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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:RAPH1-CD46 (FusionGDB2 ID:72275)

Fusion Gene Summary for RAPH1-CD46

Fusion gene summary

Fusion gene information	Fusion gene name: RAPH1-CD46
	Fusion gene ID: 72275
		Hgene	Tgene
	Gene symbol	RAPH1	CD46
	Gene ID	65059	4179
	Gene name	Ras association (RalGDS/AF-6) and pleckstrin homology domains 1	CD46 molecule
	Synonyms	ALS2CR18\|ALS2CR9\|LPD\|PREL-2\|PREL2\|RMO1\|RalGDS/AF-6	AHUS2\|MCP\|MIC10\|TLX\|TRA2.10
	Cytomap	2q33.2	1q32.2
	Type of gene	protein-coding	protein-coding
	Description	ras-associated and pleckstrin homology domains-containing protein 1amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 18amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 9lamellipodinproline-rich EVH1 ligand	membrane cofactor proteinCD46 antigen, complement regulatory proteinCD46 molecule, complement regulatory proteinantigen identified by monoclonal antibody TRA-2-10complement membrane cofactor proteinmeasles virus receptormembrane cofactor protein (CD
	Modification date	20200313	20200313
	UniProtAcc	.	P15529
	Ensembl transtripts involved in fusion gene	ENST00000308091, ENST00000319170, ENST00000374488, ENST00000374489, ENST00000453034, ENST00000457812, ENST00000374493, ENST00000418114, ENST00000419464, ENST00000423104, ENST00000439222,	ENST00000322875, ENST00000322918, ENST00000354848, ENST00000357714, ENST00000358170, ENST00000361067, ENST00000367041, ENST00000367042, ENST00000367047, ENST00000441839, ENST00000360212, ENST00000469535, ENST00000480003,
Fusion gene scores	* DoF score	5 X 5 X 2=50	16 X 13 X 7=1456
	# samples	5	17
	** MAII score	log2(5/50*10)=0	log2(17/1456*10)=-3.098403704061 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context	PubMed: RAPH1 [Title/Abstract] AND CD46 [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	RAPH1(204399834)-CD46(207958416), # 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	CD46	GO:0008593	regulation of Notch signaling pathway	23086448
Tgene	CD46	GO:0010629	negative regulation of gene expression	23086448
Tgene	CD46	GO:0032613	interleukin-10 production	23086448
Tgene	CD46	GO:0032733	positive regulation of interleukin-10 production	12540904
Tgene	CD46	GO:0035581	sequestering of extracellular ligand from receptor	23086448
Tgene	CD46	GO:0042102	positive regulation of T cell proliferation	12540904
Tgene	CD46	GO:0043382	positive regulation of memory T cell differentiation	12540904
Tgene	CD46	GO:0045591	positive regulation of regulatory T cell differentiation	12540904
Tgene	CD46	GO:0071636	positive regulation of transforming growth factor beta production	12540904

Fusion gene breakpoints across RAPH1 (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 CD46 (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
ChimerDB4	SKCM	TCGA-DA-A1I4-06A	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+

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Fusion Gene ORF analysis for RAPH1-CD46

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
5UTR-3CDS	ENST00000308091	ENST00000322875	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000308091	ENST00000322918	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000308091	ENST00000354848	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000308091	ENST00000357714	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000308091	ENST00000358170	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000308091	ENST00000361067	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000308091	ENST00000367041	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000308091	ENST00000367042	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000308091	ENST00000367047	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000308091	ENST00000441839	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000319170	ENST00000322875	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000319170	ENST00000322918	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000319170	ENST00000354848	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000319170	ENST00000357714	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000319170	ENST00000358170	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000319170	ENST00000361067	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000319170	ENST00000367041	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000319170	ENST00000367042	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000319170	ENST00000367047	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000319170	ENST00000441839	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000374488	ENST00000322875	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000374488	ENST00000322918	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000374488	ENST00000354848	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000374488	ENST00000357714	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000374488	ENST00000358170	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000374488	ENST00000361067	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000374488	ENST00000367041	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000374488	ENST00000367042	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000374488	ENST00000367047	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000374488	ENST00000441839	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000374489	ENST00000322875	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000374489	ENST00000322918	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000374489	ENST00000354848	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000374489	ENST00000357714	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000374489	ENST00000358170	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000374489	ENST00000361067	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000374489	ENST00000367041	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000374489	ENST00000367042	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000374489	ENST00000367047	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000374489	ENST00000441839	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000453034	ENST00000322875	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000453034	ENST00000322918	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000453034	ENST00000354848	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000453034	ENST00000357714	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000453034	ENST00000358170	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000453034	ENST00000361067	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000453034	ENST00000367041	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000453034	ENST00000367042	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000453034	ENST00000367047	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000453034	ENST00000441839	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000457812	ENST00000322875	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000457812	ENST00000322918	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000457812	ENST00000354848	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000457812	ENST00000357714	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000457812	ENST00000358170	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000457812	ENST00000361067	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000457812	ENST00000367041	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000457812	ENST00000367042	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000457812	ENST00000367047	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3CDS	ENST00000457812	ENST00000441839	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3UTR	ENST00000308091	ENST00000360212	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3UTR	ENST00000308091	ENST00000469535	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3UTR	ENST00000308091	ENST00000480003	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3UTR	ENST00000319170	ENST00000360212	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3UTR	ENST00000319170	ENST00000469535	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3UTR	ENST00000319170	ENST00000480003	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3UTR	ENST00000374488	ENST00000360212	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3UTR	ENST00000374488	ENST00000469535	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3UTR	ENST00000374488	ENST00000480003	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3UTR	ENST00000374489	ENST00000360212	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3UTR	ENST00000374489	ENST00000469535	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3UTR	ENST00000374489	ENST00000480003	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3UTR	ENST00000453034	ENST00000360212	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3UTR	ENST00000453034	ENST00000469535	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3UTR	ENST00000453034	ENST00000480003	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3UTR	ENST00000457812	ENST00000360212	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3UTR	ENST00000457812	ENST00000469535	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
5UTR-3UTR	ENST00000457812	ENST00000480003	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3CDS	ENST00000374493	ENST00000322875	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3CDS	ENST00000374493	ENST00000322918	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3CDS	ENST00000374493	ENST00000354848	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3CDS	ENST00000374493	ENST00000357714	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3CDS	ENST00000374493	ENST00000358170	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3CDS	ENST00000374493	ENST00000361067	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3CDS	ENST00000374493	ENST00000367041	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3CDS	ENST00000374493	ENST00000367042	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3CDS	ENST00000374493	ENST00000367047	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3CDS	ENST00000374493	ENST00000441839	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3CDS	ENST00000418114	ENST00000322875	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3CDS	ENST00000418114	ENST00000322918	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3CDS	ENST00000418114	ENST00000354848	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3CDS	ENST00000418114	ENST00000357714	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3CDS	ENST00000418114	ENST00000358170	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3CDS	ENST00000418114	ENST00000361067	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3CDS	ENST00000418114	ENST00000367041	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3CDS	ENST00000418114	ENST00000367042	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3CDS	ENST00000418114	ENST00000367047	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3CDS	ENST00000418114	ENST00000441839	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3CDS	ENST00000419464	ENST00000322875	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3CDS	ENST00000419464	ENST00000322918	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3CDS	ENST00000419464	ENST00000354848	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3CDS	ENST00000419464	ENST00000357714	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3CDS	ENST00000419464	ENST00000358170	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3CDS	ENST00000419464	ENST00000361067	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3CDS	ENST00000419464	ENST00000367041	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3CDS	ENST00000419464	ENST00000367042	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3CDS	ENST00000419464	ENST00000367047	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3CDS	ENST00000419464	ENST00000441839	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3CDS	ENST00000423104	ENST00000322875	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3CDS	ENST00000423104	ENST00000322918	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3CDS	ENST00000423104	ENST00000354848	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3CDS	ENST00000423104	ENST00000357714	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3CDS	ENST00000423104	ENST00000358170	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3CDS	ENST00000423104	ENST00000361067	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3CDS	ENST00000423104	ENST00000367041	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3CDS	ENST00000423104	ENST00000367042	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3CDS	ENST00000423104	ENST00000367047	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3CDS	ENST00000423104	ENST00000441839	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3CDS	ENST00000439222	ENST00000322875	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3CDS	ENST00000439222	ENST00000322918	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3CDS	ENST00000439222	ENST00000354848	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3CDS	ENST00000439222	ENST00000357714	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3CDS	ENST00000439222	ENST00000358170	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3CDS	ENST00000439222	ENST00000361067	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3CDS	ENST00000439222	ENST00000367041	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3CDS	ENST00000439222	ENST00000367042	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3CDS	ENST00000439222	ENST00000367047	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3CDS	ENST00000439222	ENST00000441839	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3UTR	ENST00000374493	ENST00000360212	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3UTR	ENST00000374493	ENST00000469535	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3UTR	ENST00000374493	ENST00000480003	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3UTR	ENST00000418114	ENST00000360212	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3UTR	ENST00000418114	ENST00000469535	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3UTR	ENST00000418114	ENST00000480003	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3UTR	ENST00000419464	ENST00000360212	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3UTR	ENST00000419464	ENST00000469535	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3UTR	ENST00000419464	ENST00000480003	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3UTR	ENST00000423104	ENST00000360212	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3UTR	ENST00000423104	ENST00000469535	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3UTR	ENST00000423104	ENST00000480003	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3UTR	ENST00000439222	ENST00000360212	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3UTR	ENST00000439222	ENST00000469535	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+
intron-3UTR	ENST00000439222	ENST00000480003	RAPH1	chr2	204399834	-	CD46	chr1	207958416	+

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 RAPH1-CD46

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)
RAPH1	chr2	204399833	-	CD46	chr1	207958415	+	0.003595197	0.99640477
RAPH1	chr2	204399833	-	CD46	chr1	207958415	+	0.003595197	0.99640477

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 RAPH1-CD46

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:204399834/:207958416)
- 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
.	CD46 P15529
FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.	FUNCTION: Acts as a cofactor for complement factor I, a serine protease which protects autologous cells against complement-mediated injury by cleaving C3b and C4b deposited on host tissue. May be involved in the fusion of the spermatozoa with the oocyte during fertilization. Also acts as a costimulatory factor for T-cells which induces the differentiation of CD4+ into T-regulatory 1 cells. T-regulatory 1 cells suppress immune responses by secreting interleukin-10, and therefore are thought to prevent autoimmunity. {ECO:0000269\|PubMed:10843656, ECO:0000269\|PubMed:12540904}.; FUNCTION: (Microbial infection) A number of viral and bacterial pathogens seem to bind MCP in order to exploit its immune regulation property and directly induce an immunosuppressive phenotype in T-cells.; FUNCTION: (Microbial infection) Acts as a receptor for Adenovirus subgroup B2 and Ad3. {ECO:0000269\|PubMed:12915534, ECO:0000269\|PubMed:14566335, ECO:0000269\|PubMed:15047806, ECO:0000269\|PubMed:15078926, ECO:0000269\|PubMed:15919905, ECO:0000269\|PubMed:16254377}.; FUNCTION: (Microbial infection) Acts as a receptor for cultured Measles virus. {ECO:0000269\|PubMed:10972291}.; FUNCTION: (Microbial infection) Acts as a receptor for Herpesvirus 6/HHV-6. {ECO:0000269\|PubMed:12663806, ECO:0000269\|PubMed:12724329}.; FUNCTION: (Microbial infection) May act as a receptor for pathogenic bacteria Neisseria and Streptococcus pyogenes (PubMed:7708671, PubMed:9379894, PubMed:11260136, PubMed:11971006).

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 RAPH1-CD46

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 RAPH1-CD46

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 RAPH1-CD46

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 RAPH1-CD46

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source