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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:NCOA4-ARHGAP44 (FusionGDB2 ID:57760)

Fusion Gene Summary for NCOA4-ARHGAP44

check button Fusion gene summary
Fusion gene informationFusion gene name: NCOA4-ARHGAP44
Fusion gene ID: 57760
HgeneTgene
Gene symbol

NCOA4

ARHGAP44

Gene ID

8031

9912

Gene namenuclear receptor coactivator 4Rho GTPase activating protein 44
SynonymsARA70|ELE1|PTC3|RFGNPC-A-10|RICH2
Cytomap

10q11.22

17p12

Type of geneprotein-codingprotein-coding
Descriptionnuclear receptor coactivator 470 kDa AR-activator70 kDa androgen receptor coactivatorNCoA-4RET-activating gene ELE1androgen receptor-associated protein of 70 kDaret fusedrho GTPase-activating protein 44Rho-type GTPase-activating protein RICH2RhoGAP interacting with CIP4 homologs protein 2rho GTPase-activating protein RICH2
Modification date2020031320200313
UniProtAcc

Q13772

Q17R89

Ensembl transtripts involved in fusion geneENST00000498586, ENST00000374087, 
ENST00000414907, ENST00000430396, 
ENST00000438493, ENST00000452682, 
ENST00000344348, ENST00000374082, 
ENST00000443446, 		ENST00000262444, 
ENST00000340825, ENST00000379672, 
ENST00000578087, 
Fusion gene scores* DoF score15 X 15 X 11=24759 X 9 X 7=567
# samples 2111
** MAII scorelog2(21/2475*10)=-3.55896729218821
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(11/567*10)=-2.36584521141757
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: NCOA4 [Title/Abstract] AND ARHGAP44 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointNCOA4(51565296)-ARHGAP44(12862034), # 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)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneNCOA4

GO:0006622

protein targeting to lysosome

25327288


check buttonFusion gene breakpoints across NCOA4 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across ARHGAP44 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check button 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.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChimerDB4PRADTCGA-V1-A8ML-01ANCOA4chr10

51565296

-ARHGAP44chr17

12862034

+


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Fusion Gene ORF analysis for NCOA4-ARHGAP44

check button 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.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
3UTR-3CDSENST00000498586ENST00000262444NCOA4chr10

51565296

-ARHGAP44chr17

12862034

+
3UTR-3CDSENST00000498586ENST00000340825NCOA4chr10

51565296

-ARHGAP44chr17

12862034

+
3UTR-3CDSENST00000498586ENST00000379672NCOA4chr10

51565296

-ARHGAP44chr17

12862034

+
3UTR-intronENST00000498586ENST00000578087NCOA4chr10

51565296

-ARHGAP44chr17

12862034

+
5UTR-3CDSENST00000374087ENST00000262444NCOA4chr10

51565296

-ARHGAP44chr17

12862034

+
5UTR-3CDSENST00000374087ENST00000340825NCOA4chr10

51565296

-ARHGAP44chr17

12862034

+
5UTR-3CDSENST00000374087ENST00000379672NCOA4chr10

51565296

-ARHGAP44chr17

12862034

+
5UTR-3CDSENST00000414907ENST00000262444NCOA4chr10

51565296

-ARHGAP44chr17

12862034

+
5UTR-3CDSENST00000414907ENST00000340825NCOA4chr10

51565296

-ARHGAP44chr17

12862034

+
5UTR-3CDSENST00000414907ENST00000379672NCOA4chr10

51565296

-ARHGAP44chr17

12862034

+
5UTR-3CDSENST00000430396ENST00000262444NCOA4chr10

51565296

-ARHGAP44chr17

12862034

+
5UTR-3CDSENST00000430396ENST00000340825NCOA4chr10

51565296

-ARHGAP44chr17

12862034

+
5UTR-3CDSENST00000430396ENST00000379672NCOA4chr10

51565296

-ARHGAP44chr17

12862034

+
5UTR-3CDSENST00000438493ENST00000262444NCOA4chr10

51565296

-ARHGAP44chr17

12862034

+
5UTR-3CDSENST00000438493ENST00000340825NCOA4chr10

51565296

-ARHGAP44chr17

12862034

+
5UTR-3CDSENST00000438493ENST00000379672NCOA4chr10

51565296

-ARHGAP44chr17

12862034

+
5UTR-3CDSENST00000452682ENST00000262444NCOA4chr10

51565296

-ARHGAP44chr17

12862034

+
5UTR-3CDSENST00000452682ENST00000340825NCOA4chr10

51565296

-ARHGAP44chr17

12862034

+
5UTR-3CDSENST00000452682ENST00000379672NCOA4chr10

51565296

-ARHGAP44chr17

12862034

+
5UTR-intronENST00000374087ENST00000578087NCOA4chr10

51565296

-ARHGAP44chr17

12862034

+
5UTR-intronENST00000414907ENST00000578087NCOA4chr10

51565296

-ARHGAP44chr17

12862034

+
5UTR-intronENST00000430396ENST00000578087NCOA4chr10

51565296

-ARHGAP44chr17

12862034

+
5UTR-intronENST00000438493ENST00000578087NCOA4chr10

51565296

-ARHGAP44chr17

12862034

+
5UTR-intronENST00000452682ENST00000578087NCOA4chr10

51565296

-ARHGAP44chr17

12862034

+
intron-3CDSENST00000344348ENST00000262444NCOA4chr10

51565296

-ARHGAP44chr17

12862034

+
intron-3CDSENST00000344348ENST00000340825NCOA4chr10

51565296

-ARHGAP44chr17

12862034

+
intron-3CDSENST00000344348ENST00000379672NCOA4chr10

51565296

-ARHGAP44chr17

12862034

+
intron-3CDSENST00000374082ENST00000262444NCOA4chr10

51565296

-ARHGAP44chr17

12862034

+
intron-3CDSENST00000374082ENST00000340825NCOA4chr10

51565296

-ARHGAP44chr17

12862034

+
intron-3CDSENST00000374082ENST00000379672NCOA4chr10

51565296

-ARHGAP44chr17

12862034

+
intron-3CDSENST00000443446ENST00000262444NCOA4chr10

51565296

-ARHGAP44chr17

12862034

+
intron-3CDSENST00000443446ENST00000340825NCOA4chr10

51565296

-ARHGAP44chr17

12862034

+
intron-3CDSENST00000443446ENST00000379672NCOA4chr10

51565296

-ARHGAP44chr17

12862034

+
intron-intronENST00000344348ENST00000578087NCOA4chr10

51565296

-ARHGAP44chr17

12862034

+
intron-intronENST00000374082ENST00000578087NCOA4chr10

51565296

-ARHGAP44chr17

12862034

+
intron-intronENST00000443446ENST00000578087NCOA4chr10

51565296

-ARHGAP44chr17

12862034

+

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)

check buttonDeepORF 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.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score

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Fusion Genomic Features for NCOA4-ARHGAP44


check buttonFusionAI 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.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)

check buttonDistribution 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.

check buttonDistribution 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 NCOA4-ARHGAP44


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:51565296/:12862034)
- 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.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
NCOA4

Q13772

ARHGAP44

Q17R89

FUNCTION: Enhances the androgen receptor transcriptional activity in prostate cancer cells. Ligand-independent coactivator of the peroxisome proliferator-activated receptor (PPAR) gamma. {ECO:0000269|PubMed:10347167}.FUNCTION: GTPase-activating protein (GAP) that stimulates the GTPase activity of Rho-type GTPases. Thereby, controls Rho-type GTPases cycling between their active GTP-bound and inactive GDP-bound states. Acts as a GAP at least for CDC42 and RAC1 (PubMed:11431473). In neurons, is involved in dendritic spine formation and synaptic plasticity in a specific RAC1-GAP activity (By similarity). Limits the initiation of exploratory dendritic filopodia. Recruited to actin-patches that seed filopodia, binds specifically to plasma membrane sections that are deformed inward by acto-myosin mediated contractile forces. Acts through GAP activity on RAC1 to reduce actin polymerization necessary for filopodia formation (By similarity). In association with SHANK3, promotes GRIA1 exocytosis from recycling endosomes and spine morphological changes associated to long-term potentiation (By similarity). {ECO:0000250|UniProtKB:F1LQX4, ECO:0000250|UniProtKB:Q5SSM3, ECO:0000269|PubMed:11431473}.

check buttonRetention 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.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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Fusion Gene Sequence for NCOA4-ARHGAP44


check button 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 NCOA4-ARHGAP44


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page.


check button Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs for NCOA4-ARHGAP44


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for NCOA4-ARHGAP44


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource