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1406	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1406	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1407	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1407	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1407	QGSGDLRTIPRTPIS	3	18
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1408	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1408	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1408	QGSGDLRTIPRTPIS	3	18
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1408	GDLRTIPRTPISAFS	6	21
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1411	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1411	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1411	QGSGDLRTIPRTPIS	3	18
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1411	GDLRTIPRTPISAFS	6	21
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1414	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1414	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1416	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1416	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1416	QGSGDLRTIPRTPIS	3	18
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1417	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1417	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1418	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1418	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1418	QGSGDLRTIPRTPIS	3	18
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1418	GDLRTIPRTPISAFS	6	21
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1420	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1420	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1421	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1421	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1423	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1423	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1423	QGSGDLRTIPRTPIS	3	18
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1423	GDLRTIPRTPISAFS	6	21
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1426	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1426	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1426	QGSGDLRTIPRTPIS	3	18
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1426	GDLRTIPRTPISAFS	6	21
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1428	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1428	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1428	QGSGDLRTIPRTPIS	3	18
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1428	GDLRTIPRTPISAFS	6	21
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1429	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1429	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1431	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1431	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1431	QGSGDLRTIPRTPIS	3	18
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1432	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1432	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1432	QGSGDLRTIPRTPIS	3	18
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1432	GDLRTIPRTPISAFS	6	21
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1433	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1433	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1433	QGSGDLRTIPRTPIS	3	18
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1434	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1434	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1434	QGSGDLRTIPRTPIS	3	18
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1435	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1435	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1435	QGSGDLRTIPRTPIS	3	18
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1435	GDLRTIPRTPISAFS	6	21
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1436	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1436	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1437	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1437	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1438	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1438	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1438	QGSGDLRTIPRTPIS	3	18
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1438	GDLRTIPRTPISAFS	6	21
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1439	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1439	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1439	QGSGDLRTIPRTPIS	3	18
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1442	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1442	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1443	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1443	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1443	QGSGDLRTIPRTPIS	3	18
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1443	GDLRTIPRTPISAFS	6	21
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1444	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1444	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1445	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1445	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1445	QGSGDLRTIPRTPIS	3	18
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1445	GDLRTIPRTPISAFS	6	21
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1449	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1449	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1450	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1450	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1450	QGSGDLRTIPRTPIS	3	18
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1450	GDLRTIPRTPISAFS	6	21
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1454	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1454	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1454	QGSGDLRTIPRTPIS	3	18
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1454	GDLRTIPRTPISAFS	6	21
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1455	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1455	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1455	QGSGDLRTIPRTPIS	3	18
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1456	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1456	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1456	QGSGDLRTIPRTPIS	3	18
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1456	GDLRTIPRTPISAFS	6	21
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1458	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1458	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1458	QGSGDLRTIPRTPIS	3	18
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1458	GDLRTIPRTPISAFS	6	21
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1459	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1459	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1459	QGSGDLRTIPRTPIS	3	18
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1459	GDLRTIPRTPISAFS	6	21
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1460	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1460	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1460	QGSGDLRTIPRTPIS	3	18
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1460	GDLRTIPRTPISAFS	6	21
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1461	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1461	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1461	QGSGDLRTIPRTPIS	3	18
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1461	GDLRTIPRTPISAFS	6	21
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1462	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1462	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1462	QGSGDLRTIPRTPIS	3	18
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1462	GDLRTIPRTPISAFS	6	21
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1462	NQGSGDLRTIPRTPI	2	17
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1464	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1464	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1464	QGSGDLRTIPRTPIS	3	18
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1465	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1465	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1465	QGSGDLRTIPRTPIS	3	18
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1468	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1468	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1468	QGSGDLRTIPRTPIS	3	18
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1469	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1470	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1470	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1470	QGSGDLRTIPRTPIS	3	18
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1470	GDLRTIPRTPISAFS	6	21
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1471	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1471	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1471	QGSGDLRTIPRTPIS	3	18
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1471	GDLRTIPRTPISAFS	6	21
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1472	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1472	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1472	QGSGDLRTIPRTPIS	3	18
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1473	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1473	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1473	QGSGDLRTIPRTPIS	3	18
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1474	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1474	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1474	QGSGDLRTIPRTPIS	3	18
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1475	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1475	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1475	QGSGDLRTIPRTPIS	3	18
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1475	GDLRTIPRTPISAFS	6	21
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1478	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1480	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1480	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1481	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1481	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1482	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1482	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1482	QGSGDLRTIPRTPIS	3	18
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1482	GDLRTIPRTPISAFS	6	21
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1482	NQGSGDLRTIPRTPI	2	17
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1483	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1483	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1486	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1486	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1486	QGSGDLRTIPRTPIS	3	18
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1486	GDLRTIPRTPISAFS	6	21
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1487	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1487	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1487	QGSGDLRTIPRTPIS	3	18
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1487	GDLRTIPRTPISAFS	6	21
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1488	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1488	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1488	QGSGDLRTIPRTPIS	3	18
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1488	GDLRTIPRTPISAFS	6	21
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1490	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1490	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1490	QGSGDLRTIPRTPIS	3	18
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1490	GDLRTIPRTPISAFS	6	21
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1491	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1491	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1491	QGSGDLRTIPRTPIS	3	18
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1491	GDLRTIPRTPISAFS	6	21
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1493	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1493	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1495	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1495	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1495	QGSGDLRTIPRTPIS	3	18
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1495	GDLRTIPRTPISAFS	6	21
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1496	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1496	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1496	QGSGDLRTIPRTPIS	3	18
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1496	GDLRTIPRTPISAFS	6	21
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1497	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1497	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1497	QGSGDLRTIPRTPIS	3	18
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1497	GDLRTIPRTPISAFS	6	21
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1499	GSGDLRTIPRTPISA	4	19
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1499	SGDLRTIPRTPISAF	5	20
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1499	QGSGDLRTIPRTPIS	3	18
AMD1-FIG4	chr6	111196417	chr6	110146290	431	DRB1-1499	GDLRTIPRTPISAFS	6	21

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Fusion breakpoint peptide structures of AMD1-FIG4

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
2711	GDLRTIPRTPISAF	AMD1	FIG4	chr6	111196417	chr6	110146290	431

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of AMD1-FIG4

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	2711	GDLRTIPRTPISAF	-7.9962	-8.1096
HLA-B14:02	3BVN	2711	GDLRTIPRTPISAF	-5.70842	-6.74372
HLA-B52:01	3W39	2711	GDLRTIPRTPISAF	-6.83737	-6.95077
HLA-B52:01	3W39	2711	GDLRTIPRTPISAF	-4.4836	-5.5189
HLA-A11:01	4UQ2	2711	GDLRTIPRTPISAF	-10.0067	-10.1201
HLA-A11:01	4UQ2	2711	GDLRTIPRTPISAF	-9.03915	-10.0745
HLA-A24:02	5HGA	2711	GDLRTIPRTPISAF	-6.56204	-6.67544
HLA-A24:02	5HGA	2711	GDLRTIPRTPISAF	-5.42271	-6.45801
HLA-B44:05	3DX8	2711	GDLRTIPRTPISAF	-7.85648	-8.89178
HLA-B44:05	3DX8	2711	GDLRTIPRTPISAF	-5.3978	-5.5112
HLA-A02:01	6TDR	2711	GDLRTIPRTPISAF	-3.37154	-4.40684

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Vaccine Design for the FusionNeoAntigens of AMD1-FIG4

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
AMD1-FIG4	chr6	111196417	chr6	110146290	10	20	TIPRTPISAF	TATCCCAAGAACACCCATCTCGGCTTTCTC
AMD1-FIG4	chr6	111196417	chr6	110146290	11	19	IPRTPISA	CCCAAGAACACCCATCTCGGCTTT
AMD1-FIG4	chr6	111196417	chr6	110146290	11	20	IPRTPISAF	CCCAAGAACACCCATCTCGGCTTTCTC
AMD1-FIG4	chr6	111196417	chr6	110146290	12	20	PRTPISAF	AAGAACACCCATCTCGGCTTTCTC
AMD1-FIG4	chr6	111196417	chr6	110146290	9	17	RTIPRTPI	CACTATCCCAAGAACACCCATCTC
AMD1-FIG4	chr6	111196417	chr6	110146290	9	18	RTIPRTPIS	CACTATCCCAAGAACACCCATCTCGGC
AMD1-FIG4	chr6	111196417	chr6	110146290	9	19	RTIPRTPISA	CACTATCCCAAGAACACCCATCTCGGCTTT
AMD1-FIG4	chr6	111196417	chr6	110146290	9	20	RTIPRTPISAF	CACTATCCCAAGAACACCCATCTCGGCTTTCTC

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
AMD1-FIG4	chr6	111196417	chr6	110146290	2	17	NQGSGDLRTIPRTPI	CCAAGGATCTGGGGATCTTCGCACTATCCCAAGAACACCCATCTC
AMD1-FIG4	chr6	111196417	chr6	110146290	3	18	QGSGDLRTIPRTPIS	AGGATCTGGGGATCTTCGCACTATCCCAAGAACACCCATCTCGGC
AMD1-FIG4	chr6	111196417	chr6	110146290	4	19	GSGDLRTIPRTPISA	ATCTGGGGATCTTCGCACTATCCCAAGAACACCCATCTCGGCTTT
AMD1-FIG4	chr6	111196417	chr6	110146290	5	20	SGDLRTIPRTPISAF	TGGGGATCTTCGCACTATCCCAAGAACACCCATCTCGGCTTTCTC
AMD1-FIG4	chr6	111196417	chr6	110146290	6	21	GDLRTIPRTPISAFS	GGATCTTCGCACTATCCCAAGAACACCCATCTCGGCTTTCTCGCA

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Information of the samples that have these potential fusion neoantigens of AMD1-FIG4

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
UCS	AMD1-FIG4	chr6	111196417	ENST00000368877	chr6	110146290	ENST00000230124	TCGA-NA-A5I1-01A

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Potential target of CAR-T therapy development for AMD1-FIG4

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 AMD1-FIG4

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 AMD1-FIG4

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)