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	Fusion Gene Summary
	Fusion Gene ORF analysis
	Fusion Genomic Features
	Fusion Protein Features
	Fusion Gene Sequence
	Fusion Gene PPI analysis
	Related Drugs
	Related Diseases

Fusion gene:MLLT3-KMT2A (FusionGDB2 ID:53970)

Fusion Gene Summary for MLLT3-KMT2A

Fusion gene summary

Fusion gene information	Fusion gene name: MLLT3-KMT2A
	Fusion gene ID: 53970
		Hgene	Tgene
	Gene symbol	MLLT3	KMT2A
	Gene ID	4300	4297
	Gene name	MLLT3 super elongation complex subunit	lysine methyltransferase 2A
	Synonyms	AF9\|YEATS3	ALL-1\|CXXC7\|HRX\|HTRX1\|MLL\|MLL1\|MLL1A\|TRX1\|WDSTS
	Cytomap	9p21.3	11q23.3
	Type of gene	protein-coding	protein-coding
	Description	protein AF-9ALL1-fused gene from chromosome 9 proteinKMT2A/MLLT3 fusionKMT2A/MLLT3 fusion proteinYEATS domain-containing protein 3myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog); translocated to, 3myeloid/lymphoid or mixed-lineage leu	histone-lysine N-methyltransferase 2ACXXC-type zinc finger protein 7lysine (K)-specific methyltransferase 2Alysine N-methyltransferase 2Amixed lineage leukemia 1myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)trithorax-like
	Modification date	20200327	20200319
	UniProtAcc	P42568	Q03164
	Ensembl transtripts involved in fusion gene	ENST00000380338, ENST00000355930, ENST00000429426, ENST00000475957, ENST00000380321,	ENST00000534358, ENST00000389506, ENST00000354520, ENST00000420751,
Fusion gene scores	* DoF score	18 X 14 X 11=2772	31 X 72 X 3=6696
	# samples	25	79
	** MAII score	log2(25/2772*10)=-3.47092725747513 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(79/6696*10)=-3.08337496948588 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context	PubMed: MLLT3 [Title/Abstract] AND KMT2A [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	KMT2A(118353210)-MLLT3(20365742), # samples:2 MLLT3(20360029)-KMT2A(118353560), # samples:2
Anticipated loss of major functional domain due to fusion event.

* 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	MLLT3	GO:0045893	positive regulation of transcription, DNA-templated	25417107\|27105114
Hgene	MLLT3	GO:0090090	negative regulation of canonical Wnt signaling pathway	19591803
Tgene	KMT2A	GO:0044648	histone H3-K4 dimethylation	25561738
Tgene	KMT2A	GO:0045944	positive regulation of transcription by RNA polymerase II	20861184
Tgene	KMT2A	GO:0051568	histone H3-K4 methylation	19556245
Tgene	KMT2A	GO:0065003	protein-containing complex assembly	15199122
Tgene	KMT2A	GO:0080182	histone H3-K4 trimethylation	20861184
Tgene	KMT2A	GO:0097692	histone H3-K4 monomethylation	25561738\|26324722

Fusion gene breakpoints across MLLT3 (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 KMT2A (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* All genome coordinats were lifted-over on hg19.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.

Source	Disease	Sample	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
ChiTaRS5.0	N/A	AY282402	MLLT3	chr9	20410548	-	KMT2A	chr11	118359129	+
ChiTaRS5.0	N/A	AY282403	MLLT3	chr9	20358126	-	KMT2A	chr11	118354734	+
ChiTaRS5.0	N/A	AY282404	MLLT3	chr9	20373293	-	KMT2A	chr11	118359137	+
ChiTaRS5.0	N/A	AY282405	MLLT3	chr9	20372883	-	KMT2A	chr11	118359141	+
ChiTaRS5.0	N/A	AY387662	MLLT3	chr9	20413320	-	KMT2A	chr11	118359129	+
ChiTaRS5.0	N/A	AY840547	MLLT3	chr9	20360029	+	KMT2A	chr11	118353560	-
ChiTaRS5.0	N/A	AY840550	MLLT3	chr9	20360029	+	KMT2A	chr11	118353560	-

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Fusion Gene ORF analysis for MLLT3-KMT2A

Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.

ORF	Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
intron-intron	ENST00000380338	ENST00000534358	MLLT3	chr9	20410548	-	KMT2A	chr11	118359129	+
intron-intron	ENST00000380338	ENST00000389506	MLLT3	chr9	20410548	-	KMT2A	chr11	118359129	+
intron-intron	ENST00000380338	ENST00000354520	MLLT3	chr9	20410548	-	KMT2A	chr11	118359129	+
intron-intron	ENST00000380338	ENST00000420751	MLLT3	chr9	20410548	-	KMT2A	chr11	118359129	+
intron-intron	ENST00000355930	ENST00000534358	MLLT3	chr9	20410548	-	KMT2A	chr11	118359129	+
intron-intron	ENST00000355930	ENST00000389506	MLLT3	chr9	20410548	-	KMT2A	chr11	118359129	+
intron-intron	ENST00000355930	ENST00000354520	MLLT3	chr9	20410548	-	KMT2A	chr11	118359129	+
intron-intron	ENST00000355930	ENST00000420751	MLLT3	chr9	20410548	-	KMT2A	chr11	118359129	+
intron-intron	ENST00000429426	ENST00000534358	MLLT3	chr9	20410548	-	KMT2A	chr11	118359129	+
intron-intron	ENST00000429426	ENST00000389506	MLLT3	chr9	20410548	-	KMT2A	chr11	118359129	+
intron-intron	ENST00000429426	ENST00000354520	MLLT3	chr9	20410548	-	KMT2A	chr11	118359129	+
intron-intron	ENST00000429426	ENST00000420751	MLLT3	chr9	20410548	-	KMT2A	chr11	118359129	+
intron-intron	ENST00000475957	ENST00000534358	MLLT3	chr9	20410548	-	KMT2A	chr11	118359129	+
intron-intron	ENST00000475957	ENST00000389506	MLLT3	chr9	20410548	-	KMT2A	chr11	118359129	+
intron-intron	ENST00000475957	ENST00000354520	MLLT3	chr9	20410548	-	KMT2A	chr11	118359129	+
intron-intron	ENST00000475957	ENST00000420751	MLLT3	chr9	20410548	-	KMT2A	chr11	118359129	+
intron-intron	ENST00000380321	ENST00000534358	MLLT3	chr9	20410548	-	KMT2A	chr11	118359129	+
intron-intron	ENST00000380321	ENST00000389506	MLLT3	chr9	20410548	-	KMT2A	chr11	118359129	+
intron-intron	ENST00000380321	ENST00000354520	MLLT3	chr9	20410548	-	KMT2A	chr11	118359129	+
intron-intron	ENST00000380321	ENST00000420751	MLLT3	chr9	20410548	-	KMT2A	chr11	118359129	+
intron-intron	ENST00000380338	ENST00000534358	MLLT3	chr9	20358126	-	KMT2A	chr11	118354734	+
intron-intron	ENST00000380338	ENST00000389506	MLLT3	chr9	20358126	-	KMT2A	chr11	118354734	+
intron-intron	ENST00000380338	ENST00000354520	MLLT3	chr9	20358126	-	KMT2A	chr11	118354734	+
intron-intron	ENST00000380338	ENST00000420751	MLLT3	chr9	20358126	-	KMT2A	chr11	118354734	+
intron-intron	ENST00000355930	ENST00000534358	MLLT3	chr9	20358126	-	KMT2A	chr11	118354734	+
intron-intron	ENST00000355930	ENST00000389506	MLLT3	chr9	20358126	-	KMT2A	chr11	118354734	+
intron-intron	ENST00000355930	ENST00000354520	MLLT3	chr9	20358126	-	KMT2A	chr11	118354734	+
intron-intron	ENST00000355930	ENST00000420751	MLLT3	chr9	20358126	-	KMT2A	chr11	118354734	+
intron-intron	ENST00000429426	ENST00000534358	MLLT3	chr9	20358126	-	KMT2A	chr11	118354734	+
intron-intron	ENST00000429426	ENST00000389506	MLLT3	chr9	20358126	-	KMT2A	chr11	118354734	+
intron-intron	ENST00000429426	ENST00000354520	MLLT3	chr9	20358126	-	KMT2A	chr11	118354734	+
intron-intron	ENST00000429426	ENST00000420751	MLLT3	chr9	20358126	-	KMT2A	chr11	118354734	+
intron-intron	ENST00000475957	ENST00000534358	MLLT3	chr9	20358126	-	KMT2A	chr11	118354734	+
intron-intron	ENST00000475957	ENST00000389506	MLLT3	chr9	20358126	-	KMT2A	chr11	118354734	+
intron-intron	ENST00000475957	ENST00000354520	MLLT3	chr9	20358126	-	KMT2A	chr11	118354734	+
intron-intron	ENST00000475957	ENST00000420751	MLLT3	chr9	20358126	-	KMT2A	chr11	118354734	+
intron-intron	ENST00000380321	ENST00000534358	MLLT3	chr9	20358126	-	KMT2A	chr11	118354734	+
intron-intron	ENST00000380321	ENST00000389506	MLLT3	chr9	20358126	-	KMT2A	chr11	118354734	+
intron-intron	ENST00000380321	ENST00000354520	MLLT3	chr9	20358126	-	KMT2A	chr11	118354734	+
intron-intron	ENST00000380321	ENST00000420751	MLLT3	chr9	20358126	-	KMT2A	chr11	118354734	+
intron-intron	ENST00000380338	ENST00000534358	MLLT3	chr9	20373293	-	KMT2A	chr11	118359137	+
intron-intron	ENST00000380338	ENST00000389506	MLLT3	chr9	20373293	-	KMT2A	chr11	118359137	+
intron-intron	ENST00000380338	ENST00000354520	MLLT3	chr9	20373293	-	KMT2A	chr11	118359137	+
intron-intron	ENST00000380338	ENST00000420751	MLLT3	chr9	20373293	-	KMT2A	chr11	118359137	+
intron-intron	ENST00000355930	ENST00000534358	MLLT3	chr9	20373293	-	KMT2A	chr11	118359137	+
intron-intron	ENST00000355930	ENST00000389506	MLLT3	chr9	20373293	-	KMT2A	chr11	118359137	+
intron-intron	ENST00000355930	ENST00000354520	MLLT3	chr9	20373293	-	KMT2A	chr11	118359137	+
intron-intron	ENST00000355930	ENST00000420751	MLLT3	chr9	20373293	-	KMT2A	chr11	118359137	+
intron-intron	ENST00000429426	ENST00000534358	MLLT3	chr9	20373293	-	KMT2A	chr11	118359137	+
intron-intron	ENST00000429426	ENST00000389506	MLLT3	chr9	20373293	-	KMT2A	chr11	118359137	+
intron-intron	ENST00000429426	ENST00000354520	MLLT3	chr9	20373293	-	KMT2A	chr11	118359137	+
intron-intron	ENST00000429426	ENST00000420751	MLLT3	chr9	20373293	-	KMT2A	chr11	118359137	+
intron-intron	ENST00000475957	ENST00000534358	MLLT3	chr9	20373293	-	KMT2A	chr11	118359137	+
intron-intron	ENST00000475957	ENST00000389506	MLLT3	chr9	20373293	-	KMT2A	chr11	118359137	+
intron-intron	ENST00000475957	ENST00000354520	MLLT3	chr9	20373293	-	KMT2A	chr11	118359137	+
intron-intron	ENST00000475957	ENST00000420751	MLLT3	chr9	20373293	-	KMT2A	chr11	118359137	+
intron-intron	ENST00000380321	ENST00000534358	MLLT3	chr9	20373293	-	KMT2A	chr11	118359137	+
intron-intron	ENST00000380321	ENST00000389506	MLLT3	chr9	20373293	-	KMT2A	chr11	118359137	+
intron-intron	ENST00000380321	ENST00000354520	MLLT3	chr9	20373293	-	KMT2A	chr11	118359137	+
intron-intron	ENST00000380321	ENST00000420751	MLLT3	chr9	20373293	-	KMT2A	chr11	118359137	+
intron-intron	ENST00000380338	ENST00000534358	MLLT3	chr9	20372883	-	KMT2A	chr11	118359141	+
intron-intron	ENST00000380338	ENST00000389506	MLLT3	chr9	20372883	-	KMT2A	chr11	118359141	+
intron-intron	ENST00000380338	ENST00000354520	MLLT3	chr9	20372883	-	KMT2A	chr11	118359141	+
intron-intron	ENST00000380338	ENST00000420751	MLLT3	chr9	20372883	-	KMT2A	chr11	118359141	+
intron-intron	ENST00000355930	ENST00000534358	MLLT3	chr9	20372883	-	KMT2A	chr11	118359141	+
intron-intron	ENST00000355930	ENST00000389506	MLLT3	chr9	20372883	-	KMT2A	chr11	118359141	+
intron-intron	ENST00000355930	ENST00000354520	MLLT3	chr9	20372883	-	KMT2A	chr11	118359141	+
intron-intron	ENST00000355930	ENST00000420751	MLLT3	chr9	20372883	-	KMT2A	chr11	118359141	+
intron-intron	ENST00000429426	ENST00000534358	MLLT3	chr9	20372883	-	KMT2A	chr11	118359141	+
intron-intron	ENST00000429426	ENST00000389506	MLLT3	chr9	20372883	-	KMT2A	chr11	118359141	+
intron-intron	ENST00000429426	ENST00000354520	MLLT3	chr9	20372883	-	KMT2A	chr11	118359141	+
intron-intron	ENST00000429426	ENST00000420751	MLLT3	chr9	20372883	-	KMT2A	chr11	118359141	+
intron-intron	ENST00000475957	ENST00000534358	MLLT3	chr9	20372883	-	KMT2A	chr11	118359141	+
intron-intron	ENST00000475957	ENST00000389506	MLLT3	chr9	20372883	-	KMT2A	chr11	118359141	+
intron-intron	ENST00000475957	ENST00000354520	MLLT3	chr9	20372883	-	KMT2A	chr11	118359141	+
intron-intron	ENST00000475957	ENST00000420751	MLLT3	chr9	20372883	-	KMT2A	chr11	118359141	+
intron-intron	ENST00000380321	ENST00000534358	MLLT3	chr9	20372883	-	KMT2A	chr11	118359141	+
intron-intron	ENST00000380321	ENST00000389506	MLLT3	chr9	20372883	-	KMT2A	chr11	118359141	+
intron-intron	ENST00000380321	ENST00000354520	MLLT3	chr9	20372883	-	KMT2A	chr11	118359141	+
intron-intron	ENST00000380321	ENST00000420751	MLLT3	chr9	20372883	-	KMT2A	chr11	118359141	+
intron-intron	ENST00000380338	ENST00000534358	MLLT3	chr9	20413320	-	KMT2A	chr11	118359129	+
intron-intron	ENST00000380338	ENST00000389506	MLLT3	chr9	20413320	-	KMT2A	chr11	118359129	+
intron-intron	ENST00000380338	ENST00000354520	MLLT3	chr9	20413320	-	KMT2A	chr11	118359129	+
intron-intron	ENST00000380338	ENST00000420751	MLLT3	chr9	20413320	-	KMT2A	chr11	118359129	+
intron-intron	ENST00000355930	ENST00000534358	MLLT3	chr9	20413320	-	KMT2A	chr11	118359129	+
intron-intron	ENST00000355930	ENST00000389506	MLLT3	chr9	20413320	-	KMT2A	chr11	118359129	+
intron-intron	ENST00000355930	ENST00000354520	MLLT3	chr9	20413320	-	KMT2A	chr11	118359129	+
intron-intron	ENST00000355930	ENST00000420751	MLLT3	chr9	20413320	-	KMT2A	chr11	118359129	+
intron-intron	ENST00000429426	ENST00000534358	MLLT3	chr9	20413320	-	KMT2A	chr11	118359129	+
intron-intron	ENST00000429426	ENST00000389506	MLLT3	chr9	20413320	-	KMT2A	chr11	118359129	+
intron-intron	ENST00000429426	ENST00000354520	MLLT3	chr9	20413320	-	KMT2A	chr11	118359129	+
intron-intron	ENST00000429426	ENST00000420751	MLLT3	chr9	20413320	-	KMT2A	chr11	118359129	+
intron-intron	ENST00000475957	ENST00000534358	MLLT3	chr9	20413320	-	KMT2A	chr11	118359129	+
intron-intron	ENST00000475957	ENST00000389506	MLLT3	chr9	20413320	-	KMT2A	chr11	118359129	+
intron-intron	ENST00000475957	ENST00000354520	MLLT3	chr9	20413320	-	KMT2A	chr11	118359129	+
intron-intron	ENST00000475957	ENST00000420751	MLLT3	chr9	20413320	-	KMT2A	chr11	118359129	+
intron-intron	ENST00000380321	ENST00000534358	MLLT3	chr9	20413320	-	KMT2A	chr11	118359129	+
intron-intron	ENST00000380321	ENST00000389506	MLLT3	chr9	20413320	-	KMT2A	chr11	118359129	+
intron-intron	ENST00000380321	ENST00000354520	MLLT3	chr9	20413320	-	KMT2A	chr11	118359129	+
intron-intron	ENST00000380321	ENST00000420751	MLLT3	chr9	20413320	-	KMT2A	chr11	118359129	+
intron-intron	ENST00000380338	ENST00000534358	MLLT3	chr9	20360029	+	KMT2A	chr11	118353560	-
intron-intron	ENST00000380338	ENST00000389506	MLLT3	chr9	20360029	+	KMT2A	chr11	118353560	-
intron-intron	ENST00000380338	ENST00000354520	MLLT3	chr9	20360029	+	KMT2A	chr11	118353560	-
intron-intron	ENST00000380338	ENST00000420751	MLLT3	chr9	20360029	+	KMT2A	chr11	118353560	-
intron-intron	ENST00000355930	ENST00000534358	MLLT3	chr9	20360029	+	KMT2A	chr11	118353560	-
intron-intron	ENST00000355930	ENST00000389506	MLLT3	chr9	20360029	+	KMT2A	chr11	118353560	-
intron-intron	ENST00000355930	ENST00000354520	MLLT3	chr9	20360029	+	KMT2A	chr11	118353560	-
intron-intron	ENST00000355930	ENST00000420751	MLLT3	chr9	20360029	+	KMT2A	chr11	118353560	-
intron-intron	ENST00000429426	ENST00000534358	MLLT3	chr9	20360029	+	KMT2A	chr11	118353560	-
intron-intron	ENST00000429426	ENST00000389506	MLLT3	chr9	20360029	+	KMT2A	chr11	118353560	-
intron-intron	ENST00000429426	ENST00000354520	MLLT3	chr9	20360029	+	KMT2A	chr11	118353560	-
intron-intron	ENST00000429426	ENST00000420751	MLLT3	chr9	20360029	+	KMT2A	chr11	118353560	-
intron-intron	ENST00000475957	ENST00000534358	MLLT3	chr9	20360029	+	KMT2A	chr11	118353560	-
intron-intron	ENST00000475957	ENST00000389506	MLLT3	chr9	20360029	+	KMT2A	chr11	118353560	-
intron-intron	ENST00000475957	ENST00000354520	MLLT3	chr9	20360029	+	KMT2A	chr11	118353560	-
intron-intron	ENST00000475957	ENST00000420751	MLLT3	chr9	20360029	+	KMT2A	chr11	118353560	-
intron-intron	ENST00000380321	ENST00000534358	MLLT3	chr9	20360029	+	KMT2A	chr11	118353560	-
intron-intron	ENST00000380321	ENST00000389506	MLLT3	chr9	20360029	+	KMT2A	chr11	118353560	-
intron-intron	ENST00000380321	ENST00000354520	MLLT3	chr9	20360029	+	KMT2A	chr11	118353560	-
intron-intron	ENST00000380321	ENST00000420751	MLLT3	chr9	20360029	+	KMT2A	chr11	118353560	-
5CDS-intron	ENST00000380338	ENST00000354520	MLLT3	chr9	20413718	-	KMT2A	chr11	118355576
5CDS-intron	ENST00000380338	ENST00000420751	MLLT3	chr9	20413718	-	KMT2A	chr11	118355576
5CDS-intron	ENST00000380338	ENST00000420751	MLLT3	chr9	20413718	-	KMT2A	chr11	118359328
5CDS-intron	ENST00000429426	ENST00000354520	MLLT3	chr9	20413718	-	KMT2A	chr11	118355576
5CDS-intron	ENST00000429426	ENST00000420751	MLLT3	chr9	20413718	-	KMT2A	chr11	118355576
5CDS-intron	ENST00000429426	ENST00000420751	MLLT3	chr9	20413718	-	KMT2A	chr11	118359328
5UTR-3CDS	ENST00000355930	ENST00000354520	MLLT3	chr9	20413718	-	KMT2A	chr11	118359328
5UTR-3CDS	ENST00000355930	ENST00000389506	MLLT3	chr9	20413718	-	KMT2A	chr11	118355576
5UTR-3CDS	ENST00000355930	ENST00000389506	MLLT3	chr9	20413718	-	KMT2A	chr11	118359328
5UTR-3CDS	ENST00000355930	ENST00000534358	MLLT3	chr9	20413718	-	KMT2A	chr11	118355576
5UTR-3CDS	ENST00000355930	ENST00000534358	MLLT3	chr9	20413718	-	KMT2A	chr11	118359328
5UTR-3CDS	ENST00000475957	ENST00000354520	MLLT3	chr9	20413718	-	KMT2A	chr11	118359328
5UTR-3CDS	ENST00000475957	ENST00000389506	MLLT3	chr9	20413718	-	KMT2A	chr11	118355576
5UTR-3CDS	ENST00000475957	ENST00000389506	MLLT3	chr9	20413718	-	KMT2A	chr11	118359328
5UTR-3CDS	ENST00000475957	ENST00000534358	MLLT3	chr9	20413718	-	KMT2A	chr11	118355576
5UTR-3CDS	ENST00000475957	ENST00000534358	MLLT3	chr9	20413718	-	KMT2A	chr11	118359328
5UTR-intron	ENST00000355930	ENST00000354520	MLLT3	chr9	20413718	-	KMT2A	chr11	118355576
5UTR-intron	ENST00000355930	ENST00000420751	MLLT3	chr9	20413718	-	KMT2A	chr11	118355576
5UTR-intron	ENST00000355930	ENST00000420751	MLLT3	chr9	20413718	-	KMT2A	chr11	118359328
5UTR-intron	ENST00000475957	ENST00000354520	MLLT3	chr9	20413718	-	KMT2A	chr11	118355576
5UTR-intron	ENST00000475957	ENST00000420751	MLLT3	chr9	20413718	-	KMT2A	chr11	118355576
5UTR-intron	ENST00000475957	ENST00000420751	MLLT3	chr9	20413718	-	KMT2A	chr11	118359328
In-frame	ENST00000380338	ENST00000354520	MLLT3	chr9	20413718	-	KMT2A	chr11	118359328
In-frame	ENST00000380338	ENST00000389506	MLLT3	chr9	20413718	-	KMT2A	chr11	118355576
In-frame	ENST00000380338	ENST00000389506	MLLT3	chr9	20413718	-	KMT2A	chr11	118359328
In-frame	ENST00000380338	ENST00000534358	MLLT3	chr9	20413718	-	KMT2A	chr11	118355576
In-frame	ENST00000380338	ENST00000534358	MLLT3	chr9	20413718	-	KMT2A	chr11	118359328
In-frame	ENST00000429426	ENST00000354520	MLLT3	chr9	20413718	-	KMT2A	chr11	118359328
In-frame	ENST00000429426	ENST00000389506	MLLT3	chr9	20413718	-	KMT2A	chr11	118355576
In-frame	ENST00000429426	ENST00000389506	MLLT3	chr9	20413718	-	KMT2A	chr11	118359328
In-frame	ENST00000429426	ENST00000534358	MLLT3	chr9	20413718	-	KMT2A	chr11	118355576
In-frame	ENST00000429426	ENST00000534358	MLLT3	chr9	20413718	-	KMT2A	chr11	118359328
intron-3CDS	ENST00000380321	ENST00000354520	MLLT3	chr9	20413718	-	KMT2A	chr11	118359328
intron-3CDS	ENST00000380321	ENST00000389506	MLLT3	chr9	20413718	-	KMT2A	chr11	118355576
intron-3CDS	ENST00000380321	ENST00000389506	MLLT3	chr9	20413718	-	KMT2A	chr11	118359328
intron-3CDS	ENST00000380321	ENST00000534358	MLLT3	chr9	20413718	-	KMT2A	chr11	118355576
intron-3CDS	ENST00000380321	ENST00000534358	MLLT3	chr9	20413718	-	KMT2A	chr11	118359328
intron-intron	ENST00000380321	ENST00000354520	MLLT3	chr9	20413718	-	KMT2A	chr11	118355576
intron-intron	ENST00000380321	ENST00000420751	MLLT3	chr9	20413718	-	KMT2A	chr11	118355576
intron-intron	ENST00000380321	ENST00000420751	MLLT3	chr9	20413718	-	KMT2A	chr11	118359328

ORFfinder result based on the fusion transcript sequence of in-frame fusion genes.

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)

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

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Fusion Genomic Features for MLLT3-KMT2A

FusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.

Hgene

Hchr

Hbp

Hstrand

Tgene

Tchr

Tbp

Tstrand

1-p

p (fusion gene breakpoint)

Distribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

Distribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.

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Fusion Protein Features for MLLT3-KMT2A

Go to
FGviewer for the breakpoints of chr9:20413718-chr11:118359328
.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.

Main function of each fusion partner protein. (from UniProt)

Hgene	Tgene
MLLT3 P42568	KMT2A Q03164
FUNCTION: Chromatin reader component of the super elongation complex (SEC), a complex required to increase the catalytic rate of RNA polymerase II transcription by suppressing transient pausing by the polymerase at multiple sites along the DNA (PubMed:20159561, PubMed:20471948, PubMed:25417107, PubMed:27105114, PubMed:27545619). Specifically recognizes and binds acylated histone H3, with a preference for histone H3 that is crotonylated (PubMed:25417107, PubMed:27105114, PubMed:27545619, PubMed:30374167, PubMed:30385749). Crotonylation marks active promoters and enhancers and confers resistance to transcriptional repressors (PubMed:25417107, PubMed:27105114, PubMed:27545619). Recognizes and binds histone H3 crotonylated at 'Lys-9' (H3K9cr), and with slightly lower affinity histone H3 crotonylated at 'Lys-18' (H3K18cr) (PubMed:27105114). Also recognizes and binds histone H3 acetylated and butyrylated at 'Lys-9' (H3K9ac and H3K9bu, respectively), but with lower affinity than crotonylated histone H3 (PubMed:25417107, PubMed:27105114, PubMed:30385749). In the SEC complex, MLLT3 is required to recruit the complex to crotonylated histones (PubMed:27105114, PubMed:27545619). Recruitment of the SEC complex to crotonylated histones promotes recruitment of DOT1L on active chromatin to deposit histone H3 'Lys-79' methylation (H3K79me) (PubMed:25417107). Plays a key role in hematopoietic stem cell (HSC) maintenance by preserving, rather than confering, HSC stemness (PubMed:31776511). Acts by binding to the transcription start site of active genes in HSCs and sustaining level of H3K79me2, probably by recruiting DOT1L (PubMed:31776511). {ECO:0000269\|PubMed:20159561, ECO:0000269\|PubMed:20471948, ECO:0000269\|PubMed:25417107, ECO:0000269\|PubMed:27105114, ECO:0000269\|PubMed:27545619, ECO:0000269\|PubMed:30374167, ECO:0000269\|PubMed:30385749, ECO:0000269\|PubMed:31776511}.	FUNCTION: Histone methyltransferase that plays an essential role in early development and hematopoiesis (PubMed:15960975, PubMed:12453419, PubMed:15960975, PubMed:19556245, PubMed:19187761, PubMed:20677832, PubMed:21220120, PubMed:26886794). Catalytic subunit of the MLL1/MLL complex, a multiprotein complex that mediates both methylation of 'Lys-4' of histone H3 (H3K4me) complex and acetylation of 'Lys-16' of histone H4 (H4K16ac) (PubMed:15960975, PubMed:12453419, PubMed:15960975, PubMed:19556245, PubMed:24235145, PubMed:19187761, PubMed:20677832, PubMed:21220120, PubMed:26886794). Catalyzes methyl group transfer from S-adenosyl-L-methionine to the epsilon-amino group of 'Lys-4' of histone H3 (H3K4) via a non-processive mechanism. Part of chromatin remodeling machinery predominantly forms H3K4me1 and H3K4me2 methylation marks at active chromatin sites where transcription and DNA repair take place (PubMed:25561738, PubMed:15960975, PubMed:12453419, PubMed:15960975, PubMed:19556245, PubMed:19187761, PubMed:20677832, PubMed:21220120, PubMed:26886794). Has weak methyltransferase activity by itself, and requires other component of the MLL1/MLL complex to obtain full methyltransferase activity (PubMed:19187761, PubMed:26886794). Has no activity toward histone H3 phosphorylated on 'Thr-3', less activity toward H3 dimethylated on 'Arg-8' or 'Lys-9', while it has higher activity toward H3 acetylated on 'Lys-9' (PubMed:19187761). Binds to unmethylated CpG elements in the promoter of target genes and helps maintain them in the nonmethylated state (PubMed:20010842). Required for transcriptional activation of HOXA9 (PubMed:12453419, PubMed:20677832, PubMed:20010842). Promotes PPP1R15A-induced apoptosis (PubMed:10490642). Plays a critical role in the control of circadian gene expression and is essential for the transcriptional activation mediated by the CLOCK-ARNTL/BMAL1 heterodimer (By similarity). Establishes a permissive chromatin state for circadian transcription by mediating a rhythmic methylation of 'Lys-4' of histone H3 (H3K4me) and this histone modification directs the circadian acetylation at H3K9 and H3K14 allowing the recruitment of CLOCK-ARNTL/BMAL1 to chromatin (By similarity). Also has auto-methylation activity on Cys-3882 in absence of histone H3 substrate (PubMed:24235145). {ECO:0000250\|UniProtKB:P55200, ECO:0000269\|PubMed:10490642, ECO:0000269\|PubMed:12453419, ECO:0000269\|PubMed:15960975, ECO:0000269\|PubMed:19187761, ECO:0000269\|PubMed:19556245, ECO:0000269\|PubMed:20010842, ECO:0000269\|PubMed:21220120, ECO:0000269\|PubMed:24235145, ECO:0000269\|PubMed:26886794, ECO:0000305\|PubMed:20677832}.

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, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at
download page

* Minus value of BPloci means that the break pointn is located before the CDS.

- In-frame and retained protein feature among the 13 regional features.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

- In-frame and not-retained protein feature among the 13 regional features.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

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Fusion Gene Sequence for MLLT3-KMT2A

For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.

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Fusion Gene PPI Analysis for MLLT3-KMT2A

Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in
ChiPPI page.

Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)

Hgene

Hgene's interactors

Tgene

Tgene's interactors

- Retained PPIs in in-frame fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Still interaction with

- Lost PPIs in in-frame fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

- Retained PPIs, but lost function due to frame-shift fusion.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Interaction lost with

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Related Drugs for MLLT3-KMT2A

Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)

Partner

Gene

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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Related Diseases for MLLT3-KMT2A

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner	Gene	Disease ID	Disease name	# pubmeds	Source
Hgene	MLLT3	C0005586	Bipolar Disorder	1	PSYGENET
Tgene	KMT2A	C2826025	Mixed phenotype acute leukemia	3	ORPHANET
Tgene	KMT2A	C0023418	leukemia	2	CTD_human
Tgene	KMT2A	C0023452	Childhood Acute Lymphoblastic Leukemia	2	CTD_human
Tgene	KMT2A	C0023453	L2 Acute Lymphoblastic Leukemia	2	CTD_human
Tgene	KMT2A	C0023466	Leukemia, Monocytic, Chronic	2	CTD_human
Tgene	KMT2A	C0023467	Leukemia, Myelocytic, Acute	2	CTD_human
Tgene	KMT2A	C0023470	Myeloid Leukemia	2	CTD_human
Tgene	KMT2A	C0026998	Acute Myeloid Leukemia, M1	2	CTD_human
Tgene	KMT2A	C1854630	Growth Deficiency and Mental Retardation with Facial Dysmorphism	2	CTD_human;GENOMICS_ENGLAND;ORPHANET
Tgene	KMT2A	C1879321	Acute Myeloid Leukemia (AML-M2)	2	CTD_human
Tgene	KMT2A	C1961102	Precursor Cell Lymphoblastic Leukemia Lymphoma	2	CTD_human
Tgene	KMT2A	C0001418	Adenocarcinoma	1	CTD_human
Tgene	KMT2A	C0004403	Autosome Abnormalities	1	CTD_human
Tgene	KMT2A	C0005684	Malignant neoplasm of urinary bladder	1	CTD_human
Tgene	KMT2A	C0005695	Bladder Neoplasm	1	CTD_human
Tgene	KMT2A	C0007138	Carcinoma, Transitional Cell	1	CTD_human
Tgene	KMT2A	C0008625	Chromosome Aberrations	1	CTD_human
Tgene	KMT2A	C0023448	Lymphoid leukemia	1	CTD_human
Tgene	KMT2A	C0023465	Acute monocytic leukemia	1	CTD_human
Tgene	KMT2A	C0023479	Acute myelomonocytic leukemia	1	CTD_human
Tgene	KMT2A	C0024623	Malignant neoplasm of stomach	1	CTD_human
Tgene	KMT2A	C0033578	Prostatic Neoplasms	1	CTD_human
Tgene	KMT2A	C0036341	Schizophrenia	1	PSYGENET
Tgene	KMT2A	C0038356	Stomach Neoplasms	1	CTD_human
Tgene	KMT2A	C0149925	Small cell carcinoma of lung	1	CTD_human
Tgene	KMT2A	C0205641	Adenocarcinoma, Basal Cell	1	CTD_human
Tgene	KMT2A	C0205642	Adenocarcinoma, Oxyphilic	1	CTD_human
Tgene	KMT2A	C0205643	Carcinoma, Cribriform	1	CTD_human
Tgene	KMT2A	C0205644	Carcinoma, Granular Cell	1	CTD_human
Tgene	KMT2A	C0205645	Adenocarcinoma, Tubular	1	CTD_human
Tgene	KMT2A	C0270972	Cornelia De Lange Syndrome	1	ORPHANET
Tgene	KMT2A	C0280141	Acute Undifferentiated Leukemia	1	ORPHANET
Tgene	KMT2A	C0376358	Malignant neoplasm of prostate	1	CTD_human
Tgene	KMT2A	C0856823	Undifferentiated type acute leukemia	1	ORPHANET
Tgene	KMT2A	C1535926	Neurodevelopmental Disorders	1	CTD_human
Tgene	KMT2A	C1708349	Hereditary Diffuse Gastric Cancer	1	CTD_human
Tgene	KMT2A	C2239176	Liver carcinoma	1	CTD_human
Tgene	KMT2A	C2930974	Acute erythroleukemia	1	CTD_human
Tgene	KMT2A	C2930975	Acute erythroleukemia - M6a subtype	1	CTD_human
Tgene	KMT2A	C2930976	Acute myeloid leukemia FAB-M6	1	CTD_human
Tgene	KMT2A	C2930977	Acute erythroleukemia - M6b subtype	1	CTD_human