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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:LIMCH1-ILF3 (FusionGDB2 ID:44699)

Fusion Gene Summary for LIMCH1-ILF3

Fusion gene summary

Fusion gene information	Fusion gene name: LIMCH1-ILF3
	Fusion gene ID: 44699
		Hgene	Tgene
	Gene symbol	LIMCH1	ILF3
	Gene ID	22998	3609
	Gene name	LIM and calponin homology domains 1	interleukin enhancer binding factor 3
	Synonyms	LIMCH1A\|LMO7B	CBTF\|DRBF\|DRBP76\|MMP4\|MPHOSPH4\|MPP4\|MPP4110\|NF-AT-90\|NF110\|NF110b\|NF90\|NF90a\|NF90b\|NF90c\|NF90ctv\|NFAR\|NFAR-1\|NFAR-2\|NFAR110\|NFAR2\|NFAR90\|TCP110\|TCP80
	Cytomap	4p13	19p13.2
	Type of gene	protein-coding	protein-coding
	Description	LIM and calponin homology domains-containing protein 1	interleukin enhancer-binding factor 3M phase phosphoprotein 4, nuclear factor associated with DS RNAM-phase phosphoprotein 4double-stranded RNA-binding protein, 76 kDdsRNA binding protein NFAR-2/MPP4interleukin enhancer binding factor 3, 90kDinterle
	Modification date	20200313	20200322
	UniProtAcc	Q9UPQ0	Q12906
	Ensembl transtripts involved in fusion gene	ENST00000313860, ENST00000381753, ENST00000396595, ENST00000503057, ENST00000508501, ENST00000509277, ENST00000509454, ENST00000509638, ENST00000511496, ENST00000512632, ENST00000512820, ENST00000512946, ENST00000513024, ENST00000514096, ENST00000515785,	ENST00000318511, ENST00000449870, ENST00000586544, ENST00000250241, ENST00000407004, ENST00000420083, ENST00000588657, ENST00000589998, ENST00000590261, ENST00000592763,
Fusion gene scores	* DoF score	14 X 12 X 9=1512	17 X 23 X 6=2346
	# samples	19	25
	** MAII score	log2(19/1512*10)=-2.99238681589013 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(25/2346*10)=-3.23020301336642 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context	PubMed: LIMCH1 [Title/Abstract] AND ILF3 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	LIMCH1(41630358)-ILF3(10803041), # samples:1
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
Tgene	ILF3	GO:0006468	protein phosphorylation	21123651
Tgene	ILF3	GO:0045892	negative regulation of transcription, DNA-templated	11739746
Tgene	ILF3	GO:0045893	positive regulation of transcription, DNA-templated	11739746

Fusion gene breakpoints across LIMCH1 (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 ILF3 (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	AW268677	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-

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Fusion Gene ORF analysis for LIMCH1-ILF3

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-3UTR	ENST00000313860	ENST00000318511	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-3UTR	ENST00000313860	ENST00000449870	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-3UTR	ENST00000313860	ENST00000586544	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-3UTR	ENST00000381753	ENST00000318511	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-3UTR	ENST00000381753	ENST00000449870	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-3UTR	ENST00000381753	ENST00000586544	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-3UTR	ENST00000396595	ENST00000318511	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-3UTR	ENST00000396595	ENST00000449870	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-3UTR	ENST00000396595	ENST00000586544	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-3UTR	ENST00000503057	ENST00000318511	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-3UTR	ENST00000503057	ENST00000449870	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-3UTR	ENST00000503057	ENST00000586544	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-3UTR	ENST00000508501	ENST00000318511	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-3UTR	ENST00000508501	ENST00000449870	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-3UTR	ENST00000508501	ENST00000586544	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-3UTR	ENST00000509277	ENST00000318511	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-3UTR	ENST00000509277	ENST00000449870	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-3UTR	ENST00000509277	ENST00000586544	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-3UTR	ENST00000509454	ENST00000318511	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-3UTR	ENST00000509454	ENST00000449870	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-3UTR	ENST00000509454	ENST00000586544	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-3UTR	ENST00000509638	ENST00000318511	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-3UTR	ENST00000509638	ENST00000449870	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-3UTR	ENST00000509638	ENST00000586544	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-3UTR	ENST00000511496	ENST00000318511	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-3UTR	ENST00000511496	ENST00000449870	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-3UTR	ENST00000511496	ENST00000586544	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-3UTR	ENST00000512632	ENST00000318511	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-3UTR	ENST00000512632	ENST00000449870	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-3UTR	ENST00000512632	ENST00000586544	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-3UTR	ENST00000512820	ENST00000318511	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-3UTR	ENST00000512820	ENST00000449870	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-3UTR	ENST00000512820	ENST00000586544	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-3UTR	ENST00000512946	ENST00000318511	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-3UTR	ENST00000512946	ENST00000449870	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-3UTR	ENST00000512946	ENST00000586544	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-3UTR	ENST00000513024	ENST00000318511	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-3UTR	ENST00000513024	ENST00000449870	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-3UTR	ENST00000513024	ENST00000586544	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-3UTR	ENST00000514096	ENST00000318511	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-3UTR	ENST00000514096	ENST00000449870	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-3UTR	ENST00000514096	ENST00000586544	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-3UTR	ENST00000515785	ENST00000318511	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-3UTR	ENST00000515785	ENST00000449870	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-3UTR	ENST00000515785	ENST00000586544	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000313860	ENST00000250241	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000313860	ENST00000407004	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000313860	ENST00000420083	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000313860	ENST00000588657	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000313860	ENST00000589998	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000313860	ENST00000590261	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000313860	ENST00000592763	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000381753	ENST00000250241	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000381753	ENST00000407004	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000381753	ENST00000420083	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000381753	ENST00000588657	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000381753	ENST00000589998	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000381753	ENST00000590261	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000381753	ENST00000592763	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000396595	ENST00000250241	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000396595	ENST00000407004	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000396595	ENST00000420083	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000396595	ENST00000588657	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000396595	ENST00000589998	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000396595	ENST00000590261	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000396595	ENST00000592763	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000503057	ENST00000250241	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000503057	ENST00000407004	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000503057	ENST00000420083	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000503057	ENST00000588657	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000503057	ENST00000589998	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000503057	ENST00000590261	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000503057	ENST00000592763	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000508501	ENST00000250241	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000508501	ENST00000407004	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000508501	ENST00000420083	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000508501	ENST00000588657	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000508501	ENST00000589998	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000508501	ENST00000590261	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000508501	ENST00000592763	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000509277	ENST00000250241	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000509277	ENST00000407004	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000509277	ENST00000420083	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000509277	ENST00000588657	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000509277	ENST00000589998	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000509277	ENST00000590261	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000509277	ENST00000592763	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000509454	ENST00000250241	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000509454	ENST00000407004	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000509454	ENST00000420083	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000509454	ENST00000588657	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000509454	ENST00000589998	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000509454	ENST00000590261	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000509454	ENST00000592763	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000509638	ENST00000250241	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000509638	ENST00000407004	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000509638	ENST00000420083	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000509638	ENST00000588657	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000509638	ENST00000589998	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000509638	ENST00000590261	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000509638	ENST00000592763	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000511496	ENST00000250241	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000511496	ENST00000407004	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000511496	ENST00000420083	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000511496	ENST00000588657	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000511496	ENST00000589998	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000511496	ENST00000590261	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000511496	ENST00000592763	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000512632	ENST00000250241	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000512632	ENST00000407004	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000512632	ENST00000420083	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000512632	ENST00000588657	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000512632	ENST00000589998	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000512632	ENST00000590261	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000512632	ENST00000592763	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000512820	ENST00000250241	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000512820	ENST00000407004	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000512820	ENST00000420083	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000512820	ENST00000588657	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000512820	ENST00000589998	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000512820	ENST00000590261	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000512820	ENST00000592763	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000512946	ENST00000250241	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000512946	ENST00000407004	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000512946	ENST00000420083	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000512946	ENST00000588657	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000512946	ENST00000589998	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000512946	ENST00000590261	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000512946	ENST00000592763	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000513024	ENST00000250241	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000513024	ENST00000407004	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000513024	ENST00000420083	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000513024	ENST00000588657	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000513024	ENST00000589998	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000513024	ENST00000590261	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000513024	ENST00000592763	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000514096	ENST00000250241	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000514096	ENST00000407004	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000514096	ENST00000420083	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000514096	ENST00000588657	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000514096	ENST00000589998	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000514096	ENST00000590261	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000514096	ENST00000592763	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000515785	ENST00000250241	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000515785	ENST00000407004	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000515785	ENST00000420083	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000515785	ENST00000588657	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000515785	ENST00000589998	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000515785	ENST00000590261	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-
intron-intron	ENST00000515785	ENST00000592763	LIMCH1	chr4	41630358	-	ILF3	chr19	10803041	-

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 LIMCH1-ILF3

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 LIMCH1-ILF3

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:41630358/:10803041)
- 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.

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

Hgene	Tgene
LIMCH1 Q9UPQ0	ILF3 Q12906
FUNCTION: Actin stress fibers-associated protein that activates non-muscle myosin IIa. Activates the non-muscle myosin IIa complex by promoting the phosphorylation of its regulatory subunit MRLC/MYL9. Through the activation of non-muscle myosin IIa, positively regulates actin stress fibers assembly and stabilizes focal adhesions. It therefore negatively regulates cell spreading and cell migration. {ECO:0000269\|PubMed:28228547}.	FUNCTION: RNA-binding protein that plays an essential role in the biogenesis of circular RNAs (circRNAs) which are produced by back-splicing circularization of pre-mRNAs. Within the nucleus, promotes circRNAs processing by stabilizing the regulatory elements residing in the flanking introns of the circularized exons. Plays thereby a role in the back-splicing of a subset of circRNAs (PubMed:28625552). As a consequence, participates in a wide range of transcriptional and post-transcriptional processes. Binds to poly-U elements and AU-rich elements (AREs) in the 3'-UTR of target mRNAs (PubMed:14731398). Upon viral infection, ILF3 accumulates in the cytoplasm and participates in the innate antiviral response (PubMed:21123651). Mechanistically, ILF3 becomes phosphorylated and activated by the double-stranded RNA-activated protein kinase/PKR which releases ILF3 from cellular mature circRNAs. In turn, unbound ILF3 molecules are able to interact with and thus inhibit viral mRNAs (PubMed:21123651, PubMed:28625552). {ECO:0000269\|PubMed:14731398, ECO:0000269\|PubMed:21123651, ECO:0000269\|PubMed:28625552, ECO:0000269\|PubMed:9442054}.

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 LIMCH1-ILF3

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 LIMCH1-ILF3

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 LIMCH1-ILF3

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 LIMCH1-ILF3

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source