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Fusion gene ID: 24740

FusionGeneSummary for NPM1_RARA

Fusion gene summary

Fusion gene information	Fusion gene name: NPM1_RARA
	Fusion gene ID: 24740
		Hgene	Tgene
	Gene symbol	NPM1	RARA
	Gene ID	4869	5914
	Gene name	nucleophosmin 1	retinoic acid receptor alpha
	Synonyms	B23\|NPM	NR1B1\|RAR
	Cytomap	5q35.1	17q21.2
	Type of gene	protein-coding	protein-coding
	Description	nucleophosminnucleolar protein NO38nucleophosmin (nucleolar phosphoprotein B23, numatrin)nucleophosmin/nucleoplasmin family, member 1testicular tissue protein Li 128	retinoic acid receptor alphaRAR-alphanuclear receptor subfamily 1 group B member 1nucleophosmin-retinoic acid receptor alpha fusion protein NPM-RAR long formretinoic acid nuclear receptor alpha variant 1retinoic acid nuclear receptor alpha variant 2
	Modification date	20180523	20180523
	UniProtAcc	P06748	P10276
	Ensembl transtripts involved in fusion gene	ENST00000517671, ENST00000296930, ENST00000351986, ENST00000393820,	ENST00000254066, ENST00000394089, ENST00000425707, ENST00000394086, ENST00000394081, ENST00000420042,
Fusion gene scores	* DoF score	6 X 4 X 3=72	18 X 16 X 10=2880
	# samples	7	42
	** MAII score	log2(7/72*10)=-0.0406419844973459 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(42/2880*10)=-2.77760757866355 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context	PubMed: NPM1 [Title/Abstract] AND RARA [Title/Abstract] AND fusion [Title/Abstract]
Functional or gene categories assigned by FusionGDB annotation	Oncogene involved fusion gene, in-frame and retained their domain. Tumor suppressor gene involved fusion gene, in-frame but not retained their domain. Transcription factor involved fusion gene, inframe and retained DNA-binding domain.

* 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	NPM1	GO:0006281	DNA repair	19188445
Hgene	NPM1	GO:0006334	nucleosome assembly	11602260
Hgene	NPM1	GO:0006913	nucleocytoplasmic transport	16041368
Hgene	NPM1	GO:0008104	protein localization	18420587
Hgene	NPM1	GO:0008284	positive regulation of cell proliferation	22528486
Hgene	NPM1	GO:0032071	regulation of endodeoxyribonuclease activity	19188445
Hgene	NPM1	GO:0034644	cellular response to UV	19160485
Hgene	NPM1	GO:0043066	negative regulation of apoptotic process	12882984
Hgene	NPM1	GO:0044387	negative regulation of protein kinase activity by regulation of protein phosphorylation	12882984
Hgene	NPM1	GO:0045727	positive regulation of translation	12882984
Hgene	NPM1	GO:0045893	positive regulation of transcription, DNA-templated	22528486
Hgene	NPM1	GO:0045944	positive regulation of transcription by RNA polymerase II	19160485
Hgene	NPM1	GO:0051259	protein complex oligomerization	18809582
Hgene	NPM1	GO:0060699	regulation of endoribonuclease activity	19188445
Hgene	NPM1	GO:0060735	regulation of eIF2 alpha phosphorylation by dsRNA	12882984
Hgene	NPM1	GO:1902751	positive regulation of cell cycle G2/M phase transition	22528486
Tgene	RARA	GO:0007165	signal transduction	2825025
Tgene	RARA	GO:0030853	negative regulation of granulocyte differentiation	19917671
Tgene	RARA	GO:0032689	negative regulation of interferon-gamma production	18416830
Tgene	RARA	GO:0032720	negative regulation of tumor necrosis factor production	18416830
Tgene	RARA	GO:0032736	positive regulation of interleukin-13 production	18416830
Tgene	RARA	GO:0032753	positive regulation of interleukin-4 production	18416830
Tgene	RARA	GO:0032754	positive regulation of interleukin-5 production	18416830
Tgene	RARA	GO:0045630	positive regulation of T-helper 2 cell differentiation	18416830
Tgene	RARA	GO:0045892	negative regulation of transcription, DNA-templated	20080953
Tgene	RARA	GO:0045893	positive regulation of transcription, DNA-templated	18845237\|19850744\|20080953
Tgene	RARA	GO:0045944	positive regulation of transcription by RNA polymerase II	19850744
Tgene	RARA	GO:0071300	cellular response to retinoic acid	19917671
Tgene	RARA	GO:0071391	cellular response to estrogen stimulus	20080953

Fusion gene information from three resources
(ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018))
* 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.

Data type	Source	Cancer type	Sample	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
ChiTaRS3.1			U41743	NPM1	chr5	170818803	+	RARA	chr17	38504565	+

* LD: Li Ding group's fusion gene list
RV: Roel Verhaak group's fusion gene list
ChiTaRs fusion database

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
In-frame	ENST00000517671	ENST00000254066	NPM1	chr5	170818803	+	RARA	chr17	38504565	+
In-frame	ENST00000517671	ENST00000394089	NPM1	chr5	170818803	+	RARA	chr17	38504565	+
5CDS-intron	ENST00000517671	ENST00000425707	NPM1	chr5	170818803	+	RARA	chr17	38504565	+
5CDS-intron	ENST00000517671	ENST00000394086	NPM1	chr5	170818803	+	RARA	chr17	38504565	+
5CDS-intron	ENST00000517671	ENST00000394081	NPM1	chr5	170818803	+	RARA	chr17	38504565	+
5CDS-intron	ENST00000517671	ENST00000420042	NPM1	chr5	170818803	+	RARA	chr17	38504565	+
In-frame	ENST00000296930	ENST00000254066	NPM1	chr5	170818803	+	RARA	chr17	38504565	+
In-frame	ENST00000296930	ENST00000394089	NPM1	chr5	170818803	+	RARA	chr17	38504565	+
5CDS-intron	ENST00000296930	ENST00000425707	NPM1	chr5	170818803	+	RARA	chr17	38504565	+
5CDS-intron	ENST00000296930	ENST00000394086	NPM1	chr5	170818803	+	RARA	chr17	38504565	+
5CDS-intron	ENST00000296930	ENST00000394081	NPM1	chr5	170818803	+	RARA	chr17	38504565	+
5CDS-intron	ENST00000296930	ENST00000420042	NPM1	chr5	170818803	+	RARA	chr17	38504565	+
In-frame	ENST00000351986	ENST00000254066	NPM1	chr5	170818803	+	RARA	chr17	38504565	+
In-frame	ENST00000351986	ENST00000394089	NPM1	chr5	170818803	+	RARA	chr17	38504565	+
5CDS-intron	ENST00000351986	ENST00000425707	NPM1	chr5	170818803	+	RARA	chr17	38504565	+
5CDS-intron	ENST00000351986	ENST00000394086	NPM1	chr5	170818803	+	RARA	chr17	38504565	+
5CDS-intron	ENST00000351986	ENST00000394081	NPM1	chr5	170818803	+	RARA	chr17	38504565	+
5CDS-intron	ENST00000351986	ENST00000420042	NPM1	chr5	170818803	+	RARA	chr17	38504565	+
In-frame	ENST00000393820	ENST00000254066	NPM1	chr5	170818803	+	RARA	chr17	38504565	+
In-frame	ENST00000393820	ENST00000394089	NPM1	chr5	170818803	+	RARA	chr17	38504565	+
5CDS-intron	ENST00000393820	ENST00000425707	NPM1	chr5	170818803	+	RARA	chr17	38504565	+
5CDS-intron	ENST00000393820	ENST00000394086	NPM1	chr5	170818803	+	RARA	chr17	38504565	+
5CDS-intron	ENST00000393820	ENST00000394081	NPM1	chr5	170818803	+	RARA	chr17	38504565	+
5CDS-intron	ENST00000393820	ENST00000420042	NPM1	chr5	170818803	+	RARA	chr17	38504565	+

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FusionProtFeatures for NPM1_RARA

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

Hgene	Tgene
NPM1 P06748	RARA P10276

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Fusion gene ID: 24740

FusionGeneSummary for NPM1_RARA

FusionProtFeatures for NPM1_RARA