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Fusion Protein:AGAP1-RINT1

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: AGAP1-RINT1
	FusionPDB ID: 2780
	FusionGDB2.0 ID: 2780
		Hgene	Tgene
	Gene symbol	AGAP1	RINT1
	Gene ID	116987	60561
	Gene name	ArfGAP with GTPase domain, ankyrin repeat and PH domain 1	RAD50 interactor 1
	Synonyms	AGAP-1\|CENTG2\|GGAP1\|cnt-g2	ILFS3\|RINT-1
	Cytomap	2q37.2	7q22.3
	Type of gene	protein-coding	protein-coding
	Description	arf-GAP with GTPase, ANK repeat and PH domain-containing protein 1Arf GAP with GTP-binding protein-like, ANK repeat and PH domains 1GTP-binding and GTPase-activating protein 1centaurin, gamma 2	RAD50-interacting protein 1
	Modification date	20200313	20200315
	UniProtAcc	Q9UPQ3 Main function of 5'-partner protein: FUNCTION: GTPase-activating protein for ARF1 and, to a lesser extent, ARF5. Directly and specifically regulates the adapter protein 3 (AP-3)-dependent trafficking of proteins in the endosomal-lysosomal system. {ECO:0000269\|PubMed:12640130}.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000304032, ENST00000336665, ENST00000409538, ENST00000428334, ENST00000409457,	ENST00000477285, ENST00000257700,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	49 X 18 X 17=14994	5 X 7 X 3=105
	# samples	48	7
	** MAII score	log2(48/14994*10)=-4.96520709119934 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(7/105*10)=-0.584962500721156 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: AGAP1 [Title/Abstract] AND RINT1 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: AGAP1 [Title/Abstract] AND RINT1 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	AGAP1(236792093)-RINT1(105204180), # samples:3
Anticipated loss of major functional domain due to fusion event.	AGAP1-RINT1 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. AGAP1-RINT1 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. AGAP1-RINT1 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. AGAP1-RINT1 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/chr2:236792093/chr7:105204180)
- 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 AGAP1 (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 RINT1 (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)
ENST00000336665	AGAP1	chr2	236792093	+	ENST00000257700	RINT1	chr7	105204180	+	2809	1735	421	2442	673
ENST00000304032	AGAP1	chr2	236792093	+	ENST00000257700	RINT1	chr7	105204180	+	2809	1735	421	2442	673
ENST00000409538	AGAP1	chr2	236792093	+	ENST00000257700	RINT1	chr7	105204180	+	3520	2446	418	3153	911
ENST00000428334	AGAP1	chr2	236792093	+	ENST00000257700	RINT1	chr7	105204180	+	1767	693	21	1400	459
ENST00000336665	AGAP1	chr2	236792093	+	ENST00000257700	RINT1	chr7	105204179	+	2809	1735	421	2442	673
ENST00000304032	AGAP1	chr2	236792093	+	ENST00000257700	RINT1	chr7	105204179	+	2809	1735	421	2442	673
ENST00000409538	AGAP1	chr2	236792093	+	ENST00000257700	RINT1	chr7	105204179	+	3520	2446	418	3153	911
ENST00000428334	AGAP1	chr2	236792093	+	ENST00000257700	RINT1	chr7	105204179	+	1767	693	21	1400	459

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
ENST00000336665	ENST00000257700	AGAP1	chr2	236792093	+	RINT1	chr7	105204180	+	0.000997444	0.9990025
ENST00000304032	ENST00000257700	AGAP1	chr2	236792093	+	RINT1	chr7	105204180	+	0.000997444	0.9990025
ENST00000409538	ENST00000257700	AGAP1	chr2	236792093	+	RINT1	chr7	105204180	+	0.001051212	0.9989489
ENST00000428334	ENST00000257700	AGAP1	chr2	236792093	+	RINT1	chr7	105204180	+	0.00060049	0.99939954
ENST00000336665	ENST00000257700	AGAP1	chr2	236792093	+	RINT1	chr7	105204179	+	0.000997444	0.9990025
ENST00000304032	ENST00000257700	AGAP1	chr2	236792093	+	RINT1	chr7	105204179	+	0.000997444	0.9990025
ENST00000409538	ENST00000257700	AGAP1	chr2	236792093	+	RINT1	chr7	105204179	+	0.001051212	0.9989489
ENST00000428334	ENST00000257700	AGAP1	chr2	236792093	+	RINT1	chr7	105204179	+	0.00060049	0.99939954

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 AGAP1-RINT1

+/-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
AGAP1	chr2	236792093	RINT1	chr7	105204179	1735	438	CDNGVLTYHPSLHFFLQLQQAALEVF
AGAP1	chr2	236792093	RINT1	chr7	105204179	2446	676	CDNGVLTYHPSLHFFLQLQQAALEVF
AGAP1	chr2	236792093	RINT1	chr7	105204179	693	224	CDNGVLTYHPSLHFFLQLQQAALEVF
AGAP1	chr2	236792093	RINT1	chr7	105204180	1735	438	CDNGVLTYHPSLHFFLQLQQAALEVF
AGAP1	chr2	236792093	RINT1	chr7	105204180	2446	676	CDNGVLTYHPSLHFFLQLQQAALEVF
AGAP1	chr2	236792093	RINT1	chr7	105204180	693	224	CDNGVLTYHPSLHFFLQLQQAALEVF

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Potential FusionNeoAntigen Information of AGAP1-RINT1 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.

AGAP1-RINT1_236792093_105204179.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)
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-A24:14	TYHPSLHF	0.9945	0.6265	6	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:18	YHPSLHFF	0.9944	0.6793	7	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B08:01	HPSLHFFL	0.9922	0.9272	8	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:10	YHPSLHFF	0.9921	0.6021	7	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B35:03	HPSLHFFL	0.9917	0.9401	8	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B38:01	YHPSLHFF	0.9904	0.979	7	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B38:02	YHPSLHFF	0.9903	0.9846	7	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B08:09	HPSLHFFL	0.9901	0.9192	8	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:37	YHPSLHFF	0.9748	0.646	7	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-A24:14	YHPSLHFF	0.9672	0.6302	7	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B35:02	HPSLHFFL	0.95	0.9407	8	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B35:04	HPSLHFFL	0.95	0.9407	8	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B57:01	LTYHPSLHF	0.9995	0.9299	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:25	LTYHPSLHF	0.9992	0.9365	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:17	LTYHPSLHF	0.999	0.9373	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-A24:15	TYHPSLHFF	0.9989	0.5054	6	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B58:02	LTYHPSLHF	0.9989	0.932	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:02	LTYHPSLHF	0.9988	0.9464	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B57:03	LTYHPSLHF	0.9987	0.9642	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:01	LTYHPSLHF	0.9985	0.91	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B58:01	LTYHPSLHF	0.9982	0.8683	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B39:24	YHPSLHFFL	0.9978	0.6161	7	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:16	LTYHPSLHF	0.9977	0.7681	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B39:01	YHPSLHFFL	0.9973	0.9816	7	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-A24:10	TYHPSLHFF	0.9965	0.5283	6	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B38:02	YHPSLHFFL	0.9947	0.9867	7	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B38:01	YHPSLHFFL	0.9946	0.9816	7	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-A24:17	TYHPSLHFF	0.9945	0.5345	6	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B39:06	YHPSLHFFL	0.992	0.8359	7	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:03	LTYHPSLHF	0.9918	0.8351	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-A32:13	TYHPSLHFF	0.9757	0.9862	6	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-A32:13	LTYHPSLHF	0.972	0.9773	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:10	YHPSLHFFL	0.9704	0.6113	7	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B14:02	YHPSLHFFL	0.942	0.7583	7	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B14:01	YHPSLHFFL	0.942	0.7583	7	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-A24:14	TYHPSLHFF	0.9067	0.6673	6	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-A24:14	LTYHPSLHF	0.7821	0.5583	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:18	YHPSLHFFL	0.7705	0.7102	7	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B52:01	LTYHPSLHF	0.7371	0.9631	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:18	TYHPSLHFF	0.6423	0.7942	6	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:37	YHPSLHFFL	0.618	0.6339	7	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-A30:08	LTYHPSLHF	0.5824	0.7889	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B58:02	TYHPSLHFF	0.4969	0.95	6	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-A24:14	YHPSLHFFL	0.4531	0.6296	7	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B57:01	LTYHPSLHFF	0.9999	0.926	5	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B58:02	LTYHPSLHFF	0.9997	0.9195	5	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B57:03	LTYHPSLHFF	0.9997	0.9626	5	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:17	LTYHPSLHFF	0.9994	0.9064	5	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:16	LTYHPSLHFF	0.9993	0.7395	5	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B58:01	LTYHPSLHFF	0.9993	0.8524	5	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:01	VLTYHPSLHF	0.9982	0.9121	4	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-A24:25	TYHPSLHFFL	0.997	0.5265	6	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-A24:20	TYHPSLHFFL	0.9954	0.5219	6	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-A24:15	TYHPSLHFFL	0.9952	0.5364	6	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-A24:31	TYHPSLHFFL	0.9942	0.507	6	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B57:01	VLTYHPSLHF	0.9872	0.9802	4	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-A24:17	TYHPSLHFFL	0.986	0.5633	6	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-A24:10	TYHPSLHFFL	0.9846	0.6054	6	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B35:03	HPSLHFFLQL	0.9799	0.9439	8	18
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B39:06	LHFFLQLQQA	0.9792	0.9948	11	21
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B07:05	HPSLHFFLQL	0.9759	0.6265	8	18
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B07:02	HPSLHFFLQL	0.974	0.5426	8	18
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B57:03	VLTYHPSLHF	0.9724	0.987	4	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:25	VLTYHPSLHF	0.9712	0.9431	4	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-A32:13	LTYHPSLHFF	0.9682	0.9799	5	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-A24:14	LTYHPSLHFF	0.9569	0.5837	5	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-A24:14	TYHPSLHFFL	0.9521	0.6239	6	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-A32:13	VLTYHPSLHF	0.9466	0.9793	4	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:16	VLTYHPSLHF	0.9234	0.793	4	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:17	VLTYHPSLHF	0.916	0.9245	4	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B58:02	VLTYHPSLHF	0.9001	0.9721	4	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B81:01	HPSLHFFLQL	0.8392	0.5534	8	18
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B58:01	VLTYHPSLHF	0.7474	0.9456	4	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B82:01	HPSLHFFLQL	0.6897	0.6308	8	18
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B39:06	LHFFLQLQQAA	0.9979	0.9936	11	22
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B57:03	GVLTYHPSLHF	0.9944	0.9826	3	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:16	GVLTYHPSLHF	0.9909	0.7931	3	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:17	GVLTYHPSLHF	0.99	0.8618	3	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-A24:14	VLTYHPSLHFF	0.9358	0.5465	4	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:29	YHPSLHFF	0.999	0.9691	7	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:13	YHPSLHFF	0.9986	0.927	7	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:19	YHPSLHFF	0.9985	0.7392	7	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:95	YHPSLHFF	0.9985	0.7369	7	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:27	YHPSLHFF	0.9984	0.9586	7	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:67	YHPSLHFF	0.9984	0.932	7	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:80	YHPSLHFF	0.9984	0.932	7	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:10	YHPSLHFF	0.998	0.9594	7	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:19	TYHPSLHF	0.9969	0.8124	6	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:10	TYHPSLHF	0.9968	0.9751	6	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:80	TYHPSLHF	0.9968	0.9594	6	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:67	TYHPSLHF	0.9968	0.9594	6	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B39:09	YHPSLHFF	0.9968	0.7106	7	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C12:16	TYHPSLHF	0.9967	0.9759	6	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:46	YHPSLHFF	0.9967	0.8406	7	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:46	TYHPSLHF	0.9964	0.8998	6	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B42:02	HPSLHFFL	0.9963	0.9344	8	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:29	TYHPSLHF	0.9956	0.9778	6	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:05	TYHPSLHF	0.9948	0.9819	6	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B39:12	YHPSLHFF	0.9947	0.979	7	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B42:01	HPSLHFFL	0.9935	0.9305	8	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:27	TYHPSLHF	0.993	0.9728	6	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:13	TYHPSLHF	0.9926	0.9531	6	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B39:05	YHPSLHFF	0.9837	0.9703	7	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C04:14	TYHPSLHF	0.9832	0.7312	6	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C12:16	YHPSLHFF	0.9828	0.9759	7	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B35:12	HPSLHFFL	0.95	0.9407	8	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B39:10	HPSLHFFL	0.8678	0.9865	8	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:21	LTYHPSLHF	0.9988	0.9358	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:07	LTYHPSLHF	0.9987	0.755	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B39:09	YHPSLHFFL	0.9984	0.7598	7	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C03:08	LTYHPSLHF	0.9971	0.9338	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B39:12	YHPSLHFFL	0.9963	0.9836	7	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B39:05	YHPSLHFFL	0.995	0.9756	7	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C15:04	LTYHPSLHF	0.9918	0.9381	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C03:19	LTYHPSLHF	0.9903	0.9885	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:05	LTYHPSLHF	0.9846	0.8843	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C03:07	LTYHPSLHF	0.9846	0.9905	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:31	LTYHPSLHF	0.9807	0.8958	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:04	LTYHPSLHF	0.9799	0.8888	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C15:06	LTYHPSLHF	0.9777	0.9595	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:19	LTYHPSLHF	0.9777	0.7597	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C12:12	LTYHPSLHF	0.9671	0.9731	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:95	LTYHPSLHF	0.967	0.7657	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C03:14	LTYHPSLHF	0.957	0.9876	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C04:06	LTYHPSLHF	0.9514	0.9042	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:21	TYHPSLHFF	0.933	0.9288	6	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C06:03	LTYHPSLHF	0.8499	0.9967	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C12:04	LTYHPSLHF	0.8408	0.997	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:05	YHPSLHFFL	0.7563	0.9793	7	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:05	TYHPSLHFF	0.7478	0.982	6	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:80	TYHPSLHFF	0.7448	0.96	6	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:67	TYHPSLHFF	0.7448	0.96	6	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:10	TYHPSLHFF	0.7411	0.9764	6	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:27	TYHPSLHFF	0.7357	0.9746	6	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:95	YHPSLHFFL	0.7334	0.8046	7	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:27	YHPSLHFFL	0.7323	0.9643	7	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:29	TYHPSLHFF	0.7255	0.9775	6	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C12:16	TYHPSLHFF	0.7237	0.9776	6	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:19	TYHPSLHFF	0.719	0.8161	6	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:67	YHPSLHFFL	0.7085	0.9419	7	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:80	YHPSLHFFL	0.7085	0.9419	7	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:13	YHPSLHFFL	0.7022	0.9324	7	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:29	YHPSLHFFL	0.6899	0.9714	7	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:95	TYHPSLHFF	0.6867	0.8189	6	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:13	TYHPSLHFF	0.6684	0.9505	6	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:19	YHPSLHFFL	0.6668	0.781	7	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:46	TYHPSLHFF	0.6604	0.8959	6	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:10	YHPSLHFFL	0.6311	0.9676	7	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:46	YHPSLHFFL	0.6249	0.864	7	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C03:14	TYHPSLHFF	0.6154	0.9905	6	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C04:14	YHPSLHFFL	0.4059	0.813	7	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B14:03	YHPSLHFFL	0.3742	0.9555	7	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C02:06	LTYHPSLHF	0.324	0.9829	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C04:14	TYHPSLHFF	0.2516	0.7316	6	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C12:16	YHPSLHFFL	0.0591	0.9802	7	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C04:07	YHPSLHFFL	0.0321	0.8798	7	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C04:10	YHPSLHFFL	0.0316	0.8481	7	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C04:07	TYHPSLHFF	0.0106	0.856	6	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C04:10	TYHPSLHFF	0.0106	0.8194	6	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C15:04	LTYHPSLHFF	0.9992	0.9163	5	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:07	VLTYHPSLHF	0.9979	0.8101	4	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-A24:02	TYHPSLHFFL	0.9954	0.5219	6	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B07:12	HPSLHFFLQL	0.9742	0.6838	8	18
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C15:04	VLTYHPSLHF	0.9728	0.9455	4	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B07:04	HPSLHFFLQL	0.9645	0.5583	8	18
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B42:02	HPSLHFFLQL	0.9508	0.9678	8	18
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B42:01	HPSLHFFLQL	0.9338	0.9654	8	18
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:29	TYHPSLHFFL	0.8852	0.9759	6	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B39:10	HPSLHFFLQL	0.8715	0.9791	8	18
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:13	TYHPSLHFFL	0.856	0.9536	6	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B39:09	YHPSLHFFLQL	0.9998	0.9593	7	18
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:29	YHPSLHFFLQL	0.9956	0.9725	7	18
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:13	YHPSLHFFLQL	0.9951	0.928	7	18
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:17	YHPSLHFF	0.9986	0.9764	7	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:02	YHPSLHFF	0.9984	0.932	7	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:17	TYHPSLHF	0.9982	0.9815	6	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:02	TYHPSLHF	0.9968	0.9594	6	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C03:67	TYHPSLHF	0.9959	0.9818	6	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B08:18	HPSLHFFL	0.9922	0.9272	8	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B38:05	YHPSLHFF	0.9904	0.979	7	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C04:04	TYHPSLHF	0.9822	0.8643	6	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C06:06	YHPSLHFF	0.967	0.9941	7	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C14:03	YHPSLHFF	0.9573	0.9803	7	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C14:02	YHPSLHFF	0.9573	0.9803	7	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C06:06	TYHPSLHF	0.9514	0.9953	6	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B35:09	HPSLHFFL	0.95	0.9407	8	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C18:01	TYHPSLHF	0.9445	0.8435	6	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:09	YHPSLHFF	0.9368	0.5623	7	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B67:01	HPSLHFFL	0.9282	0.8496	8	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C14:03	TYHPSLHF	0.9108	0.9807	6	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C14:02	TYHPSLHF	0.9108	0.9807	6	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B08:12	HPSLHFFL	0.9069	0.9682	8	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B57:10	LTYHPSLHF	0.9995	0.9299	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B57:04	LTYHPSLHF	0.9995	0.7945	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:39	LTYHPSLHF	0.9992	0.8732	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B58:06	LTYHPSLHF	0.999	0.8924	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C03:02	LTYHPSLHF	0.9987	0.9664	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:35	LTYHPSLHF	0.9987	0.8833	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:34	LTYHPSLHF	0.9985	0.91	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:33	LTYHPSLHF	0.9985	0.91	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:27	LTYHPSLHF	0.9985	0.9024	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:125	LTYHPSLHF	0.9985	0.91	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:11	LTYHPSLHF	0.9985	0.8654	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:08	LTYHPSLHF	0.9985	0.8717	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:135	LTYHPSLHF	0.9983	0.9078	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B57:02	LTYHPSLHF	0.9982	0.94	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B35:43	LTYHPSLHF	0.9981	0.8704	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:50	LTYHPSLHF	0.998	0.9453	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:24	LTYHPSLHF	0.998	0.8718	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:53	LTYHPSLHF	0.9976	0.9012	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B39:31	YHPSLHFFL	0.9973	0.9817	7	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C03:04	LTYHPSLHF	0.9972	0.9882	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C03:03	LTYHPSLHF	0.9972	0.9882	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C03:67	LTYHPSLHF	0.9971	0.9824	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:13	LTYHPSLHF	0.9971	0.7428	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B38:05	YHPSLHFFL	0.9946	0.9816	7	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C16:04	LTYHPSLHF	0.9928	0.9922	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-A32:01	LTYHPSLHF	0.9923	0.9814	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C03:05	LTYHPSLHF	0.9918	0.9203	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C15:09	LTYHPSLHF	0.9918	0.9381	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C03:17	LTYHPSLHF	0.9916	0.9798	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:20	LTYHPSLHF	0.9864	0.9184	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B35:28	LTYHPSLHF	0.9796	0.9173	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:01	LTYHPSLHF	0.9715	0.7563	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:12	LTYHPSLHF	0.9709	0.8964	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C12:03	LTYHPSLHF	0.9704	0.9898	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C15:05	LTYHPSLHF	0.967	0.9118	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C15:02	LTYHPSLHF	0.9612	0.9093	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:09	YHPSLHFFL	0.9568	0.5986	7	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C04:04	LTYHPSLHF	0.947	0.8908	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C12:02	LTYHPSLHF	0.9287	0.979	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C16:01	LTYHPSLHF	0.9222	0.9891	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-A25:01	LTYHPSLHF	0.9161	0.9532	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:30	LTYHPSLHF	0.8848	0.9645	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C03:06	LTYHPSLHF	0.8706	0.9906	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:13	TYHPSLHFF	0.8519	0.7546	6	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C16:02	LTYHPSLHF	0.8373	0.9953	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C03:67	TYHPSLHFF	0.7777	0.9751	6	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:22	TYHPSLHFF	0.7667	0.8674	6	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:17	TYHPSLHFF	0.7637	0.9846	6	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:02	TYHPSLHFF	0.7448	0.96	6	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:17	YHPSLHFFL	0.7188	0.9751	7	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B39:11	YHPSLHFFL	0.7157	0.9428	7	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:01	YHPSLHFFL	0.7124	0.7756	7	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:02	YHPSLHFFL	0.7085	0.9419	7	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:01	TYHPSLHFF	0.6958	0.8014	6	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C03:67	YHPSLHFFL	0.6775	0.9697	7	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:22	YHPSLHFFL	0.5804	0.8399	7	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C04:04	YHPSLHFFL	0.4585	0.842	7	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C02:02	LTYHPSLHF	0.4423	0.9867	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C02:10	LTYHPSLHF	0.4423	0.9867	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:04	YHPSLHFFL	0.4065	0.9771	7	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C07:04	TYHPSLHFF	0.3795	0.9704	6	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C06:02	TYHPSLHFF	0.3183	0.9969	6	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C06:17	TYHPSLHFF	0.3183	0.9969	6	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C14:03	TYHPSLHFF	0.1926	0.9851	6	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C14:02	TYHPSLHFF	0.1926	0.9851	6	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C04:04	TYHPSLHFF	0.1568	0.8162	6	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C17:01	LTYHPSLHF	0.1259	0.9238	5	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C06:08	YHPSLHFFL	0.113	0.9938	7	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C06:08	TYHPSLHFF	0.0789	0.9935	6	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C06:17	YHPSLHFFL	0.0687	0.9972	7	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C06:02	YHPSLHFFL	0.0687	0.9972	7	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C06:06	YHPSLHFFL	0.0526	0.9936	7	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C18:01	YHPSLHFFL	0.0392	0.8899	7	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C06:06	TYHPSLHFF	0.038	0.9959	6	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C04:01	YHPSLHFFL	0.0321	0.8798	7	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C18:01	TYHPSLHFF	0.0108	0.8612	6	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C04:01	TYHPSLHFF	0.0106	0.856	6	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B57:04	LTYHPSLHFF	0.9999	0.7805	5	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B57:10	LTYHPSLHFF	0.9999	0.926	5	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B58:06	LTYHPSLHFF	0.9997	0.8651	5	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B57:02	LTYHPSLHFF	0.9996	0.9483	5	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:24	LTYHPSLHFF	0.9994	0.8487	5	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C15:09	LTYHPSLHFF	0.9992	0.9163	5	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:33	VLTYHPSLHF	0.9982	0.9121	4	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:125	VLTYHPSLHF	0.9982	0.9121	4	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:34	VLTYHPSLHF	0.9982	0.9121	4	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:27	VLTYHPSLHF	0.9981	0.9068	4	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:135	VLTYHPSLHF	0.9981	0.9114	4	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:50	VLTYHPSLHF	0.9981	0.9621	4	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:24	VLTYHPSLHF	0.9979	0.8785	4	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:35	VLTYHPSLHF	0.9978	0.9015	4	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:12	VLTYHPSLHF	0.9944	0.9109	4	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-A32:01	LTYHPSLHFF	0.9921	0.9833	5	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B57:10	VLTYHPSLHF	0.9872	0.9802	4	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C14:02	LTYHPSLHFF	0.9777	0.982	5	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C14:03	LTYHPSLHFF	0.9777	0.982	5	15
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B07:09	HPSLHFFLQL	0.9753	0.5567	8	18
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B07:22	HPSLHFFLQL	0.974	0.5426	8	18
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B57:04	VLTYHPSLHF	0.9732	0.8473	4	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C15:09	VLTYHPSLHF	0.9728	0.9455	4	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:39	VLTYHPSLHF	0.9722	0.8753	4	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B55:04	HPSLHFFLQL	0.9582	0.6495	8	18
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B58:06	VLTYHPSLHF	0.9549	0.8899	4	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B57:02	VLTYHPSLHF	0.9494	0.9722	4	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-A32:01	VLTYHPSLHF	0.9412	0.9883	4	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B15:13	VLTYHPSLHF	0.9239	0.7532	4	14
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B67:01	HPSLHFFLQL	0.8627	0.8167	8	18
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C14:03	TYHPSLHFFL	0.8033	0.9857	6	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-C14:02	TYHPSLHFFL	0.8033	0.9857	6	16
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-B82:02	HPSLHFFLQL	0.6897	0.6308	8	18
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	HLA-A32:01	GVLTYHPSLHF	0.9935	0.9801	3	14

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Potential FusionNeoAntigen Information of AGAP1-RINT1 in HLA II

AGAP1-RINT1_236792093_105204179.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)
AGAP1-RINT1	chr2	236792093	chr7	105204179	1735	DRB1-1510	NGVLTYHPSLHFFLQ	2	17

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Fusion breakpoint peptide structures of AGAP1-RINT1

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
9762	TYHPSLHFFLQLQQ	AGAP1	RINT1	chr2	236792093	chr7	105204179	1735

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of AGAP1-RINT1

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	9762	TYHPSLHFFLQLQQ	-5.42908	-5.54248
HLA-B14:02	3BVN	9762	TYHPSLHFFLQLQQ	-5.06008	-6.09538
HLA-B52:01	3W39	9762	TYHPSLHFFLQLQQ	-9.1987	-9.3121
HLA-B52:01	3W39	9762	TYHPSLHFFLQLQQ	-7.53083	-8.56613
HLA-A11:01	4UQ2	9762	TYHPSLHFFLQLQQ	-8.87547	-8.98887
HLA-A24:02	5HGA	9762	TYHPSLHFFLQLQQ	-7.78065	-7.89405
HLA-A24:02	5HGA	9762	TYHPSLHFFLQLQQ	-7.11918	-8.15448
HLA-B27:05	6PYJ	9762	TYHPSLHFFLQLQQ	-7.64943	-7.76283
HLA-B27:05	6PYJ	9762	TYHPSLHFFLQLQQ	-6.50173	-7.53703
HLA-B44:05	3DX8	9762	TYHPSLHFFLQLQQ	-7.26947	-7.38287
HLA-B44:05	3DX8	9762	TYHPSLHFFLQLQQ	-6.09544	-7.13074

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Vaccine Design for the FusionNeoAntigens of AGAP1-RINT1

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
AGAP1-RINT1	chr2	236792093	chr7	105204179	11	21	LHFFLQLQQA	TTACATTTCTTTCTACAACTTCAACAGGCT
AGAP1-RINT1	chr2	236792093	chr7	105204179	11	22	LHFFLQLQQAA	TTACATTTCTTTCTACAACTTCAACAGGCTGCA
AGAP1-RINT1	chr2	236792093	chr7	105204179	3	14	GVLTYHPSLHF	GGCGTGCTGACCTATCATCCCAGTTTACATTTC
AGAP1-RINT1	chr2	236792093	chr7	105204179	4	14	VLTYHPSLHF	GTGCTGACCTATCATCCCAGTTTACATTTC
AGAP1-RINT1	chr2	236792093	chr7	105204179	4	15	VLTYHPSLHFF	GTGCTGACCTATCATCCCAGTTTACATTTCTTT
AGAP1-RINT1	chr2	236792093	chr7	105204179	5	14	LTYHPSLHF	CTGACCTATCATCCCAGTTTACATTTC
AGAP1-RINT1	chr2	236792093	chr7	105204179	5	15	LTYHPSLHFF	CTGACCTATCATCCCAGTTTACATTTCTTT
AGAP1-RINT1	chr2	236792093	chr7	105204179	6	14	TYHPSLHF	ACCTATCATCCCAGTTTACATTTC
AGAP1-RINT1	chr2	236792093	chr7	105204179	6	15	TYHPSLHFF	ACCTATCATCCCAGTTTACATTTCTTT
AGAP1-RINT1	chr2	236792093	chr7	105204179	6	16	TYHPSLHFFL	ACCTATCATCCCAGTTTACATTTCTTTCTA
AGAP1-RINT1	chr2	236792093	chr7	105204179	7	15	YHPSLHFF	TATCATCCCAGTTTACATTTCTTT
AGAP1-RINT1	chr2	236792093	chr7	105204179	7	16	YHPSLHFFL	TATCATCCCAGTTTACATTTCTTTCTA
AGAP1-RINT1	chr2	236792093	chr7	105204179	7	18	YHPSLHFFLQL	TATCATCCCAGTTTACATTTCTTTCTACAACTT
AGAP1-RINT1	chr2	236792093	chr7	105204179	8	16	HPSLHFFL	CATCCCAGTTTACATTTCTTTCTA
AGAP1-RINT1	chr2	236792093	chr7	105204179	8	18	HPSLHFFLQL	CATCCCAGTTTACATTTCTTTCTACAACTT

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
AGAP1-RINT1	chr2	236792093	chr7	105204179	2	17	NGVLTYHPSLHFFLQ	AATGGCGTGCTGACCTATCATCCCAGTTTACATTTCTTTCTACAA

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Information of the samples that have these potential fusion neoantigens of AGAP1-RINT1

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	AGAP1-RINT1	chr2	236792093	ENST00000304032	chr7	105204179	ENST00000257700	TCGA-A7-A0DA

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Potential target of CAR-T therapy development for AGAP1-RINT1

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 AGAP1-RINT1

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 AGAP1-RINT1

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)