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Fusion Protein:RUNX1-RUNX1T1

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: RUNX1-RUNX1T1
	FusionPDB ID: 78673
	FusionGDB2.0 ID: 78673
		Hgene	Tgene
	Gene symbol	RUNX1	RUNX1T1
	Gene ID	861	862
	Gene name	RUNX family transcription factor 1	RUNX1 partner transcriptional co-repressor 1
	Synonyms	AML1\|AML1-EVI-1\|AMLCR1\|CBF2alpha\|CBFA2\|EVI-1\|PEBP2aB\|PEBP2alpha	AML1-MTG8\|AML1T1\|CBFA2T1\|CDR\|ETO\|MTG8\|ZMYND2
	Cytomap	21q22.12	8q21.3
	Type of gene	protein-coding	protein-coding
	Description	runt-related transcription factor 1AML1-EVI-1 fusion proteinPEA2-alpha BPEBP2-alpha BSL3-3 enhancer factor 1 alpha B subunitSL3/AKV core-binding factor alpha B subunitacute myeloid leukemia 1 proteincore-binding factor, runt domain, alpha subunit 2	protein CBFA2T1RUNX1 translocation partner 1acute myelogenous leukemia 1 translocation 1, cyclin-D relatedcore-binding factor, runt domain, alpha subunit 2; translocated to, 1; cyclin D-relatedeight twenty one proteinmyeloid translocation gene on 8q2
	Modification date	20200322	20200315
	UniProtAcc	Q06455 Main function of 5'-partner protein: FUNCTION: Transcriptional corepressor which facilitates transcriptional repression via its association with DNA-binding transcription factors and recruitment of other corepressors and histone-modifying enzymes (PubMed:12559562, PubMed:15203199, PubMed:10688654). Can repress the expression of MMP7 in a ZBTB33-dependent manner (PubMed:23251453). Can repress transactivation mediated by TCF12 (PubMed:16803958). Acts as a negative regulator of adipogenesis (By similarity). The AML1-MTG8/ETO fusion protein frequently found in leukemic cells is involved in leukemogenesis and contributes to hematopoietic stem/progenitor cell self-renewal (PubMed:23812588). {ECO:0000250\|UniProtKB:Q61909, ECO:0000269\|PubMed:10688654, ECO:0000269\|PubMed:10973986, ECO:0000269\|PubMed:16803958, ECO:0000269\|PubMed:23251453, ECO:0000269\|PubMed:23812588, ECO:0000303\|PubMed:12559562, ECO:0000303\|PubMed:15203199}.	Q06455 Main function of 5'-partner protein: FUNCTION: Transcriptional corepressor which facilitates transcriptional repression via its association with DNA-binding transcription factors and recruitment of other corepressors and histone-modifying enzymes (PubMed:12559562, PubMed:15203199, PubMed:10688654). Can repress the expression of MMP7 in a ZBTB33-dependent manner (PubMed:23251453). Can repress transactivation mediated by TCF12 (PubMed:16803958). Acts as a negative regulator of adipogenesis (By similarity). The AML1-MTG8/ETO fusion protein frequently found in leukemic cells is involved in leukemogenesis and contributes to hematopoietic stem/progenitor cell self-renewal (PubMed:23812588). {ECO:0000250\|UniProtKB:Q61909, ECO:0000269\|PubMed:10688654, ECO:0000269\|PubMed:10973986, ECO:0000269\|PubMed:16803958, ECO:0000269\|PubMed:23251453, ECO:0000269\|PubMed:23812588, ECO:0000303\|PubMed:12559562, ECO:0000303\|PubMed:15203199}.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000300305, ENST00000325074, ENST00000344691, ENST00000358356, ENST00000399240, ENST00000437180, ENST00000486278, ENST00000494829,	ENST00000360348, ENST00000396218, ENST00000422361, ENST00000436581, ENST00000518844, ENST00000520724, ENST00000521553, ENST00000522163, ENST00000265814, ENST00000523629,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	46 X 68 X 13=40664	7 X 47 X 4=1316
	# samples	89	50
	** MAII score	log2(89/40664*10)=-5.51380298959468 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(50/1316*10)=-1.39615948907315 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: RUNX1 [Title/Abstract] AND RUNX1T1 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: RUNX1 [Title/Abstract] AND RUNX1T1 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	RUNX1(36231771)-RUNX1T1(93029591), # samples:50 RUNX1T1(93074774)-RUNX1(36231875), # samples:1 RUNX1T1(93066670)-RUNX1(36229669), # samples:1 RUNX1T1(93076651)-RUNX1(36226882), # samples:1 RUNX1T1(93077979)-RUNX1(36221594), # samples:1 RUNX1T1(93077103)-RUNX1(36220613), # samples:1 RUNX1T1(93086037)-RUNX1(36216148), # samples:1 RUNX1T1(93077765)-RUNX1(36215526), # samples:1 RUNX1T1(93084407)-RUNX1(36210978), # samples:1 RUNX1T1(93082089)-RUNX1(36209907), # samples:1 RUNX1T1(93080031)-RUNX1(36208793), # samples:1 RUNX1T1(93086896)-RUNX1(36211486), # samples:1 RUNX1T1(93082546)-RUNX1(36219456), # samples:1 RUNX1T1(93088282)-RUNX1(36209989), # samples:1 RUNX1T1(92972535)-RUNX1(36259385), # samples:1
Anticipated loss of major functional domain due to fusion event.	RUNX1-RUNX1T1 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. RUNX1-RUNX1T1 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. RUNX1-RUNX1T1 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. RUNX1-RUNX1T1 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. RUNX1-RUNX1T1 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF. RUNX1-RUNX1T1 seems lost the major protein functional domain in Hgene partner, which is a transcription factor due to the frame-shifted ORF. RUNX1-RUNX1T1 seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF. RUNX1-RUNX1T1 seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF. RUNX1-RUNX1T1 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF. RUNX1T1-RUNX1 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF. RUNX1T1-RUNX1 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF. RUNX1T1-RUNX1 seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF. RUNX1T1-RUNX1 seems lost the major protein functional domain in Tgene partner, which is a transcription factor due to the frame-shifted ORF. RUNX1T1-RUNX1 seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor due to the frame-shifted ORF.

* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner	Gene	GO ID	GO term	PubMed ID
Hgene	RUNX1	GO:0030097	hemopoiesis	21873977
Hgene	RUNX1	GO:0045893	positive regulation of transcription, DNA-templated	10207087\|14970218
Hgene	RUNX1	GO:0045944	positive regulation of transcription by RNA polymerase II	9199349\|10207087\|14970218\|21873977
Tgene	RUNX1T1	GO:0045892	negative regulation of transcription, DNA-templated	23251453

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr21:36231771/chr8:93029591)
- 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 RUNX1 (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 RUNX1T1 (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)
ENST00000344691	RUNX1	chr21	36231770	-	ENST00000523629	RUNX1T1	chr8	93029591	-	9104	2110	1578	3836	752
ENST00000344691	RUNX1	chr21	36231770	-	ENST00000396218	RUNX1T1	chr8	93029591	-	5155	2110	1578	3836	752
ENST00000344691	RUNX1	chr21	36231770	-	ENST00000265814	RUNX1T1	chr8	93029591	-	5155	2110	1578	3836	752
ENST00000325074	RUNX1	chr21	36231770	-	ENST00000523629	RUNX1T1	chr8	93029591	-	7571	577	0	2303	767
ENST00000325074	RUNX1	chr21	36231770	-	ENST00000396218	RUNX1T1	chr8	93029591	-	3622	577	0	2303	767
ENST00000325074	RUNX1	chr21	36231770	-	ENST00000265814	RUNX1T1	chr8	93029591	-	3622	577	0	2303	767
ENST00000300305	RUNX1	chr21	36231770	-	ENST00000523629	RUNX1T1	chr8	93029591	-	8052	1058	445	2784	779
ENST00000300305	RUNX1	chr21	36231770	-	ENST00000396218	RUNX1T1	chr8	93029591	-	4103	1058	445	2784	779
ENST00000300305	RUNX1	chr21	36231770	-	ENST00000265814	RUNX1T1	chr8	93029591	-	4103	1058	445	2784	779
ENST00000399240	RUNX1	chr21	36231770	-	ENST00000523629	RUNX1T1	chr8	93029591	-	7597	603	71	2329	752
ENST00000399240	RUNX1	chr21	36231770	-	ENST00000396218	RUNX1T1	chr8	93029591	-	3648	603	71	2329	752
ENST00000399240	RUNX1	chr21	36231770	-	ENST00000265814	RUNX1T1	chr8	93029591	-	3648	603	71	2329	752
ENST00000486278	RUNX1	chr21	36231770	-	ENST00000523629	RUNX1T1	chr8	93029591	-	7751	757	144	2483	779
ENST00000486278	RUNX1	chr21	36231770	-	ENST00000396218	RUNX1T1	chr8	93029591	-	3802	757	144	2483	779
ENST00000486278	RUNX1	chr21	36231770	-	ENST00000265814	RUNX1T1	chr8	93029591	-	3802	757	144	2483	779
ENST00000358356	RUNX1	chr21	36231770	-	ENST00000523629	RUNX1T1	chr8	93029591	-	9104	2110	1578	3836	752
ENST00000358356	RUNX1	chr21	36231770	-	ENST00000396218	RUNX1T1	chr8	93029591	-	5155	2110	1578	3836	752
ENST00000358356	RUNX1	chr21	36231770	-	ENST00000265814	RUNX1T1	chr8	93029591	-	5155	2110	1578	3836	752
ENST00000344691	RUNX1	chr21	36231771	-	ENST00000523629	RUNX1T1	chr8	93029591	-	9104	2110	1578	3836	752
ENST00000344691	RUNX1	chr21	36231771	-	ENST00000396218	RUNX1T1	chr8	93029591	-	5155	2110	1578	3836	752
ENST00000344691	RUNX1	chr21	36231771	-	ENST00000265814	RUNX1T1	chr8	93029591	-	5155	2110	1578	3836	752
ENST00000325074	RUNX1	chr21	36231771	-	ENST00000523629	RUNX1T1	chr8	93029591	-	7571	577	0	2303	767
ENST00000325074	RUNX1	chr21	36231771	-	ENST00000396218	RUNX1T1	chr8	93029591	-	3622	577	0	2303	767
ENST00000325074	RUNX1	chr21	36231771	-	ENST00000265814	RUNX1T1	chr8	93029591	-	3622	577	0	2303	767
ENST00000300305	RUNX1	chr21	36231771	-	ENST00000523629	RUNX1T1	chr8	93029591	-	8052	1058	445	2784	779
ENST00000300305	RUNX1	chr21	36231771	-	ENST00000396218	RUNX1T1	chr8	93029591	-	4103	1058	445	2784	779
ENST00000300305	RUNX1	chr21	36231771	-	ENST00000265814	RUNX1T1	chr8	93029591	-	4103	1058	445	2784	779
ENST00000399240	RUNX1	chr21	36231771	-	ENST00000523629	RUNX1T1	chr8	93029591	-	7597	603	71	2329	752
ENST00000399240	RUNX1	chr21	36231771	-	ENST00000396218	RUNX1T1	chr8	93029591	-	3648	603	71	2329	752
ENST00000399240	RUNX1	chr21	36231771	-	ENST00000265814	RUNX1T1	chr8	93029591	-	3648	603	71	2329	752
ENST00000486278	RUNX1	chr21	36231771	-	ENST00000523629	RUNX1T1	chr8	93029591	-	7751	757	144	2483	779
ENST00000486278	RUNX1	chr21	36231771	-	ENST00000396218	RUNX1T1	chr8	93029591	-	3802	757	144	2483	779
ENST00000486278	RUNX1	chr21	36231771	-	ENST00000265814	RUNX1T1	chr8	93029591	-	3802	757	144	2483	779
ENST00000358356	RUNX1	chr21	36231771	-	ENST00000523629	RUNX1T1	chr8	93029591	-	9104	2110	1578	3836	752
ENST00000358356	RUNX1	chr21	36231771	-	ENST00000396218	RUNX1T1	chr8	93029591	-	5155	2110	1578	3836	752
ENST00000358356	RUNX1	chr21	36231771	-	ENST00000265814	RUNX1T1	chr8	93029591	-	5155	2110	1578	3836	752
ENST00000344691	RUNX1	chr21	36252854	-	ENST00000523629	RUNX1T1	chr8	93029593	-	8999	2005	1578	3731	717
ENST00000344691	RUNX1	chr21	36252854	-	ENST00000396218	RUNX1T1	chr8	93029593	-	5050	2005	1578	3731	717
ENST00000344691	RUNX1	chr21	36252854	-	ENST00000265814	RUNX1T1	chr8	93029593	-	5050	2005	1578	3731	717
ENST00000325074	RUNX1	chr21	36252854	-	ENST00000523629	RUNX1T1	chr8	93029593	-	7466	472	0	2198	732
ENST00000325074	RUNX1	chr21	36252854	-	ENST00000396218	RUNX1T1	chr8	93029593	-	3517	472	0	2198	732
ENST00000325074	RUNX1	chr21	36252854	-	ENST00000265814	RUNX1T1	chr8	93029593	-	3517	472	0	2198	732
ENST00000300305	RUNX1	chr21	36252854	-	ENST00000523629	RUNX1T1	chr8	93029593	-	7947	953	445	2679	744
ENST00000300305	RUNX1	chr21	36252854	-	ENST00000396218	RUNX1T1	chr8	93029593	-	3998	953	445	2679	744
ENST00000300305	RUNX1	chr21	36252854	-	ENST00000265814	RUNX1T1	chr8	93029593	-	3998	953	445	2679	744
ENST00000399240	RUNX1	chr21	36252854	-	ENST00000523629	RUNX1T1	chr8	93029593	-	7492	498	71	2224	717
ENST00000399240	RUNX1	chr21	36252854	-	ENST00000396218	RUNX1T1	chr8	93029593	-	3543	498	71	2224	717
ENST00000399240	RUNX1	chr21	36252854	-	ENST00000265814	RUNX1T1	chr8	93029593	-	3543	498	71	2224	717
ENST00000486278	RUNX1	chr21	36252854	-	ENST00000523629	RUNX1T1	chr8	93029593	-	7646	652	144	2378	744
ENST00000486278	RUNX1	chr21	36252854	-	ENST00000396218	RUNX1T1	chr8	93029593	-	3697	652	144	2378	744
ENST00000486278	RUNX1	chr21	36252854	-	ENST00000265814	RUNX1T1	chr8	93029593	-	3697	652	144	2378	744
ENST00000358356	RUNX1	chr21	36252854	-	ENST00000523629	RUNX1T1	chr8	93029593	-	8999	2005	1578	3731	717
ENST00000358356	RUNX1	chr21	36252854	-	ENST00000396218	RUNX1T1	chr8	93029593	-	5050	2005	1578	3731	717
ENST00000358356	RUNX1	chr21	36252854	-	ENST00000265814	RUNX1T1	chr8	93029593	-	5050	2005	1578	3731	717
ENST00000344691	RUNX1	chr21	36231771	-	ENST00000523629	RUNX1T1	chr8	92988201	-	7913	2110	1578	2645	355
ENST00000344691	RUNX1	chr21	36231771	-	ENST00000396218	RUNX1T1	chr8	92988201	-	3964	2110	1578	2645	355
ENST00000344691	RUNX1	chr21	36231771	-	ENST00000265814	RUNX1T1	chr8	92988201	-	3964	2110	1578	2645	355
ENST00000344691	RUNX1	chr21	36231771	-	ENST00000360348	RUNX1T1	chr8	92988201	-	3101	2110	1578	2645	355
ENST00000344691	RUNX1	chr21	36231771	-	ENST00000436581	RUNX1T1	chr8	92988201	-	2757	2110	1578	2645	355
ENST00000344691	RUNX1	chr21	36231771	-	ENST00000520724	RUNX1T1	chr8	92988201	-	2757	2110	1578	2645	355
ENST00000344691	RUNX1	chr21	36231771	-	ENST00000518844	RUNX1T1	chr8	92988201	-	2646	2110	1578	2645	355
ENST00000325074	RUNX1	chr21	36231771	-	ENST00000523629	RUNX1T1	chr8	92988201	-	6380	577	0	1112	370
ENST00000325074	RUNX1	chr21	36231771	-	ENST00000396218	RUNX1T1	chr8	92988201	-	2431	577	0	1112	370
ENST00000325074	RUNX1	chr21	36231771	-	ENST00000265814	RUNX1T1	chr8	92988201	-	2431	577	0	1112	370
ENST00000325074	RUNX1	chr21	36231771	-	ENST00000360348	RUNX1T1	chr8	92988201	-	1568	577	0	1112	370
ENST00000325074	RUNX1	chr21	36231771	-	ENST00000436581	RUNX1T1	chr8	92988201	-	1224	577	0	1112	370
ENST00000325074	RUNX1	chr21	36231771	-	ENST00000520724	RUNX1T1	chr8	92988201	-	1224	577	0	1112	370
ENST00000325074	RUNX1	chr21	36231771	-	ENST00000518844	RUNX1T1	chr8	92988201	-	1113	577	0	1112	370
ENST00000300305	RUNX1	chr21	36231771	-	ENST00000523629	RUNX1T1	chr8	92988201	-	6861	1058	445	1593	382
ENST00000300305	RUNX1	chr21	36231771	-	ENST00000396218	RUNX1T1	chr8	92988201	-	2912	1058	445	1593	382
ENST00000300305	RUNX1	chr21	36231771	-	ENST00000265814	RUNX1T1	chr8	92988201	-	2912	1058	445	1593	382
ENST00000300305	RUNX1	chr21	36231771	-	ENST00000360348	RUNX1T1	chr8	92988201	-	2049	1058	445	1593	382
ENST00000300305	RUNX1	chr21	36231771	-	ENST00000436581	RUNX1T1	chr8	92988201	-	1705	1058	445	1593	382
ENST00000300305	RUNX1	chr21	36231771	-	ENST00000520724	RUNX1T1	chr8	92988201	-	1705	1058	445	1593	382
ENST00000300305	RUNX1	chr21	36231771	-	ENST00000518844	RUNX1T1	chr8	92988201	-	1594	1058	445	1593	383
ENST00000399240	RUNX1	chr21	36231771	-	ENST00000523629	RUNX1T1	chr8	92988201	-	6406	603	71	1138	355
ENST00000399240	RUNX1	chr21	36231771	-	ENST00000396218	RUNX1T1	chr8	92988201	-	2457	603	71	1138	355
ENST00000399240	RUNX1	chr21	36231771	-	ENST00000265814	RUNX1T1	chr8	92988201	-	2457	603	71	1138	355
ENST00000399240	RUNX1	chr21	36231771	-	ENST00000360348	RUNX1T1	chr8	92988201	-	1594	603	71	1138	355
ENST00000399240	RUNX1	chr21	36231771	-	ENST00000436581	RUNX1T1	chr8	92988201	-	1250	603	71	1138	355
ENST00000399240	RUNX1	chr21	36231771	-	ENST00000520724	RUNX1T1	chr8	92988201	-	1250	603	71	1138	355
ENST00000399240	RUNX1	chr21	36231771	-	ENST00000518844	RUNX1T1	chr8	92988201	-	1139	603	71	1138	356
ENST00000486278	RUNX1	chr21	36231771	-	ENST00000523629	RUNX1T1	chr8	92988201	-	6560	757	144	1292	382
ENST00000486278	RUNX1	chr21	36231771	-	ENST00000396218	RUNX1T1	chr8	92988201	-	2611	757	144	1292	382
ENST00000486278	RUNX1	chr21	36231771	-	ENST00000265814	RUNX1T1	chr8	92988201	-	2611	757	144	1292	382
ENST00000486278	RUNX1	chr21	36231771	-	ENST00000360348	RUNX1T1	chr8	92988201	-	1748	757	144	1292	382
ENST00000486278	RUNX1	chr21	36231771	-	ENST00000436581	RUNX1T1	chr8	92988201	-	1404	757	144	1292	382
ENST00000486278	RUNX1	chr21	36231771	-	ENST00000520724	RUNX1T1	chr8	92988201	-	1404	757	144	1292	382
ENST00000486278	RUNX1	chr21	36231771	-	ENST00000518844	RUNX1T1	chr8	92988201	-	1293	757	144	1292	382
ENST00000358356	RUNX1	chr21	36231771	-	ENST00000523629	RUNX1T1	chr8	92988201	-	7913	2110	1578	2645	355
ENST00000358356	RUNX1	chr21	36231771	-	ENST00000396218	RUNX1T1	chr8	92988201	-	3964	2110	1578	2645	355
ENST00000358356	RUNX1	chr21	36231771	-	ENST00000265814	RUNX1T1	chr8	92988201	-	3964	2110	1578	2645	355
ENST00000358356	RUNX1	chr21	36231771	-	ENST00000360348	RUNX1T1	chr8	92988201	-	3101	2110	1578	2645	355
ENST00000358356	RUNX1	chr21	36231771	-	ENST00000436581	RUNX1T1	chr8	92988201	-	2757	2110	1578	2645	355
ENST00000358356	RUNX1	chr21	36231771	-	ENST00000520724	RUNX1T1	chr8	92988201	-	2757	2110	1578	2645	355
ENST00000358356	RUNX1	chr21	36231771	-	ENST00000518844	RUNX1T1	chr8	92988201	-	2646	2110	1578	2645	355
ENST00000437180	RUNX1	chr21	36231771	-	ENST00000523629	RUNX1T1	chr8	93004117	-	7145	803	834	1877	347
ENST00000437180	RUNX1	chr21	36231771	-	ENST00000396218	RUNX1T1	chr8	93004117	-	3196	803	834	1877	347
ENST00000437180	RUNX1	chr21	36231771	-	ENST00000265814	RUNX1T1	chr8	93004117	-	3196	803	834	1877	347
ENST00000437180	RUNX1	chr21	36231771	-	ENST00000360348	RUNX1T1	chr8	93004117	-	2333	803	834	1877	347
ENST00000437180	RUNX1	chr21	36231771	-	ENST00000436581	RUNX1T1	chr8	93004117	-	1989	803	834	1877	347
ENST00000437180	RUNX1	chr21	36231771	-	ENST00000520724	RUNX1T1	chr8	93004117	-	1989	803	834	1877	347
ENST00000437180	RUNX1	chr21	36231771	-	ENST00000518844	RUNX1T1	chr8	93004117	-	1878	803	834	1877	347
ENST00000344691	RUNX1	chr21	36231771	-	ENST00000523629	RUNX1T1	chr8	92983076	-	7844	2110	1578	2576	332
ENST00000344691	RUNX1	chr21	36231771	-	ENST00000396218	RUNX1T1	chr8	92983076	-	3895	2110	1578	2576	332
ENST00000344691	RUNX1	chr21	36231771	-	ENST00000265814	RUNX1T1	chr8	92983076	-	3895	2110	1578	2576	332
ENST00000344691	RUNX1	chr21	36231771	-	ENST00000360348	RUNX1T1	chr8	92983076	-	3032	2110	1578	2576	332
ENST00000344691	RUNX1	chr21	36231771	-	ENST00000436581	RUNX1T1	chr8	92983076	-	2688	2110	1578	2576	332
ENST00000344691	RUNX1	chr21	36231771	-	ENST00000520724	RUNX1T1	chr8	92983076	-	2688	2110	1578	2576	332
ENST00000344691	RUNX1	chr21	36231771	-	ENST00000518844	RUNX1T1	chr8	92983076	-	2577	2110	1578	2576	332
ENST00000325074	RUNX1	chr21	36231771	-	ENST00000523629	RUNX1T1	chr8	92983076	-	6311	577	0	1043	347
ENST00000325074	RUNX1	chr21	36231771	-	ENST00000396218	RUNX1T1	chr8	92983076	-	2362	577	0	1043	347
ENST00000325074	RUNX1	chr21	36231771	-	ENST00000265814	RUNX1T1	chr8	92983076	-	2362	577	0	1043	347
ENST00000325074	RUNX1	chr21	36231771	-	ENST00000360348	RUNX1T1	chr8	92983076	-	1499	577	0	1043	347
ENST00000325074	RUNX1	chr21	36231771	-	ENST00000436581	RUNX1T1	chr8	92983076	-	1155	577	0	1043	347
ENST00000325074	RUNX1	chr21	36231771	-	ENST00000520724	RUNX1T1	chr8	92983076	-	1155	577	0	1043	347
ENST00000325074	RUNX1	chr21	36231771	-	ENST00000518844	RUNX1T1	chr8	92983076	-	1044	577	0	1043	347
ENST00000300305	RUNX1	chr21	36231771	-	ENST00000523629	RUNX1T1	chr8	92983076	-	6792	1058	445	1524	359
ENST00000300305	RUNX1	chr21	36231771	-	ENST00000396218	RUNX1T1	chr8	92983076	-	2843	1058	445	1524	359
ENST00000300305	RUNX1	chr21	36231771	-	ENST00000265814	RUNX1T1	chr8	92983076	-	2843	1058	445	1524	359
ENST00000300305	RUNX1	chr21	36231771	-	ENST00000360348	RUNX1T1	chr8	92983076	-	1980	1058	445	1524	359
ENST00000300305	RUNX1	chr21	36231771	-	ENST00000436581	RUNX1T1	chr8	92983076	-	1636	1058	445	1524	359
ENST00000300305	RUNX1	chr21	36231771	-	ENST00000520724	RUNX1T1	chr8	92983076	-	1636	1058	445	1524	359
ENST00000300305	RUNX1	chr21	36231771	-	ENST00000518844	RUNX1T1	chr8	92983076	-	1525	1058	445	1524	360
ENST00000399240	RUNX1	chr21	36231771	-	ENST00000523629	RUNX1T1	chr8	92983076	-	6337	603	71	1069	332
ENST00000399240	RUNX1	chr21	36231771	-	ENST00000396218	RUNX1T1	chr8	92983076	-	2388	603	71	1069	332
ENST00000399240	RUNX1	chr21	36231771	-	ENST00000265814	RUNX1T1	chr8	92983076	-	2388	603	71	1069	332
ENST00000399240	RUNX1	chr21	36231771	-	ENST00000360348	RUNX1T1	chr8	92983076	-	1525	603	71	1069	332
ENST00000399240	RUNX1	chr21	36231771	-	ENST00000436581	RUNX1T1	chr8	92983076	-	1181	603	71	1069	332
ENST00000399240	RUNX1	chr21	36231771	-	ENST00000520724	RUNX1T1	chr8	92983076	-	1181	603	71	1069	332
ENST00000399240	RUNX1	chr21	36231771	-	ENST00000518844	RUNX1T1	chr8	92983076	-	1070	603	71	1069	333
ENST00000486278	RUNX1	chr21	36231771	-	ENST00000523629	RUNX1T1	chr8	92983076	-	6491	757	144	1223	359
ENST00000486278	RUNX1	chr21	36231771	-	ENST00000396218	RUNX1T1	chr8	92983076	-	2542	757	144	1223	359
ENST00000486278	RUNX1	chr21	36231771	-	ENST00000265814	RUNX1T1	chr8	92983076	-	2542	757	144	1223	359
ENST00000486278	RUNX1	chr21	36231771	-	ENST00000360348	RUNX1T1	chr8	92983076	-	1679	757	144	1223	359
ENST00000486278	RUNX1	chr21	36231771	-	ENST00000436581	RUNX1T1	chr8	92983076	-	1335	757	144	1223	359
ENST00000486278	RUNX1	chr21	36231771	-	ENST00000520724	RUNX1T1	chr8	92983076	-	1335	757	144	1223	359
ENST00000486278	RUNX1	chr21	36231771	-	ENST00000518844	RUNX1T1	chr8	92983076	-	1224	757	144	1223	359
ENST00000358356	RUNX1	chr21	36231771	-	ENST00000523629	RUNX1T1	chr8	92983076	-	7844	2110	1578	2576	332
ENST00000358356	RUNX1	chr21	36231771	-	ENST00000396218	RUNX1T1	chr8	92983076	-	3895	2110	1578	2576	332
ENST00000358356	RUNX1	chr21	36231771	-	ENST00000265814	RUNX1T1	chr8	92983076	-	3895	2110	1578	2576	332
ENST00000358356	RUNX1	chr21	36231771	-	ENST00000360348	RUNX1T1	chr8	92983076	-	3032	2110	1578	2576	332
ENST00000358356	RUNX1	chr21	36231771	-	ENST00000436581	RUNX1T1	chr8	92983076	-	2688	2110	1578	2576	332
ENST00000358356	RUNX1	chr21	36231771	-	ENST00000520724	RUNX1T1	chr8	92983076	-	2688	2110	1578	2576	332
ENST00000358356	RUNX1	chr21	36231771	-	ENST00000518844	RUNX1T1	chr8	92983076	-	2577	2110	1578	2576	332
ENST00000344691	RUNX1	chr21	36231771	-	ENST00000523629	RUNX1T1	chr8	92972745	-	7653	2110	3330	2755	191
ENST00000344691	RUNX1	chr21	36231771	-	ENST00000396218	RUNX1T1	chr8	92972745	-	3704	2110	3330	2755	191
ENST00000344691	RUNX1	chr21	36231771	-	ENST00000265814	RUNX1T1	chr8	92972745	-	3704	2110	3330	2755	191
ENST00000325074	RUNX1	chr21	36231771	-	ENST00000523629	RUNX1T1	chr8	92972745	-	6120	577	0	599	199
ENST00000325074	RUNX1	chr21	36231771	-	ENST00000396218	RUNX1T1	chr8	92972745	-	2171	577	0	599	199
ENST00000325074	RUNX1	chr21	36231771	-	ENST00000265814	RUNX1T1	chr8	92972745	-	2171	577	0	599	199
ENST00000437180	RUNX1	chr21	36231771	-	ENST00000360348	RUNX1T1	chr8	92972745	-	1534	803	190	825	211
ENST00000437180	RUNX1	chr21	36231771	-	ENST00000520724	RUNX1T1	chr8	92972745	-	1190	803	190	825	211
ENST00000300305	RUNX1	chr21	36231771	-	ENST00000523629	RUNX1T1	chr8	92972745	-	6601	1058	445	1080	211
ENST00000300305	RUNX1	chr21	36231771	-	ENST00000396218	RUNX1T1	chr8	92972745	-	2652	1058	445	1080	211
ENST00000300305	RUNX1	chr21	36231771	-	ENST00000265814	RUNX1T1	chr8	92972745	-	2652	1058	445	1080	211
ENST00000399240	RUNX1	chr21	36231771	-	ENST00000523629	RUNX1T1	chr8	92972745	-	6146	603	1823	1248	191
ENST00000399240	RUNX1	chr21	36231771	-	ENST00000396218	RUNX1T1	chr8	92972745	-	2197	603	1823	1248	191
ENST00000399240	RUNX1	chr21	36231771	-	ENST00000265814	RUNX1T1	chr8	92972745	-	2197	603	1823	1248	191
ENST00000486278	RUNX1	chr21	36231771	-	ENST00000523629	RUNX1T1	chr8	92972745	-	6300	757	144	779	211
ENST00000486278	RUNX1	chr21	36231771	-	ENST00000396218	RUNX1T1	chr8	92972745	-	2351	757	144	779	211
ENST00000486278	RUNX1	chr21	36231771	-	ENST00000265814	RUNX1T1	chr8	92972745	-	2351	757	144	779	211
ENST00000358356	RUNX1	chr21	36231771	-	ENST00000523629	RUNX1T1	chr8	92972745	-	7653	2110	3330	2755	191
ENST00000358356	RUNX1	chr21	36231771	-	ENST00000396218	RUNX1T1	chr8	92972745	-	3704	2110	3330	2755	191
ENST00000358356	RUNX1	chr21	36231771	-	ENST00000265814	RUNX1T1	chr8	92972745	-	3704	2110	3330	2755	191
ENST00000437180	RUNX1	chr21	36421139	-	ENST00000360348	RUNX1T1	chr8	92972747	-	979	248	310	627	105
ENST00000437180	RUNX1	chr21	36421139	-	ENST00000520724	RUNX1T1	chr8	92972747	-	635	248	310	627	105
ENST00000300305	RUNX1	chr21	36421139	-	ENST00000436581	RUNX1T1	chr8	92972747	-	890	503	565	882	105
ENST00000300305	RUNX1	chr21	36421139	-	ENST00000518844	RUNX1T1	chr8	92972747	-	779	503	472	227	81

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
ENST00000344691	ENST00000523629	RUNX1	chr21	36231771	-	RUNX1T1	chr8	93029591	-	0.002271168	0.9977289
ENST00000344691	ENST00000396218	RUNX1	chr21	36231771	-	RUNX1T1	chr8	93029591	-	0.009559119	0.99044085
ENST00000344691	ENST00000265814	RUNX1	chr21	36231771	-	RUNX1T1	chr8	93029591	-	0.009559119	0.99044085
ENST00000325074	ENST00000523629	RUNX1	chr21	36231771	-	RUNX1T1	chr8	93029591	-	0.001385115	0.9986149
ENST00000325074	ENST00000396218	RUNX1	chr21	36231771	-	RUNX1T1	chr8	93029591	-	0.011407558	0.9885924
ENST00000325074	ENST00000265814	RUNX1	chr21	36231771	-	RUNX1T1	chr8	93029591	-	0.011407558	0.9885924
ENST00000300305	ENST00000523629	RUNX1	chr21	36231771	-	RUNX1T1	chr8	93029591	-	0.001879364	0.9981206
ENST00000300305	ENST00000396218	RUNX1	chr21	36231771	-	RUNX1T1	chr8	93029591	-	0.00936235	0.99063766
ENST00000300305	ENST00000265814	RUNX1	chr21	36231771	-	RUNX1T1	chr8	93029591	-	0.00936235	0.99063766
ENST00000399240	ENST00000523629	RUNX1	chr21	36231771	-	RUNX1T1	chr8	93029591	-	0.002143072	0.9978569
ENST00000399240	ENST00000396218	RUNX1	chr21	36231771	-	RUNX1T1	chr8	93029591	-	0.013254603	0.9867454
ENST00000399240	ENST00000265814	RUNX1	chr21	36231771	-	RUNX1T1	chr8	93029591	-	0.013254603	0.9867454
ENST00000486278	ENST00000523629	RUNX1	chr21	36231771	-	RUNX1T1	chr8	93029591	-	0.001879426	0.9981206
ENST00000486278	ENST00000396218	RUNX1	chr21	36231771	-	RUNX1T1	chr8	93029591	-	0.01054403	0.989456
ENST00000486278	ENST00000265814	RUNX1	chr21	36231771	-	RUNX1T1	chr8	93029591	-	0.01054403	0.989456
ENST00000358356	ENST00000523629	RUNX1	chr21	36231771	-	RUNX1T1	chr8	93029591	-	0.002271168	0.9977289
ENST00000358356	ENST00000396218	RUNX1	chr21	36231771	-	RUNX1T1	chr8	93029591	-	0.009559119	0.99044085
ENST00000358356	ENST00000265814	RUNX1	chr21	36231771	-	RUNX1T1	chr8	93029591	-	0.009559119	0.99044085
ENST00000344691	ENST00000523629	RUNX1	chr21	36252854	-	RUNX1T1	chr8	93029593	-	0.002531766	0.99746823
ENST00000344691	ENST00000396218	RUNX1	chr21	36252854	-	RUNX1T1	chr8	93029593	-	0.012180953	0.9878191
ENST00000344691	ENST00000265814	RUNX1	chr21	36252854	-	RUNX1T1	chr8	93029593	-	0.012180953	0.9878191
ENST00000325074	ENST00000523629	RUNX1	chr21	36252854	-	RUNX1T1	chr8	93029593	-	0.001941259	0.99805874
ENST00000325074	ENST00000396218	RUNX1	chr21	36252854	-	RUNX1T1	chr8	93029593	-	0.01646135	0.9835386
ENST00000325074	ENST00000265814	RUNX1	chr21	36252854	-	RUNX1T1	chr8	93029593	-	0.01646135	0.9835386
ENST00000300305	ENST00000523629	RUNX1	chr21	36252854	-	RUNX1T1	chr8	93029593	-	0.002407298	0.9975926
ENST00000300305	ENST00000396218	RUNX1	chr21	36252854	-	RUNX1T1	chr8	93029593	-	0.013164954	0.98683506
ENST00000300305	ENST00000265814	RUNX1	chr21	36252854	-	RUNX1T1	chr8	93029593	-	0.013164954	0.98683506
ENST00000399240	ENST00000523629	RUNX1	chr21	36252854	-	RUNX1T1	chr8	93029593	-	0.002424022	0.99757594
ENST00000399240	ENST00000396218	RUNX1	chr21	36252854	-	RUNX1T1	chr8	93029593	-	0.017924359	0.98207563
ENST00000399240	ENST00000265814	RUNX1	chr21	36252854	-	RUNX1T1	chr8	93029593	-	0.017924359	0.98207563
ENST00000486278	ENST00000523629	RUNX1	chr21	36252854	-	RUNX1T1	chr8	93029593	-	0.002388991	0.99761105
ENST00000486278	ENST00000396218	RUNX1	chr21	36252854	-	RUNX1T1	chr8	93029593	-	0.014826166	0.98517376
ENST00000486278	ENST00000265814	RUNX1	chr21	36252854	-	RUNX1T1	chr8	93029593	-	0.014826166	0.98517376
ENST00000358356	ENST00000523629	RUNX1	chr21	36252854	-	RUNX1T1	chr8	93029593	-	0.002531766	0.99746823
ENST00000358356	ENST00000396218	RUNX1	chr21	36252854	-	RUNX1T1	chr8	93029593	-	0.012180953	0.9878191
ENST00000358356	ENST00000265814	RUNX1	chr21	36252854	-	RUNX1T1	chr8	93029593	-	0.012180953	0.9878191
ENST00000344691	ENST00000523629	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92988201	-	0.001440369	0.99855965
ENST00000344691	ENST00000396218	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92988201	-	0.008265964	0.991734
ENST00000344691	ENST00000265814	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92988201	-	0.008265964	0.991734
ENST00000344691	ENST00000360348	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92988201	-	0.030244337	0.9697557
ENST00000344691	ENST00000436581	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92988201	-	0.042954557	0.9570455
ENST00000344691	ENST00000520724	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92988201	-	0.042954557	0.9570455
ENST00000344691	ENST00000518844	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92988201	-	0.042186633	0.9578134
ENST00000325074	ENST00000523629	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92988201	-	0.001353386	0.9986467
ENST00000325074	ENST00000396218	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92988201	-	0.011780153	0.98821986
ENST00000325074	ENST00000265814	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92988201	-	0.011780153	0.98821986
ENST00000325074	ENST00000360348	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92988201	-	0.060509145	0.9394909
ENST00000325074	ENST00000436581	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92988201	-	0.072090164	0.9279098
ENST00000325074	ENST00000520724	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92988201	-	0.072090164	0.9279098
ENST00000325074	ENST00000518844	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92988201	-	0.08731598	0.9126841
ENST00000300305	ENST00000523629	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92988201	-	0.002055152	0.9979449
ENST00000300305	ENST00000396218	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92988201	-	0.013631212	0.9863688
ENST00000300305	ENST00000265814	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92988201	-	0.013631212	0.9863688
ENST00000300305	ENST00000360348	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92988201	-	0.047485176	0.9525149
ENST00000300305	ENST00000436581	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92988201	-	0.08329787	0.9167021
ENST00000300305	ENST00000520724	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92988201	-	0.08329787	0.9167021
ENST00000300305	ENST00000518844	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92988201	-	0.07711417	0.9228859
ENST00000399240	ENST00000523629	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92988201	-	0.001213952	0.99878603
ENST00000399240	ENST00000396218	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92988201	-	0.009773422	0.9902265
ENST00000399240	ENST00000265814	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92988201	-	0.009773422	0.9902265
ENST00000399240	ENST00000360348	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92988201	-	0.049508676	0.95049137
ENST00000399240	ENST00000436581	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92988201	-	0.058641292	0.9413587
ENST00000399240	ENST00000520724	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92988201	-	0.058641292	0.9413587
ENST00000399240	ENST00000518844	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92988201	-	0.07027788	0.9297222
ENST00000486278	ENST00000523629	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92988201	-	0.002075462	0.99792457
ENST00000486278	ENST00000396218	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92988201	-	0.015623352	0.98437667
ENST00000486278	ENST00000265814	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92988201	-	0.015623352	0.98437667
ENST00000486278	ENST00000360348	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92988201	-	0.06135508	0.93864495
ENST00000486278	ENST00000436581	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92988201	-	0.10530863	0.89469135
ENST00000486278	ENST00000520724	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92988201	-	0.10530863	0.89469135
ENST00000486278	ENST00000518844	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92988201	-	0.106937185	0.89306283
ENST00000358356	ENST00000523629	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92988201	-	0.001440369	0.99855965
ENST00000358356	ENST00000396218	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92988201	-	0.008265964	0.991734
ENST00000358356	ENST00000265814	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92988201	-	0.008265964	0.991734
ENST00000358356	ENST00000360348	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92988201	-	0.030244337	0.9697557
ENST00000358356	ENST00000436581	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92988201	-	0.042954557	0.9570455
ENST00000358356	ENST00000520724	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92988201	-	0.042954557	0.9570455
ENST00000358356	ENST00000518844	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92988201	-	0.042186633	0.9578134
ENST00000437180	ENST00000523629	RUNX1	chr21	36231771	-	RUNX1T1	chr8	93004117	-	0.003633878	0.99636614
ENST00000437180	ENST00000396218	RUNX1	chr21	36231771	-	RUNX1T1	chr8	93004117	-	0.03023193	0.96976805
ENST00000437180	ENST00000265814	RUNX1	chr21	36231771	-	RUNX1T1	chr8	93004117	-	0.03023193	0.96976805
ENST00000437180	ENST00000360348	RUNX1	chr21	36231771	-	RUNX1T1	chr8	93004117	-	0.08312257	0.91687745
ENST00000437180	ENST00000436581	RUNX1	chr21	36231771	-	RUNX1T1	chr8	93004117	-	0.0720756	0.9279244
ENST00000437180	ENST00000520724	RUNX1	chr21	36231771	-	RUNX1T1	chr8	93004117	-	0.0720756	0.9279244
ENST00000437180	ENST00000518844	RUNX1	chr21	36231771	-	RUNX1T1	chr8	93004117	-	0.078110516	0.9218895
ENST00000344691	ENST00000523629	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92983076	-	0.0022064	0.99779356
ENST00000344691	ENST00000396218	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92983076	-	0.011794517	0.98820555
ENST00000344691	ENST00000265814	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92983076	-	0.011794517	0.98820555
ENST00000344691	ENST00000360348	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92983076	-	0.03826727	0.96173275
ENST00000344691	ENST00000436581	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92983076	-	0.055535987	0.9444641
ENST00000344691	ENST00000520724	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92983076	-	0.055535987	0.9444641
ENST00000344691	ENST00000518844	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92983076	-	0.05385059	0.9461494
ENST00000325074	ENST00000523629	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92983076	-	0.001520155	0.9984799
ENST00000325074	ENST00000396218	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92983076	-	0.012501073	0.98749894
ENST00000325074	ENST00000265814	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92983076	-	0.012501073	0.98749894
ENST00000325074	ENST00000360348	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92983076	-	0.06407947	0.93592054
ENST00000325074	ENST00000436581	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92983076	-	0.06682698	0.93317306
ENST00000325074	ENST00000520724	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92983076	-	0.06682698	0.93317306
ENST00000325074	ENST00000518844	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92983076	-	0.08434551	0.9156544
ENST00000300305	ENST00000523629	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92983076	-	0.001344896	0.9986551
ENST00000300305	ENST00000396218	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92983076	-	0.009010749	0.99098927
ENST00000300305	ENST00000265814	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92983076	-	0.009010749	0.99098927
ENST00000300305	ENST00000360348	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92983076	-	0.03640927	0.9635907
ENST00000300305	ENST00000436581	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92983076	-	0.06465493	0.9353451
ENST00000300305	ENST00000520724	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92983076	-	0.06465493	0.9353451
ENST00000300305	ENST00000518844	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92983076	-	0.0628321	0.93716794
ENST00000399240	ENST00000523629	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92983076	-	0.001864854	0.9981351
ENST00000399240	ENST00000396218	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92983076	-	0.013760687	0.98623925
ENST00000399240	ENST00000265814	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92983076	-	0.013760687	0.98623925
ENST00000399240	ENST00000360348	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92983076	-	0.061295517	0.9387045
ENST00000399240	ENST00000436581	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92983076	-	0.055001646	0.9449984
ENST00000399240	ENST00000520724	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92983076	-	0.055001646	0.9449984
ENST00000399240	ENST00000518844	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92983076	-	0.071467735	0.9285323
ENST00000486278	ENST00000523629	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92983076	-	0.001360972	0.99863905
ENST00000486278	ENST00000396218	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92983076	-	0.010189991	0.98981
ENST00000486278	ENST00000265814	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92983076	-	0.010189991	0.98981
ENST00000486278	ENST00000360348	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92983076	-	0.04935325	0.95064676
ENST00000486278	ENST00000436581	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92983076	-	0.08481978	0.91518027
ENST00000486278	ENST00000520724	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92983076	-	0.08481978	0.91518027
ENST00000486278	ENST00000518844	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92983076	-	0.08885891	0.9111411
ENST00000358356	ENST00000523629	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92983076	-	0.0022064	0.99779356
ENST00000358356	ENST00000396218	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92983076	-	0.011794517	0.98820555
ENST00000358356	ENST00000265814	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92983076	-	0.011794517	0.98820555
ENST00000358356	ENST00000360348	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92983076	-	0.03826727	0.96173275
ENST00000358356	ENST00000436581	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92983076	-	0.055535987	0.9444641
ENST00000358356	ENST00000520724	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92983076	-	0.055535987	0.9444641
ENST00000358356	ENST00000518844	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92983076	-	0.05385059	0.9461494
ENST00000344691	ENST00000523629	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92972745	-	0.005822868	0.9941771
ENST00000344691	ENST00000396218	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92972745	-	0.014974858	0.9850251
ENST00000344691	ENST00000265814	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92972745	-	0.014974858	0.9850251
ENST00000325074	ENST00000523629	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92972745	-	0.010566011	0.98943394
ENST00000325074	ENST00000396218	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92972745	-	0.034443542	0.9655565
ENST00000325074	ENST00000265814	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92972745	-	0.034443542	0.9655565
ENST00000437180	ENST00000360348	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92972745	-	0.044447735	0.9555523
ENST00000437180	ENST00000520724	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92972745	-	0.04196979	0.95803016
ENST00000300305	ENST00000523629	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92972745	-	0.004745795	0.9952543
ENST00000300305	ENST00000396218	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92972745	-	0.02532898	0.97467095
ENST00000300305	ENST00000265814	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92972745	-	0.02532898	0.97467095
ENST00000399240	ENST00000523629	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92972745	-	0.005351608	0.9946484
ENST00000399240	ENST00000396218	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92972745	-	0.019886127	0.9801138
ENST00000399240	ENST00000265814	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92972745	-	0.019886127	0.9801138
ENST00000486278	ENST00000523629	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92972745	-	0.004507794	0.9954922
ENST00000486278	ENST00000396218	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92972745	-	0.020541225	0.97945875
ENST00000486278	ENST00000265814	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92972745	-	0.020541225	0.97945875
ENST00000358356	ENST00000523629	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92972745	-	0.005822868	0.9941771
ENST00000358356	ENST00000396218	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92972745	-	0.014974858	0.9850251
ENST00000358356	ENST00000265814	RUNX1	chr21	36231771	-	RUNX1T1	chr8	92972745	-	0.014974858	0.9850251
ENST00000437180	ENST00000360348	RUNX1	chr21	36421139	-	RUNX1T1	chr8	92972747	-	0.77087396	0.22912602
ENST00000437180	ENST00000520724	RUNX1	chr21	36421139	-	RUNX1T1	chr8	92972747	-	0.41287094	0.58712906
ENST00000300305	ENST00000436581	RUNX1	chr21	36421139	-	RUNX1T1	chr8	92972747	-	0.9216228	0.078377165
ENST00000300305	ENST00000518844	RUNX1	chr21	36421139	-	RUNX1T1	chr8	92972747	-	0.95541745	0.044582564

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 RUNX1-RUNX1T1

+/-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
RUNX1	chr21	36231770	RUNX1T1	chr8	93029591	1058	205	IKITVDGPREPRNRTEKHSTMPDSPV
RUNX1	chr21	36231770	RUNX1T1	chr8	93029591	2110	178	IKITVDGPREPRNRTEKHSTMPDSPV
RUNX1	chr21	36231770	RUNX1T1	chr8	93029591	577	193	IKITVDGPREPRNRTEKHSTMPDSPV
RUNX1	chr21	36231770	RUNX1T1	chr8	93029591	603	178	IKITVDGPREPRNRTEKHSTMPDSPV
RUNX1	chr21	36231770	RUNX1T1	chr8	93029591	757	205	IKITVDGPREPRNRTEKHSTMPDSPV
RUNX1	chr21	36231771	RUNX1T1	chr8	92972745	2110	38	TARMLINCRLSLLLVCVCVCVCVCVC
RUNX1	chr21	36231771	RUNX1T1	chr8	92972745	603	38	TARMLINCRLSLLLVCVCVCVCVCVC
RUNX1	chr21	36231771	RUNX1T1	chr8	92983076	1058	205	IKITVDGPREPRKEAVNEVKRQAMTE
RUNX1	chr21	36231771	RUNX1T1	chr8	92983076	2110	178	IKITVDGPREPRKEAVNEVKRQAMTE
RUNX1	chr21	36231771	RUNX1T1	chr8	92983076	577	193	IKITVDGPREPRKEAVNEVKRQAMTE
RUNX1	chr21	36231771	RUNX1T1	chr8	92983076	603	178	IKITVDGPREPRKEAVNEVKRQAMTE
RUNX1	chr21	36231771	RUNX1T1	chr8	92983076	757	205	IKITVDGPREPRKEAVNEVKRQAMTE
RUNX1	chr21	36231771	RUNX1T1	chr8	92988201	1058	205	IKITVDGPREPRNAHREFLHRPASGY
RUNX1	chr21	36231771	RUNX1T1	chr8	92988201	2110	178	IKITVDGPREPRNAHREFLHRPASGY
RUNX1	chr21	36231771	RUNX1T1	chr8	92988201	577	193	IKITVDGPREPRNAHREFLHRPASGY
RUNX1	chr21	36231771	RUNX1T1	chr8	92988201	603	178	IKITVDGPREPRNAHREFLHRPASGY
RUNX1	chr21	36231771	RUNX1T1	chr8	92988201	757	205	IKITVDGPREPRNAHREFLHRPASGY
RUNX1	chr21	36231771	RUNX1T1	chr8	93029591	1058	205	IKITVDGPREPRNRTEKHSTMPDSPV
RUNX1	chr21	36231771	RUNX1T1	chr8	93029591	2110	178	IKITVDGPREPRNRTEKHSTMPDSPV
RUNX1	chr21	36231771	RUNX1T1	chr8	93029591	577	193	IKITVDGPREPRNRTEKHSTMPDSPV
RUNX1	chr21	36231771	RUNX1T1	chr8	93029591	603	178	IKITVDGPREPRNRTEKHSTMPDSPV
RUNX1	chr21	36231771	RUNX1T1	chr8	93029591	757	205	IKITVDGPREPRNRTEKHSTMPDSPV
RUNX1	chr21	36252854	RUNX1T1	chr8	93029593	2005	142	RFNDLRFVGRSGRDRTEKHSTMPDSP
RUNX1	chr21	36252854	RUNX1T1	chr8	93029593	472	157	RFNDLRFVGRSGRDRTEKHSTMPDSP
RUNX1	chr21	36252854	RUNX1T1	chr8	93029593	498	142	RFNDLRFVGRSGRDRTEKHSTMPDSP
RUNX1	chr21	36252854	RUNX1T1	chr8	93029593	652	169	RFNDLRFVGRSGRDRTEKHSTMPDSP
RUNX1	chr21	36252854	RUNX1T1	chr8	93029593	953	169	RFNDLRFVGRSGRDRTEKHSTMPDSP

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Potential FusionNeoAntigen Information of RUNX1-RUNX1T1 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.

RUNX1-RUNX1T1_36231770_93029591.msa
RUNX1-RUNX1T1_36231771_92972745.msa
RUNX1-RUNX1T1_36231771_92983076.msa
RUNX1-RUNX1T1_36231771_92988201.msa
RUNX1-RUNX1T1_36252854_93029593.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)
RUNX1-RUNX1T1	chr21	36231770	chr8	93029591	1058	HLA-B27:04	NRTEKHSTM	0.9978	0.7297	12	21
RUNX1-RUNX1T1	chr21	36231770	chr8	93029591	1058	HLA-B14:02	NRTEKHSTM	0.9935	0.6019	12	21
RUNX1-RUNX1T1	chr21	36231770	chr8	93029591	1058	HLA-B14:01	NRTEKHSTM	0.9935	0.6019	12	21
RUNX1-RUNX1T1	chr21	36231770	chr8	93029591	1058	HLA-B39:01	NRTEKHSTM	0.9922	0.8934	12	21
RUNX1-RUNX1T1	chr21	36231770	chr8	93029591	1058	HLA-B39:06	NRTEKHSTM	0.9892	0.7641	12	21
RUNX1-RUNX1T1	chr21	36231770	chr8	93029591	1058	HLA-B07:05	GPREPRNRT	0.9882	0.6177	6	15
RUNX1-RUNX1T1	chr21	36231770	chr8	93029591	1058	HLA-B07:02	GPREPRNRT	0.9874	0.688	6	15
RUNX1-RUNX1T1	chr21	36231770	chr8	93029591	1058	HLA-B38:02	NRTEKHSTM	0.971	0.9527	12	21
RUNX1-RUNX1T1	chr21	36231770	chr8	93029591	1058	HLA-B15:10	NRTEKHSTM	0.9174	0.5676	12	21
RUNX1-RUNX1T1	chr21	36231770	chr8	93029591	1058	HLA-B15:37	NRTEKHSTM	0.7363	0.5794	12	21
RUNX1-RUNX1T1	chr21	36231770	chr8	93029591	1058	HLA-B15:18	NRTEKHSTM	0.7098	0.6959	12	21
RUNX1-RUNX1T1	chr21	36231770	chr8	93029591	1058	HLA-C07:95	NRTEKHSTM	0.9955	0.6936	12	21
RUNX1-RUNX1T1	chr21	36231770	chr8	93029591	1058	HLA-C07:05	NRTEKHSTM	0.9952	0.9613	12	21
RUNX1-RUNX1T1	chr21	36231770	chr8	93029591	1058	HLA-B39:09	NRTEKHSTM	0.9937	0.6062	12	21
RUNX1-RUNX1T1	chr21	36231770	chr8	93029591	1058	HLA-C07:27	NRTEKHSTM	0.993	0.935	12	21
RUNX1-RUNX1T1	chr21	36231770	chr8	93029591	1058	HLA-B39:12	NRTEKHSTM	0.9914	0.8984	12	21
RUNX1-RUNX1T1	chr21	36231770	chr8	93029591	1058	HLA-C07:29	NRTEKHSTM	0.9904	0.9239	12	21
RUNX1-RUNX1T1	chr21	36231770	chr8	93029591	1058	HLA-C07:13	NRTEKHSTM	0.9897	0.9045	12	21
RUNX1-RUNX1T1	chr21	36231770	chr8	93029591	1058	HLA-B39:05	NRTEKHSTM	0.9712	0.8823	12	21
RUNX1-RUNX1T1	chr21	36231770	chr8	93029591	1058	HLA-C07:46	NRTEKHSTM	0.915	0.88	12	21
RUNX1-RUNX1T1	chr21	36231770	chr8	93029591	1058	HLA-C07:67	NRTEKHSTM	0.8793	0.9311	12	21
RUNX1-RUNX1T1	chr21	36231770	chr8	93029591	1058	HLA-C07:80	NRTEKHSTM	0.8793	0.9311	12	21
RUNX1-RUNX1T1	chr21	36231770	chr8	93029591	1058	HLA-C07:19	NRTEKHSTM	0.8724	0.7416	12	21
RUNX1-RUNX1T1	chr21	36231770	chr8	93029591	1058	HLA-C07:10	NRTEKHSTM	0.8499	0.9519	12	21
RUNX1-RUNX1T1	chr21	36231770	chr8	93029591	1058	HLA-B73:01	NRTEKHSTM	0.8167	0.641	12	21
RUNX1-RUNX1T1	chr21	36231770	chr8	93029591	1058	HLA-B14:03	NRTEKHSTM	0.6072	0.6783	12	21
RUNX1-RUNX1T1	chr21	36231770	chr8	93029591	1058	HLA-B07:04	GPREPRNRT	0.5491	0.6163	6	15
RUNX1-RUNX1T1	chr21	36231770	chr8	93029591	1058	HLA-C12:16	NRTEKHSTM	0.1725	0.9467	12	21
RUNX1-RUNX1T1	chr21	36231770	chr8	93029591	1058	HLA-B27:06	NRTEKHSTM	0.9974	0.7105	12	21
RUNX1-RUNX1T1	chr21	36231770	chr8	93029591	1058	HLA-C07:01	NRTEKHSTM	0.9954	0.6558	12	21
RUNX1-RUNX1T1	chr21	36231770	chr8	93029591	1058	HLA-B39:31	NRTEKHSTM	0.9892	0.8942	12	21
RUNX1-RUNX1T1	chr21	36231770	chr8	93029591	1058	HLA-B07:22	GPREPRNRT	0.9874	0.688	6	15
RUNX1-RUNX1T1	chr21	36231770	chr8	93029591	1058	HLA-B07:09	GPREPRNRT	0.9837	0.6751	6	15
RUNX1-RUNX1T1	chr21	36231770	chr8	93029591	1058	HLA-C07:17	NRTEKHSTM	0.9824	0.9539	12	21
RUNX1-RUNX1T1	chr21	36231770	chr8	93029591	1058	HLA-C07:04	NRTEKHSTM	0.9409	0.8866	12	21
RUNX1-RUNX1T1	chr21	36231770	chr8	93029591	1058	HLA-C06:08	NRTEKHSTM	0.9149	0.9726	12	21
RUNX1-RUNX1T1	chr21	36231770	chr8	93029591	1058	HLA-C07:02	NRTEKHSTM	0.8793	0.9311	12	21
RUNX1-RUNX1T1	chr21	36231770	chr8	93029591	1058	HLA-B15:09	NRTEKHSTM	0.789	0.578	12	21
RUNX1-RUNX1T1	chr21	36231770	chr8	93029591	1058	HLA-C07:22	NRTEKHSTM	0.7861	0.7493	12	21
RUNX1-RUNX1T1	chr21	36231770	chr8	93029591	1058	HLA-B39:11	NRTEKHSTM	0.612	0.6772	12	21
RUNX1-RUNX1T1	chr21	36231770	chr8	93029591	1058	HLA-C03:67	NRTEKHSTM	0.5312	0.9643	12	21
RUNX1-RUNX1T1	chr21	36231770	chr8	93029591	1058	HLA-C06:06	NRTEKHSTM	0.5165	0.9761	12	21
RUNX1-RUNX1T1	chr21	36231770	chr8	93029591	1058	HLA-C06:17	NRTEKHSTM	0.1819	0.9853	12	21
RUNX1-RUNX1T1	chr21	36231770	chr8	93029591	1058	HLA-C06:02	NRTEKHSTM	0.1819	0.9853	12	21
RUNX1-RUNX1T1	chr21	36231770	chr8	93029591	1058	HLA-B07:26	GPREPRNRT	0.1136	0.528	6	15
RUNX1-RUNX1T1	chr21	36231770	chr8	93029591	1058	HLA-B27:06	RNRTEKHSTM	0.9725	0.652	11	21
RUNX1-RUNX1T1	chr21	36231771	chr8	92972745	2110	HLA-A02:60	RLSLLLVCV	0.947	0.7529	8	17
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	HLA-B07:05	GPREPRKEA	0.9991	0.6474	6	15
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	HLA-B07:02	GPREPRKEA	0.999	0.6477	6	15
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	HLA-B08:09	GPREPRKEA	0.7555	0.6337	6	15
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	HLA-B07:05	GPREPRKEAV	0.9979	0.6614	6	16
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	HLA-B07:02	GPREPRKEAV	0.9979	0.6602	6	16
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	HLA-B82:01	GPREPRKEAV	0.533	0.6344	6	16
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	HLA-B81:01	GPREPRKEAV	0.427	0.7179	6	16
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	HLA-B45:01	KEAVNEVKRQA	0.9995	0.9326	12	23
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	HLA-B50:02	KEAVNEVKRQA	0.9987	0.7433	12	23
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	HLA-B41:01	KEAVNEVKRQA	0.9962	0.8466	12	23
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	HLA-B07:12	GPREPRKEA	0.9239	0.7506	6	15
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	HLA-B07:04	GPREPRKEA	0.8707	0.5767	6	15
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	HLA-B42:02	GPREPRKEA	0.8281	0.5315	6	15
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	HLA-B42:01	GPREPRKEA	0.8059	0.5242	6	15
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	HLA-B78:01	GPREPRKEA	0.0732	0.5373	6	15
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	HLA-B07:12	GPREPRKEAV	0.9841	0.7414	6	16
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	HLA-B07:04	GPREPRKEAV	0.8953	0.5709	6	16
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	HLA-B40:06	KEAVNEVKRQA	0.9998	0.7363	12	23
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	HLA-B40:06	REPRKEAVNEV	0.9991	0.6595	8	19
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	HLA-B07:04	VDGPREPRKEA	0.9954	0.6213	4	15
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	HLA-B07:22	GPREPRKEA	0.999	0.6477	6	15
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	HLA-B07:09	GPREPRKEA	0.998	0.646	6	15
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	HLA-B55:04	GPREPRKEA	0.6608	0.5544	6	15
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	HLA-B07:26	GPREPRKEA	0.2932	0.5856	6	15
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	HLA-B07:22	GPREPRKEAV	0.9979	0.6602	6	16
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	HLA-B07:09	GPREPRKEAV	0.9973	0.654	6	16
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	HLA-B55:04	GPREPRKEAV	0.6577	0.5101	6	16
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	HLA-B07:26	GPREPRKEAV	0.6236	0.553	6	16
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	HLA-B82:02	GPREPRKEAV	0.533	0.6344	6	16
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	HLA-B07:26	VDGPREPRKEA	0.9964	0.5859	4	15
RUNX1-RUNX1T1	chr21	36231771	chr8	92988201	1058	HLA-B07:02	GPREPRNAH	0.9969	0.5628	6	15
RUNX1-RUNX1T1	chr21	36231771	chr8	92988201	1058	HLA-B35:01	EPRNAHREF	0.8729	0.7806	9	18
RUNX1-RUNX1T1	chr21	36231771	chr8	92988201	1058	HLA-B35:08	EPRNAHREF	0.8623	0.7173	9	18
RUNX1-RUNX1T1	chr21	36231771	chr8	92988201	1058	HLA-B07:12	GPREPRNAH	0.8082	0.7439	6	15
RUNX1-RUNX1T1	chr21	36231771	chr8	92988201	1058	HLA-B42:02	GPREPRNAH	0.298	0.502	6	15
RUNX1-RUNX1T1	chr21	36231771	chr8	92988201	1058	HLA-B07:09	GPREPRNA	0.9997	0.6155	6	14
RUNX1-RUNX1T1	chr21	36231771	chr8	92988201	1058	HLA-B07:09	GPREPRNAH	0.9973	0.5204	6	15
RUNX1-RUNX1T1	chr21	36231771	chr8	92988201	1058	HLA-B07:22	GPREPRNAH	0.9969	0.5628	6	15
RUNX1-RUNX1T1	chr21	36231771	chr8	92988201	1058	HLA-B35:23	EPRNAHREF	0.8737	0.754	9	18
RUNX1-RUNX1T1	chr21	36231771	chr8	92988201	1058	HLA-B35:77	EPRNAHREF	0.8729	0.7806	9	18
RUNX1-RUNX1T1	chr21	36231771	chr8	92988201	1058	HLA-B35:24	EPRNAHREF	0.7866	0.8132	9	18
RUNX1-RUNX1T1	chr21	36231771	chr8	92988201	1058	HLA-B35:30	EPRNAHREF	0.728	0.6076	9	18
RUNX1-RUNX1T1	chr21	36231771	chr8	92988201	1058	HLA-B35:17	EPRNAHREF	0.728	0.6076	9	18
RUNX1-RUNX1T1	chr21	36231771	chr8	92988201	1058	HLA-B35:11	EPRNAHREF	0.6826	0.7936	9	18
RUNX1-RUNX1T1	chr21	36231771	chr8	92988201	1058	HLA-B18:07	EPRNAHREF	0.0915	0.8152	9	18
RUNX1-RUNX1T1	chr21	36231771	chr8	92988201	1058	HLA-B35:43	EPRNAHREF	0.0737	0.6903	9	18
RUNX1-RUNX1T1	chr21	36231771	chr8	92988201	1058	HLA-B15:08	EPRNAHREF	0.0671	0.6666	9	18
RUNX1-RUNX1T1	chr21	36231771	chr8	92988201	1058	HLA-B15:11	EPRNAHREF	0.061	0.6734	9	18
RUNX1-RUNX1T1	chr21	36231771	chr8	92988201	1058	HLA-B15:53	REPRNAHREF	0.9773	0.8599	8	18
RUNX1-RUNX1T1	chr21	36231771	chr8	92988201	1058	HLA-B07:09	VDGPREPRNAH	0.9871	0.6461	4	15
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	HLA-A30:01	RSGRDRTEK	0.9877	0.8483	9	18
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	HLA-B27:06	RDRTEKHSTM	0.9712	0.747	12	22

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Potential FusionNeoAntigen Information of RUNX1-RUNX1T1 in HLA II

RUNX1-RUNX1T1_36231771_92983076.msa
RUNX1-RUNX1T1_36252854_93029593.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)
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	DRB1-1117	RKEAVNEVKRQAMTE	11	26
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	DRB1-1152	RKEAVNEVKRQAMTE	11	26
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	DRB1-1189	RKEAVNEVKRQAMTE	11	26
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	DRB1-1354	RKEAVNEVKRQAMTE	11	26
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	DRB1-1377	RKEAVNEVKRQAMTE	11	26
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	DRB1-1401	RKEAVNEVKRQAMTE	11	26
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	DRB1-1401	PRKEAVNEVKRQAMT	10	25
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	DRB1-1404	RKEAVNEVKRQAMTE	11	26
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	DRB1-1405	RKEAVNEVKRQAMTE	11	26
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	DRB1-1408	RKEAVNEVKRQAMTE	11	26
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	DRB1-1411	RKEAVNEVKRQAMTE	11	26
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	DRB1-1416	RKEAVNEVKRQAMTE	11	26
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	DRB1-1418	RKEAVNEVKRQAMTE	11	26
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	DRB1-1423	RKEAVNEVKRQAMTE	11	26
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	DRB1-1426	RKEAVNEVKRQAMTE	11	26
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	DRB1-1426	PRKEAVNEVKRQAMT	10	25
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	DRB1-1428	RKEAVNEVKRQAMTE	11	26
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	DRB1-1432	RKEAVNEVKRQAMTE	11	26
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	DRB1-1433	RKEAVNEVKRQAMTE	11	26
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	DRB1-1435	RKEAVNEVKRQAMTE	11	26
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	DRB1-1438	RKEAVNEVKRQAMTE	11	26
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	DRB1-1443	RKEAVNEVKRQAMTE	11	26
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	DRB1-1445	RKEAVNEVKRQAMTE	11	26
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	DRB1-1450	RKEAVNEVKRQAMTE	11	26
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	DRB1-1454	RKEAVNEVKRQAMTE	11	26
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	DRB1-1454	PRKEAVNEVKRQAMT	10	25
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	DRB1-1455	RKEAVNEVKRQAMTE	11	26
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	DRB1-1456	RKEAVNEVKRQAMTE	11	26
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	DRB1-1458	RKEAVNEVKRQAMTE	11	26
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	DRB1-1458	PRKEAVNEVKRQAMT	10	25
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	DRB1-1459	RKEAVNEVKRQAMTE	11	26
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	DRB1-1460	RKEAVNEVKRQAMTE	11	26
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	DRB1-1460	PRKEAVNEVKRQAMT	10	25
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	DRB1-1461	RKEAVNEVKRQAMTE	11	26
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	DRB1-1462	RKEAVNEVKRQAMTE	11	26
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	DRB1-1464	RKEAVNEVKRQAMTE	11	26
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	DRB1-1470	RKEAVNEVKRQAMTE	11	26
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	DRB1-1471	RKEAVNEVKRQAMTE	11	26
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	DRB1-1472	RKEAVNEVKRQAMTE	11	26
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	DRB1-1475	RKEAVNEVKRQAMTE	11	26
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	DRB1-1475	PRKEAVNEVKRQAMT	10	25
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	DRB1-1482	RKEAVNEVKRQAMTE	11	26
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	DRB1-1486	RKEAVNEVKRQAMTE	11	26
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	DRB1-1486	PRKEAVNEVKRQAMT	10	25
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	DRB1-1487	RKEAVNEVKRQAMTE	11	26
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	DRB1-1487	PRKEAVNEVKRQAMT	10	25
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	DRB1-1488	RKEAVNEVKRQAMTE	11	26
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	DRB1-1488	PRKEAVNEVKRQAMT	10	25
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	DRB1-1490	RKEAVNEVKRQAMTE	11	26
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	DRB1-1490	PRKEAVNEVKRQAMT	10	25
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	DRB1-1491	RKEAVNEVKRQAMTE	11	26
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	DRB1-1495	RKEAVNEVKRQAMTE	11	26
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	DRB1-1496	RKEAVNEVKRQAMTE	11	26
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	DRB1-1497	RKEAVNEVKRQAMTE	11	26
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	DRB1-1497	PRKEAVNEVKRQAMT	10	25
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	DRB1-1499	RKEAVNEVKRQAMTE	11	26
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	1058	DRB1-1499	PRKEAVNEVKRQAMT	10	25
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1102	FNDLRFVGRSGRDRT	1	16
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1102	RFNDLRFVGRSGRDR	0	15
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1114	FNDLRFVGRSGRDRT	1	16
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1116	FNDLRFVGRSGRDRT	1	16
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1116	RFNDLRFVGRSGRDR	0	15
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1120	FNDLRFVGRSGRDRT	1	16
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1121	FNDLRFVGRSGRDRT	1	16
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1121	RFNDLRFVGRSGRDR	0	15
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1136	FNDLRFVGRSGRDRT	1	16
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1136	RFNDLRFVGRSGRDR	0	15
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1148	FNDLRFVGRSGRDRT	1	16
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1148	RFNDLRFVGRSGRDR	0	15
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1159	FNDLRFVGRSGRDRT	1	16
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1165	FNDLRFVGRSGRDRT	1	16
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1165	RFNDLRFVGRSGRDR	0	15
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1168	FNDLRFVGRSGRDRT	1	16
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1186	FNDLRFVGRSGRDRT	1	16
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1186	NDLRFVGRSGRDRTE	2	17
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1186	RFNDLRFVGRSGRDR	0	15
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1301	FNDLRFVGRSGRDRT	1	16
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1301	RFNDLRFVGRSGRDR	0	15
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1302	FNDLRFVGRSGRDRT	1	16
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1308	FNDLRFVGRSGRDRT	1	16
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1308	RFNDLRFVGRSGRDR	0	15
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1315	FNDLRFVGRSGRDRT	1	16
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1316	FNDLRFVGRSGRDRT	1	16
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1316	NDLRFVGRSGRDRTE	2	17
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1316	RFNDLRFVGRSGRDR	0	15
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1317	FNDLRFVGRSGRDRT	1	16
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1319	FNDLRFVGRSGRDRT	1	16
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1320	FNDLRFVGRSGRDRT	1	16
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1320	RFNDLRFVGRSGRDR	0	15
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1322	FNDLRFVGRSGRDRT	1	16
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1322	RFNDLRFVGRSGRDR	0	15
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1323	FNDLRFVGRSGRDRT	1	16
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1327	FNDLRFVGRSGRDRT	1	16
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1327	RFNDLRFVGRSGRDR	0	15
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1327	NDLRFVGRSGRDRTE	2	17
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1329	FNDLRFVGRSGRDRT	1	16
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1334	FNDLRFVGRSGRDRT	1	16
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1335	FNDLRFVGRSGRDRT	1	16
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1335	RFNDLRFVGRSGRDR	0	15
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1339	FNDLRFVGRSGRDRT	1	16
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1341	FNDLRFVGRSGRDRT	1	16
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1351	FNDLRFVGRSGRDRT	1	16
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1351	RFNDLRFVGRSGRDR	0	15
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1352	FNDLRFVGRSGRDRT	1	16
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1352	RFNDLRFVGRSGRDR	0	15
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1353	FNDLRFVGRSGRDRT	1	16
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1357	FNDLRFVGRSGRDRT	1	16
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1359	FNDLRFVGRSGRDRT	1	16
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1359	RFNDLRFVGRSGRDR	0	15
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1361	FNDLRFVGRSGRDRT	1	16
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1361	RFNDLRFVGRSGRDR	0	15
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1364	FNDLRFVGRSGRDRT	1	16
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1364	RFNDLRFVGRSGRDR	0	15
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1368	FNDLRFVGRSGRDRT	1	16
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1368	RFNDLRFVGRSGRDR	0	15
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1369	FNDLRFVGRSGRDRT	1	16
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1369	RFNDLRFVGRSGRDR	0	15
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1370	FNDLRFVGRSGRDRT	1	16
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1370	RFNDLRFVGRSGRDR	0	15
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1371	FNDLRFVGRSGRDRT	1	16
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1371	RFNDLRFVGRSGRDR	0	15
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1371	NDLRFVGRSGRDRTE	2	17
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1372	FNDLRFVGRSGRDRT	1	16
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1372	RFNDLRFVGRSGRDR	0	15
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1373	FNDLRFVGRSGRDRT	1	16
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1374	FNDLRFVGRSGRDRT	1	16
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1376	FNDLRFVGRSGRDRT	1	16
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1376	RFNDLRFVGRSGRDR	0	15
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1378	FNDLRFVGRSGRDRT	1	16
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1378	RFNDLRFVGRSGRDR	0	15
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1379	FNDLRFVGRSGRDRT	1	16
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1379	RFNDLRFVGRSGRDR	0	15
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1380	FNDLRFVGRSGRDRT	1	16
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1380	RFNDLRFVGRSGRDR	0	15
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1383	FNDLRFVGRSGRDRT	1	16
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1383	RFNDLRFVGRSGRDR	0	15
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1384	FNDLRFVGRSGRDRT	1	16
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1384	RFNDLRFVGRSGRDR	0	15
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1387	FNDLRFVGRSGRDRT	1	16
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1387	RFNDLRFVGRSGRDR	0	15
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1391	FNDLRFVGRSGRDRT	1	16
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1391	RFNDLRFVGRSGRDR	0	15
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1392	FNDLRFVGRSGRDRT	1	16
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1392	RFNDLRFVGRSGRDR	0	15
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1397	FNDLRFVGRSGRDRT	1	16
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1398	FNDLRFVGRSGRDRT	1	16
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1398	RFNDLRFVGRSGRDR	0	15
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB1-1399	FNDLRFVGRSGRDRT	1	16
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	953	DRB5-0103	DLRFVGRSGRDRTEK	3	18

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Fusion breakpoint peptide structures of RUNX1-RUNX1T1

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
2605	FVGRSGRDRTEKHS	RUNX1	RUNX1T1	chr21	36252854	chr8	93029593	953

File name	BPseq	Hgene	Tgene	Hchr	Hbp	Tchr	Tbp	AAlen
3032	GPREPRKEAVNEVK	RUNX1	RUNX1T1	chr21	36231771	chr8	92983076	1058

File name	BPseq	Hgene	Tgene	Hchr	Hbp	Tchr	Tbp	AAlen
3033	GPREPRNAHREFLH	RUNX1	RUNX1T1	chr21	36231771	chr8	92988201	1058

File name	BPseq	Hgene	Tgene	Hchr	Hbp	Tchr	Tbp	AAlen
3034	GPREPRNRTEKHST	RUNX1	RUNX1T1	chr21	36231770	chr8	93029591	1058

File name	BPseq	Hgene	Tgene	Hchr	Hbp	Tchr	Tbp	AAlen
6102	NCRLSLLLVCVCVC	RUNX1	RUNX1T1	chr21	36231771	chr8	92972745	2110

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of RUNX1-RUNX1T1

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	2605	FVGRSGRDRTEKHS	-6.67724	-7.72034
HLA-B14:02	3BVN	2605	FVGRSGRDRTEKHS	-5.32474	-5.43654
HLA-B52:01	3W39	2605	FVGRSGRDRTEKHS	-6.90447	-7.01627
HLA-B52:01	3W39	2605	FVGRSGRDRTEKHS	-5.41738	-6.46048
HLA-A24:02	5HGA	2605	FVGRSGRDRTEKHS	-6.29703	-7.34013
HLA-A24:02	5HGA	2605	FVGRSGRDRTEKHS	-6.04399	-6.15579
HLA-B44:05	3DX8	2605	FVGRSGRDRTEKHS	-6.53068	-6.64248
HLA-B44:05	3DX8	2605	FVGRSGRDRTEKHS	-3.16704	-4.21014
HLA-B14:02	3BVN	3032	GPREPRKEAVNEVK	-7.9962	-8.1096
HLA-B14:02	3BVN	3032	GPREPRKEAVNEVK	-5.70842	-6.74372
HLA-B52:01	3W39	3032	GPREPRKEAVNEVK	-6.83737	-6.95077
HLA-B52:01	3W39	3032	GPREPRKEAVNEVK	-4.4836	-5.5189
HLA-A11:01	4UQ2	3032	GPREPRKEAVNEVK	-10.0067	-10.1201
HLA-A11:01	4UQ2	3032	GPREPRKEAVNEVK	-9.03915	-10.0745
HLA-A24:02	5HGA	3032	GPREPRKEAVNEVK	-6.56204	-6.67544
HLA-A24:02	5HGA	3032	GPREPRKEAVNEVK	-5.42271	-6.45801
HLA-B44:05	3DX8	3032	GPREPRKEAVNEVK	-7.85648	-8.89178
HLA-B44:05	3DX8	3032	GPREPRKEAVNEVK	-5.3978	-5.5112
HLA-A02:01	6TDR	3032	GPREPRKEAVNEVK	-3.37154	-4.40684
HLA-B14:02	3BVN	3033	GPREPRNAHREFLH	-7.9962	-8.1096
HLA-B14:02	3BVN	3033	GPREPRNAHREFLH	-5.70842	-6.74372
HLA-B52:01	3W39	3033	GPREPRNAHREFLH	-6.83737	-6.95077
HLA-B52:01	3W39	3033	GPREPRNAHREFLH	-4.4836	-5.5189
HLA-A11:01	4UQ2	3033	GPREPRNAHREFLH	-10.0067	-10.1201
HLA-A11:01	4UQ2	3033	GPREPRNAHREFLH	-9.03915	-10.0745
HLA-A24:02	5HGA	3033	GPREPRNAHREFLH	-6.56204	-6.67544
HLA-A24:02	5HGA	3033	GPREPRNAHREFLH	-5.42271	-6.45801
HLA-B44:05	3DX8	3033	GPREPRNAHREFLH	-7.85648	-8.89178
HLA-B44:05	3DX8	3033	GPREPRNAHREFLH	-5.3978	-5.5112
HLA-A02:01	6TDR	3033	GPREPRNAHREFLH	-3.37154	-4.40684
HLA-B14:02	3BVN	3034	GPREPRNRTEKHST	-7.9962	-8.1096
HLA-B14:02	3BVN	3034	GPREPRNRTEKHST	-5.70842	-6.74372
HLA-B52:01	3W39	3034	GPREPRNRTEKHST	-6.83737	-6.95077
HLA-B52:01	3W39	3034	GPREPRNRTEKHST	-4.4836	-5.5189
HLA-A11:01	4UQ2	3034	GPREPRNRTEKHST	-10.0067	-10.1201
HLA-A11:01	4UQ2	3034	GPREPRNRTEKHST	-9.03915	-10.0745
HLA-A24:02	5HGA	3034	GPREPRNRTEKHST	-6.56204	-6.67544
HLA-A24:02	5HGA	3034	GPREPRNRTEKHST	-5.42271	-6.45801
HLA-B44:05	3DX8	3034	GPREPRNRTEKHST	-7.85648	-8.89178
HLA-B44:05	3DX8	3034	GPREPRNRTEKHST	-5.3978	-5.5112
HLA-A02:01	6TDR	3034	GPREPRNRTEKHST	-3.37154	-4.40684
HLA-B14:02	3BVN	6102	NCRLSLLLVCVCVC	-7.9962	-8.1096
HLA-B14:02	3BVN	6102	NCRLSLLLVCVCVC	-5.70842	-6.74372
HLA-B52:01	3W39	6102	NCRLSLLLVCVCVC	-6.83737	-6.95077
HLA-B52:01	3W39	6102	NCRLSLLLVCVCVC	-4.4836	-5.5189
HLA-A11:01	4UQ2	6102	NCRLSLLLVCVCVC	-10.0067	-10.1201
HLA-A11:01	4UQ2	6102	NCRLSLLLVCVCVC	-9.03915	-10.0745
HLA-A24:02	5HGA	6102	NCRLSLLLVCVCVC	-6.56204	-6.67544
HLA-A24:02	5HGA	6102	NCRLSLLLVCVCVC	-5.42271	-6.45801
HLA-B44:05	3DX8	6102	NCRLSLLLVCVCVC	-7.85648	-8.89178
HLA-B44:05	3DX8	6102	NCRLSLLLVCVCVC	-5.3978	-5.5112
HLA-A02:01	6TDR	6102	NCRLSLLLVCVCVC	-3.37154	-4.40684

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Vaccine Design for the FusionNeoAntigens of RUNX1-RUNX1T1

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
RUNX1-RUNX1T1	chr21	36231770	chr8	93029591	11	21	RNRTEKHSTM	CTCGAAATCGTACTGAGAAGCACTCCACAA
RUNX1-RUNX1T1	chr21	36231770	chr8	93029591	12	21	NRTEKHSTM	GAAATCGTACTGAGAAGCACTCCACAA
RUNX1-RUNX1T1	chr21	36231770	chr8	93029591	6	15	GPREPRNRT	ATGGGCCCCGAGAACCTCGAAATCGTA
RUNX1-RUNX1T1	chr21	36231771	chr8	92972745	8	17	RLSLLLVCV	CCCGAGAACCTCGAAAGTTGCTGGAAT
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	12	23	KEAVNEVKRQA	GAAAGGAGGCCGTCAATGAGGTGAAGCGCCAGG
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	4	15	VDGPREPRKEA	CAGTGGATGGGCCCCGAGAACCTCGAAAGGAGG
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	6	15	GPREPRKEA	ATGGGCCCCGAGAACCTCGAAAGGAGG
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	6	16	GPREPRKEAV	ATGGGCCCCGAGAACCTCGAAAGGAGGCCG
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	8	19	REPRKEAVNEV	CCCGAGAACCTCGAAAGGAGGCCGTCAATGAGG
RUNX1-RUNX1T1	chr21	36231771	chr8	92988201	4	15	VDGPREPRNAH	CAGTGGATGGGCCCCGAGAACCTCGAAACGCGC
RUNX1-RUNX1T1	chr21	36231771	chr8	92988201	6	14	GPREPRNA	ATGGGCCCCGAGAACCTCGAAACG
RUNX1-RUNX1T1	chr21	36231771	chr8	92988201	6	15	GPREPRNAH	ATGGGCCCCGAGAACCTCGAAACGCGC
RUNX1-RUNX1T1	chr21	36231771	chr8	92988201	8	18	REPRNAHREF	CCCGAGAACCTCGAAACGCGCATCGGGAAT
RUNX1-RUNX1T1	chr21	36231771	chr8	92988201	9	18	EPRNAHREF	GAGAACCTCGAAACGCGCATCGGGAAT
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	12	22	RDRTEKHSTM	GAGATCGTACTGAGAAGCACTCCACAATGC
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	9	18	RSGRDRTEK	GAAGTGGAAGAGATCGTACTGAGAAGC

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
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	10	25	PRKEAVNEVKRQAMT	AACCTCGAAAGGAGGCCGTCAATGAGGTGAAGCGCCAGGCGATGA
RUNX1-RUNX1T1	chr21	36231771	chr8	92983076	11	26	RKEAVNEVKRQAMTE	CTCGAAAGGAGGCCGTCAATGAGGTGAAGCGCCAGGCGATGACGG
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	0	15	RFNDLRFVGRSGRDR	GATTTAATGACCTCAGGTTTGTCGGTCGAAGTGGAAGAGATCGTA
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	1	16	FNDLRFVGRSGRDRT	TTAATGACCTCAGGTTTGTCGGTCGAAGTGGAAGAGATCGTACTG
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	2	17	NDLRFVGRSGRDRTE	ATGACCTCAGGTTTGTCGGTCGAAGTGGAAGAGATCGTACTGAGA
RUNX1-RUNX1T1	chr21	36252854	chr8	93029593	3	18	DLRFVGRSGRDRTEK	ACCTCAGGTTTGTCGGTCGAAGTGGAAGAGATCGTACTGAGAAGC

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Information of the samples that have these potential fusion neoantigens of RUNX1-RUNX1T1

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
N/A	RUNX1-RUNX1T1	chr21	36252854	ENST00000300305	chr8	93029593	ENST00000265814	JZ534324
N/A	RUNX1-RUNX1T1	chr21	36231771	ENST00000300305	chr8	92988201	ENST00000265814	JZ534340
N/A	RUNX1-RUNX1T1	chr21	36231771	ENST00000300305	chr8	92983076	ENST00000265814	JZ534355
N/A	RUNX1-RUNX1T1	chr21	36231771	ENST00000344691	chr8	92972745	ENST00000265814	JZ534359

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Potential target of CAR-T therapy development for RUNX1-RUNX1T1

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 RUNX1-RUNX1T1

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

Hgene	Tgene	Drug	Source	PMID
RUNX1	RUNX1T1	Imatinib	PubMed	19167615

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Related Diseases to RUNX1-RUNX1T1

Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)

Hgene	Tgene	Disease	Source	PMID
RUNX1	RUNX1T1	Therapy Associated Myelodysplastic Syndrome (T-Mds)	PubMed	19167615
RUNX1	RUNX1T1	Lung Adenocarcinoma	MyCancerGenome
RUNX1	RUNX1T1	Acute Myeloid Leukemia	MyCancerGenome
RUNX1	RUNX1T1	Breast Invasive Ductal Carcinoma	MyCancerGenome
RUNX1	RUNX1T1	Acute Myeloid Leukemia With T(8;21); (Q22; Q22.1); Runx1-Runx1t1	MyCancerGenome
RUNX1	RUNX1T1	Adenocarcinoma Of The Gastroesophageal Junction	MyCancerGenome

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner	Gene	Disease ID	Disease name	# pubmeds	Source
Hgene	RUNX1	C1832388	Platelet Disorder, Familial, with Associated Myeloid Malignancy	11	CLINGEN;CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
Hgene	RUNX1	C0023467	Leukemia, Myelocytic, Acute	4	CGI;CTD_human;GENOMICS_ENGLAND
Hgene	RUNX1	C0026998	Acute Myeloid Leukemia, M1	3	CTD_human
Hgene	RUNX1	C1879321	Acute Myeloid Leukemia (AML-M2)	3	CTD_human
Hgene	RUNX1	C0023485	Precursor B-Cell Lymphoblastic Leukemia-Lymphoma	2	CTD_human
Hgene	RUNX1	C0003873	Rheumatoid Arthritis	1	CTD_human
Hgene	RUNX1	C0006413	Burkitt Lymphoma	1	ORPHANET
Hgene	RUNX1	C0017636	Glioblastoma	1	CTD_human
Hgene	RUNX1	C0023452	Childhood Acute Lymphoblastic Leukemia	1	CTD_human
Hgene	RUNX1	C0023453	L2 Acute Lymphoblastic Leukemia	1	CTD_human
Hgene	RUNX1	C0023473	Myeloid Leukemia, Chronic	1	ORPHANET
Hgene	RUNX1	C0033578	Prostatic Neoplasms	1	CTD_human
Hgene	RUNX1	C0040034	Thrombocytopenia	1	GENOMICS_ENGLAND
Hgene	RUNX1	C0334588	Giant Cell Glioblastoma	1	CTD_human
Hgene	RUNX1	C0349639	Juvenile Myelomonocytic Leukemia	1	CTD_human
Hgene	RUNX1	C0376358	Malignant neoplasm of prostate	1	CTD_human
Hgene	RUNX1	C1292769	Precursor B-cell lymphoblastic leukemia	1	ORPHANET
Hgene	RUNX1	C1621958	Glioblastoma Multiforme	1	CTD_human
Hgene	RUNX1	C1961102	Precursor Cell Lymphoblastic Leukemia Lymphoma	1	CTD_human
Hgene	RUNX1	C2713368	Hematopoetic Myelodysplasia	1	CTD_human
Hgene	RUNX1	C3463824	MYELODYSPLASTIC SYNDROME	1	CTD_human
Tgene	RUNX1T1	C0023467	Leukemia, Myelocytic, Acute	2	CTD_human
Tgene	RUNX1T1	C0026998	Acute Myeloid Leukemia, M1	2	CTD_human
Tgene	RUNX1T1	C1879321	Acute Myeloid Leukemia (AML-M2)	2	CTD_human
Tgene	RUNX1T1	C0149925	Small cell carcinoma of lung	1	CTD_human

	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)