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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:IL3RA-CSF2RA (FusionGDB2 ID:39540)

Fusion Gene Summary for IL3RA-CSF2RA

Fusion gene summary

Fusion gene information	Fusion gene name: IL3RA-CSF2RA
	Fusion gene ID: 39540
		Hgene	Tgene
	Gene symbol	IL3RA	CSF2RA
	Gene ID	3563	1438
	Gene name	interleukin 3 receptor subunit alpha	colony stimulating factor 2 receptor subunit alpha
	Synonyms	CD123\|IL3R\|IL3RAY\|IL3RX\|IL3RY\|hIL-3Ra	CD116\|CDw116\|CSF2R\|CSF2RAX\|CSF2RAY\|CSF2RX\|CSF2RY\|GM-CSF-R-alpha\|GMCSFR\|GMCSFR-alpha\|GMR\|GMR-alpha\|SMDP4\|alphaGMR
	Cytomap	Xp22.33 and Yp11.2	Xp22.33 and Yp11.2
	Type of gene	protein-coding	protein-coding
	Description	interleukin-3 receptor subunit alphaCD123 antigenIL-3 receptor alpha SP2 isoformIL-3 receptor subunit alphaIL-3R subunit alphaIL-3R-alphaIL-3RAinterleukin 3 receptor, alpha (low affinity)	granulocyte-macrophage colony-stimulating factor receptor subunit alphaCD116 antigenGM-CSF receptor alpha subunitalpha-GM-CSF receptorcolony stimulating factor 2 receptor alpha subunitcolony stimulating factor 2 receptor, alpha, low-affinity (granulo
	Modification date	20200313	20200326
	UniProtAcc	P26951	P15509
	Ensembl transtripts involved in fusion gene	ENST00000331035, ENST00000381469,	ENST00000361536, ENST00000381509, ENST00000381524, ENST00000501036, ENST00000355432, ENST00000355805, ENST00000381500, ENST00000381529, ENST00000417535, ENST00000432318, ENST00000494969, ENST00000498153,
Fusion gene scores	* DoF score	3 X 4 X 2=24	8 X 9 X 3=216
	# samples	3	8
	** MAII score	log2(3/24*10)=0.321928094887362 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0	log2(8/216*10)=-1.43295940727611 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Context	PubMed: IL3RA [Title/Abstract] AND CSF2RA [Title/Abstract] AND fusion [Title/Abstract]
Most frequent breakpoint	IL3RA(1410722)-CSF2RA(1357412), # samples:1 IL3RA(1460722)-CSF2RA(1407412), # samples:1 IL3RA(1460722)-CSF2RA(1357412), # samples:1 IL3RA(1410722)-CSF2RA(1407412), # samples:1
Anticipated loss of major functional domain due to fusion event.	IL3RA-CSF2RA seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF. IL3RA-CSF2RA seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target 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

Fusion gene breakpoints across IL3RA (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 CSF2RA (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	Non-Cancer	ERR188335	IL3RA	chrX	1460722	+	CSF2RA	chrX	1407412	+
ChimerDB4	Non-Cancer	ERR188335	IL3RA	chrX	1460722	+	CSF2RA	chrY	1357412	+
ChimerDB4	Non-Cancer	ERR188335	IL3RA	chrY	1410722	+	CSF2RA	chrX	1407412	+
ChimerDB4	Non-Cancer	ERR188335	IL3RA	chrY	1410722	+	CSF2RA	chrY	1357412	+

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Fusion Gene ORF analysis for IL3RA-CSF2RA

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
5CDS-5UTR	ENST00000331035	ENST00000361536	IL3RA	chrY	1410722	+	CSF2RA	chrY	1357412	+
5CDS-5UTR	ENST00000331035	ENST00000381509	IL3RA	chrY	1410722	+	CSF2RA	chrY	1357412	+
5CDS-5UTR	ENST00000331035	ENST00000381524	IL3RA	chrY	1410722	+	CSF2RA	chrY	1357412	+
5CDS-5UTR	ENST00000331035	ENST00000501036	IL3RA	chrY	1410722	+	CSF2RA	chrY	1357412	+
5CDS-5UTR	ENST00000381469	ENST00000361536	IL3RA	chrY	1410722	+	CSF2RA	chrY	1357412	+
5CDS-5UTR	ENST00000381469	ENST00000381509	IL3RA	chrY	1410722	+	CSF2RA	chrY	1357412	+
5CDS-5UTR	ENST00000381469	ENST00000381524	IL3RA	chrY	1410722	+	CSF2RA	chrY	1357412	+
5CDS-5UTR	ENST00000381469	ENST00000501036	IL3RA	chrY	1410722	+	CSF2RA	chrY	1357412	+
5CDS-intron	ENST00000331035	ENST00000355432	IL3RA	chrY	1410722	+	CSF2RA	chrX	1407412	+
5CDS-intron	ENST00000331035	ENST00000355432	IL3RA	chrY	1410722	+	CSF2RA	chrY	1357412	+
5CDS-intron	ENST00000331035	ENST00000355805	IL3RA	chrY	1410722	+	CSF2RA	chrX	1407412	+
5CDS-intron	ENST00000331035	ENST00000355805	IL3RA	chrY	1410722	+	CSF2RA	chrY	1357412	+
5CDS-intron	ENST00000331035	ENST00000361536	IL3RA	chrY	1410722	+	CSF2RA	chrX	1407412	+
5CDS-intron	ENST00000331035	ENST00000381500	IL3RA	chrY	1410722	+	CSF2RA	chrX	1407412	+
5CDS-intron	ENST00000331035	ENST00000381500	IL3RA	chrY	1410722	+	CSF2RA	chrY	1357412	+
5CDS-intron	ENST00000331035	ENST00000381509	IL3RA	chrY	1410722	+	CSF2RA	chrX	1407412	+
5CDS-intron	ENST00000331035	ENST00000381524	IL3RA	chrY	1410722	+	CSF2RA	chrX	1407412	+
5CDS-intron	ENST00000331035	ENST00000381529	IL3RA	chrY	1410722	+	CSF2RA	chrX	1407412	+
5CDS-intron	ENST00000331035	ENST00000417535	IL3RA	chrY	1410722	+	CSF2RA	chrX	1407412	+
5CDS-intron	ENST00000331035	ENST00000417535	IL3RA	chrY	1410722	+	CSF2RA	chrY	1357412	+
5CDS-intron	ENST00000331035	ENST00000432318	IL3RA	chrY	1410722	+	CSF2RA	chrX	1407412	+
5CDS-intron	ENST00000331035	ENST00000494969	IL3RA	chrY	1410722	+	CSF2RA	chrX	1407412	+
5CDS-intron	ENST00000331035	ENST00000494969	IL3RA	chrY	1410722	+	CSF2RA	chrY	1357412	+
5CDS-intron	ENST00000331035	ENST00000498153	IL3RA	chrY	1410722	+	CSF2RA	chrX	1407412	+
5CDS-intron	ENST00000331035	ENST00000498153	IL3RA	chrY	1410722	+	CSF2RA	chrY	1357412	+
5CDS-intron	ENST00000331035	ENST00000501036	IL3RA	chrY	1410722	+	CSF2RA	chrX	1407412	+
5CDS-intron	ENST00000381469	ENST00000355432	IL3RA	chrY	1410722	+	CSF2RA	chrX	1407412	+
5CDS-intron	ENST00000381469	ENST00000355432	IL3RA	chrY	1410722	+	CSF2RA	chrY	1357412	+
5CDS-intron	ENST00000381469	ENST00000355805	IL3RA	chrY	1410722	+	CSF2RA	chrX	1407412	+
5CDS-intron	ENST00000381469	ENST00000355805	IL3RA	chrY	1410722	+	CSF2RA	chrY	1357412	+
5CDS-intron	ENST00000381469	ENST00000361536	IL3RA	chrY	1410722	+	CSF2RA	chrX	1407412	+
5CDS-intron	ENST00000381469	ENST00000381500	IL3RA	chrY	1410722	+	CSF2RA	chrX	1407412	+
5CDS-intron	ENST00000381469	ENST00000381500	IL3RA	chrY	1410722	+	CSF2RA	chrY	1357412	+
5CDS-intron	ENST00000381469	ENST00000381509	IL3RA	chrY	1410722	+	CSF2RA	chrX	1407412	+
5CDS-intron	ENST00000381469	ENST00000381524	IL3RA	chrY	1410722	+	CSF2RA	chrX	1407412	+
5CDS-intron	ENST00000381469	ENST00000381529	IL3RA	chrY	1410722	+	CSF2RA	chrX	1407412	+
5CDS-intron	ENST00000381469	ENST00000417535	IL3RA	chrY	1410722	+	CSF2RA	chrX	1407412	+
5CDS-intron	ENST00000381469	ENST00000417535	IL3RA	chrY	1410722	+	CSF2RA	chrY	1357412	+
5CDS-intron	ENST00000381469	ENST00000432318	IL3RA	chrY	1410722	+	CSF2RA	chrX	1407412	+
5CDS-intron	ENST00000381469	ENST00000494969	IL3RA	chrY	1410722	+	CSF2RA	chrX	1407412	+
5CDS-intron	ENST00000381469	ENST00000494969	IL3RA	chrY	1410722	+	CSF2RA	chrY	1357412	+
5CDS-intron	ENST00000381469	ENST00000498153	IL3RA	chrY	1410722	+	CSF2RA	chrX	1407412	+
5CDS-intron	ENST00000381469	ENST00000498153	IL3RA	chrY	1410722	+	CSF2RA	chrY	1357412	+
5CDS-intron	ENST00000381469	ENST00000501036	IL3RA	chrY	1410722	+	CSF2RA	chrX	1407412	+
Frame-shift	ENST00000331035	ENST00000381529	IL3RA	chrY	1410722	+	CSF2RA	chrY	1357412	+
Frame-shift	ENST00000331035	ENST00000432318	IL3RA	chrY	1410722	+	CSF2RA	chrY	1357412	+
Frame-shift	ENST00000381469	ENST00000381529	IL3RA	chrY	1410722	+	CSF2RA	chrY	1357412	+
Frame-shift	ENST00000381469	ENST00000432318	IL3RA	chrY	1410722	+	CSF2RA	chrY	1357412	+
intron-3CDS	ENST00000331035	ENST00000381529	IL3RA	chrX	1460722	+	CSF2RA	chrY	1357412	+
intron-3CDS	ENST00000331035	ENST00000432318	IL3RA	chrX	1460722	+	CSF2RA	chrY	1357412	+
intron-3CDS	ENST00000381469	ENST00000381529	IL3RA	chrX	1460722	+	CSF2RA	chrY	1357412	+
intron-3CDS	ENST00000381469	ENST00000432318	IL3RA	chrX	1460722	+	CSF2RA	chrY	1357412	+
intron-5UTR	ENST00000331035	ENST00000361536	IL3RA	chrX	1460722	+	CSF2RA	chrY	1357412	+
intron-5UTR	ENST00000331035	ENST00000381509	IL3RA	chrX	1460722	+	CSF2RA	chrY	1357412	+
intron-5UTR	ENST00000331035	ENST00000381524	IL3RA	chrX	1460722	+	CSF2RA	chrY	1357412	+
intron-5UTR	ENST00000331035	ENST00000501036	IL3RA	chrX	1460722	+	CSF2RA	chrY	1357412	+
intron-5UTR	ENST00000381469	ENST00000361536	IL3RA	chrX	1460722	+	CSF2RA	chrY	1357412	+
intron-5UTR	ENST00000381469	ENST00000381509	IL3RA	chrX	1460722	+	CSF2RA	chrY	1357412	+
intron-5UTR	ENST00000381469	ENST00000381524	IL3RA	chrX	1460722	+	CSF2RA	chrY	1357412	+
intron-5UTR	ENST00000381469	ENST00000501036	IL3RA	chrX	1460722	+	CSF2RA	chrY	1357412	+
intron-intron	ENST00000331035	ENST00000355432	IL3RA	chrX	1460722	+	CSF2RA	chrX	1407412	+
intron-intron	ENST00000331035	ENST00000355432	IL3RA	chrX	1460722	+	CSF2RA	chrY	1357412	+
intron-intron	ENST00000331035	ENST00000355805	IL3RA	chrX	1460722	+	CSF2RA	chrX	1407412	+
intron-intron	ENST00000331035	ENST00000355805	IL3RA	chrX	1460722	+	CSF2RA	chrY	1357412	+
intron-intron	ENST00000331035	ENST00000361536	IL3RA	chrX	1460722	+	CSF2RA	chrX	1407412	+
intron-intron	ENST00000331035	ENST00000381500	IL3RA	chrX	1460722	+	CSF2RA	chrX	1407412	+
intron-intron	ENST00000331035	ENST00000381500	IL3RA	chrX	1460722	+	CSF2RA	chrY	1357412	+
intron-intron	ENST00000331035	ENST00000381509	IL3RA	chrX	1460722	+	CSF2RA	chrX	1407412	+
intron-intron	ENST00000331035	ENST00000381524	IL3RA	chrX	1460722	+	CSF2RA	chrX	1407412	+
intron-intron	ENST00000331035	ENST00000381529	IL3RA	chrX	1460722	+	CSF2RA	chrX	1407412	+
intron-intron	ENST00000331035	ENST00000417535	IL3RA	chrX	1460722	+	CSF2RA	chrX	1407412	+
intron-intron	ENST00000331035	ENST00000417535	IL3RA	chrX	1460722	+	CSF2RA	chrY	1357412	+
intron-intron	ENST00000331035	ENST00000432318	IL3RA	chrX	1460722	+	CSF2RA	chrX	1407412	+
intron-intron	ENST00000331035	ENST00000494969	IL3RA	chrX	1460722	+	CSF2RA	chrX	1407412	+
intron-intron	ENST00000331035	ENST00000494969	IL3RA	chrX	1460722	+	CSF2RA	chrY	1357412	+
intron-intron	ENST00000331035	ENST00000498153	IL3RA	chrX	1460722	+	CSF2RA	chrX	1407412	+
intron-intron	ENST00000331035	ENST00000498153	IL3RA	chrX	1460722	+	CSF2RA	chrY	1357412	+
intron-intron	ENST00000331035	ENST00000501036	IL3RA	chrX	1460722	+	CSF2RA	chrX	1407412	+
intron-intron	ENST00000381469	ENST00000355432	IL3RA	chrX	1460722	+	CSF2RA	chrX	1407412	+
intron-intron	ENST00000381469	ENST00000355432	IL3RA	chrX	1460722	+	CSF2RA	chrY	1357412	+
intron-intron	ENST00000381469	ENST00000355805	IL3RA	chrX	1460722	+	CSF2RA	chrX	1407412	+
intron-intron	ENST00000381469	ENST00000355805	IL3RA	chrX	1460722	+	CSF2RA	chrY	1357412	+
intron-intron	ENST00000381469	ENST00000361536	IL3RA	chrX	1460722	+	CSF2RA	chrX	1407412	+
intron-intron	ENST00000381469	ENST00000381500	IL3RA	chrX	1460722	+	CSF2RA	chrX	1407412	+
intron-intron	ENST00000381469	ENST00000381500	IL3RA	chrX	1460722	+	CSF2RA	chrY	1357412	+
intron-intron	ENST00000381469	ENST00000381509	IL3RA	chrX	1460722	+	CSF2RA	chrX	1407412	+
intron-intron	ENST00000381469	ENST00000381524	IL3RA	chrX	1460722	+	CSF2RA	chrX	1407412	+
intron-intron	ENST00000381469	ENST00000381529	IL3RA	chrX	1460722	+	CSF2RA	chrX	1407412	+
intron-intron	ENST00000381469	ENST00000417535	IL3RA	chrX	1460722	+	CSF2RA	chrX	1407412	+
intron-intron	ENST00000381469	ENST00000417535	IL3RA	chrX	1460722	+	CSF2RA	chrY	1357412	+
intron-intron	ENST00000381469	ENST00000432318	IL3RA	chrX	1460722	+	CSF2RA	chrX	1407412	+
intron-intron	ENST00000381469	ENST00000494969	IL3RA	chrX	1460722	+	CSF2RA	chrX	1407412	+
intron-intron	ENST00000381469	ENST00000494969	IL3RA	chrX	1460722	+	CSF2RA	chrY	1357412	+
intron-intron	ENST00000381469	ENST00000498153	IL3RA	chrX	1460722	+	CSF2RA	chrX	1407412	+
intron-intron	ENST00000381469	ENST00000498153	IL3RA	chrX	1460722	+	CSF2RA	chrY	1357412	+
intron-intron	ENST00000381469	ENST00000501036	IL3RA	chrX	1460722	+	CSF2RA	chrX	1407412	+

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 IL3RA-CSF2RA

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)
IL3RA	chrY	1410722	+	CSF2RA	chrY	1357411	+	2.58E-07	0.99999976
IL3RA	chrX	1460722	+	CSF2RA	chrX	1407411	+	2.58E-07	0.99999976
IL3RA	chrX	1460722	+	CSF2RA	chrY	1357411	+	2.58E-07	0.99999976
IL3RA	chrY	1410722	+	CSF2RA	chrX	1407411	+	2.58E-07	0.99999976
IL3RA	chrY	1410722	+	CSF2RA	chrY	1357411	+	2.58E-07	0.99999976
IL3RA	chrX	1460722	+	CSF2RA	chrX	1407411	+	2.58E-07	0.99999976
IL3RA	chrX	1460722	+	CSF2RA	chrY	1357411	+	2.58E-07	0.99999976
IL3RA	chrY	1410722	+	CSF2RA	chrX	1407411	+	2.58E-07	0.99999976

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 IL3RA-CSF2RA

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:1410722/:1357412)
- 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
IL3RA P26951	CSF2RA P15509
FUNCTION: This is a receptor for interleukin-3.	FUNCTION: Low affinity receptor for granulocyte-macrophage colony-stimulating factor. Transduces a signal that results in the proliferation, differentiation, and functional activation of hematopoietic cells.

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 IL3RA-CSF2RA

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 IL3RA-CSF2RA

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 IL3RA-CSF2RA

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 IL3RA-CSF2RA

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source