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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:PCGF3-NCOA1 (FusionGDB2 ID:63295)

Fusion Gene Summary for PCGF3-NCOA1

check button Fusion gene summary
Fusion gene informationFusion gene name: PCGF3-NCOA1
Fusion gene ID: 63295
HgeneTgene
Gene symbol

PCGF3

NCOA1

Gene ID

10336

8648

Gene namepolycomb group ring finger 3nuclear receptor coactivator 1
SynonymsDONG1|RNF3|RNF3AF-SRC-1|KAT13A|RIP160|SRC1|bHLHe42|bHLHe74
Cytomap

4p16.3

2p23.3

Type of geneprotein-codingprotein-coding
Descriptionpolycomb group RING finger protein 3RING finger protein 3Aring finger protein 3nuclear receptor coactivator 1Hin-2 proteinclass E basic helix-loop-helix protein 74renal carcinoma antigen NY-REN-52steroid receptor coactivator-1
Modification date2020031320200313
UniProtAcc.

Q15788

Ensembl transtripts involved in fusion geneENST00000362003, ENST00000400151, 
ENST00000470161, ENST00000482726, 
ENST00000505655, ENST00000521023, 
ENST00000406961, ENST00000288599, 
ENST00000348332, ENST00000395856, 
ENST00000405141, ENST00000407230, 
ENST00000469850, ENST00000538539, 
Fusion gene scores* DoF score14 X 8 X 8=89611 X 13 X 7=1001
# samples 1813
** MAII scorelog2(18/896*10)=-2.31550182572793
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(13/1001*10)=-2.94485844580754
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: PCGF3 [Title/Abstract] AND NCOA1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPCGF3(702588)-NCOA1(24930064), # 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)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
TgeneNCOA1

GO:0000435

positive regulation of transcription from RNA polymerase II promoter by galactose

10207113

TgeneNCOA1

GO:0006351

transcription, DNA-templated

9223431

TgeneNCOA1

GO:0045893

positive regulation of transcription, DNA-templated

11891224|15367689

TgeneNCOA1

GO:0045944

positive regulation of transcription by RNA polymerase II

15919756


check buttonFusion gene breakpoints across PCGF3 (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 NCOA1 (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
ChiTaRS5.0N/ABQ956364PCGF3chr4

702588

-NCOA1chr2

24930064

+


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Fusion Gene ORF analysis for PCGF3-NCOA1

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
intron-3CDSENST00000362003ENST00000406961PCGF3chr4

702588

-NCOA1chr2

24930064

+
intron-3CDSENST00000400151ENST00000406961PCGF3chr4

702588

-NCOA1chr2

24930064

+
intron-3CDSENST00000470161ENST00000406961PCGF3chr4

702588

-NCOA1chr2

24930064

+
intron-3CDSENST00000482726ENST00000406961PCGF3chr4

702588

-NCOA1chr2

24930064

+
intron-3CDSENST00000505655ENST00000406961PCGF3chr4

702588

-NCOA1chr2

24930064

+
intron-3CDSENST00000521023ENST00000406961PCGF3chr4

702588

-NCOA1chr2

24930064

+
intron-intronENST00000362003ENST00000288599PCGF3chr4

702588

-NCOA1chr2

24930064

+
intron-intronENST00000362003ENST00000348332PCGF3chr4

702588

-NCOA1chr2

24930064

+
intron-intronENST00000362003ENST00000395856PCGF3chr4

702588

-NCOA1chr2

24930064

+
intron-intronENST00000362003ENST00000405141PCGF3chr4

702588

-NCOA1chr2

24930064

+
intron-intronENST00000362003ENST00000407230PCGF3chr4

702588

-NCOA1chr2

24930064

+
intron-intronENST00000362003ENST00000469850PCGF3chr4

702588

-NCOA1chr2

24930064

+
intron-intronENST00000362003ENST00000538539PCGF3chr4

702588

-NCOA1chr2

24930064

+
intron-intronENST00000400151ENST00000288599PCGF3chr4

702588

-NCOA1chr2

24930064

+
intron-intronENST00000400151ENST00000348332PCGF3chr4

702588

-NCOA1chr2

24930064

+
intron-intronENST00000400151ENST00000395856PCGF3chr4

702588

-NCOA1chr2

24930064

+
intron-intronENST00000400151ENST00000405141PCGF3chr4

702588

-NCOA1chr2

24930064

+
intron-intronENST00000400151ENST00000407230PCGF3chr4

702588

-NCOA1chr2

24930064

+
intron-intronENST00000400151ENST00000469850PCGF3chr4

702588

-NCOA1chr2

24930064

+
intron-intronENST00000400151ENST00000538539PCGF3chr4

702588

-NCOA1chr2

24930064

+
intron-intronENST00000470161ENST00000288599PCGF3chr4

702588

-NCOA1chr2

24930064

+
intron-intronENST00000470161ENST00000348332PCGF3chr4

702588

-NCOA1chr2

24930064

+
intron-intronENST00000470161ENST00000395856PCGF3chr4

702588

-NCOA1chr2

24930064

+
intron-intronENST00000470161ENST00000405141PCGF3chr4

702588

-NCOA1chr2

24930064

+
intron-intronENST00000470161ENST00000407230PCGF3chr4

702588

-NCOA1chr2

24930064

+
intron-intronENST00000470161ENST00000469850PCGF3chr4

702588

-NCOA1chr2

24930064

+
intron-intronENST00000470161ENST00000538539PCGF3chr4

702588

-NCOA1chr2

24930064

+
intron-intronENST00000482726ENST00000288599PCGF3chr4

702588

-NCOA1chr2

24930064

+
intron-intronENST00000482726ENST00000348332PCGF3chr4

702588

-NCOA1chr2

24930064

+
intron-intronENST00000482726ENST00000395856PCGF3chr4

702588

-NCOA1chr2

24930064

+
intron-intronENST00000482726ENST00000405141PCGF3chr4

702588

-NCOA1chr2

24930064

+
intron-intronENST00000482726ENST00000407230PCGF3chr4

702588

-NCOA1chr2

24930064

+
intron-intronENST00000482726ENST00000469850PCGF3chr4

702588

-NCOA1chr2

24930064

+
intron-intronENST00000482726ENST00000538539PCGF3chr4

702588

-NCOA1chr2

24930064

+
intron-intronENST00000505655ENST00000288599PCGF3chr4

702588

-NCOA1chr2

24930064

+
intron-intronENST00000505655ENST00000348332PCGF3chr4

702588

-NCOA1chr2

24930064

+
intron-intronENST00000505655ENST00000395856PCGF3chr4

702588

-NCOA1chr2

24930064

+
intron-intronENST00000505655ENST00000405141PCGF3chr4

702588

-NCOA1chr2

24930064

+
intron-intronENST00000505655ENST00000407230PCGF3chr4

702588

-NCOA1chr2

24930064

+
intron-intronENST00000505655ENST00000469850PCGF3chr4

702588

-NCOA1chr2

24930064

+
intron-intronENST00000505655ENST00000538539PCGF3chr4

702588

-NCOA1chr2

24930064

+
intron-intronENST00000521023ENST00000288599PCGF3chr4

702588

-NCOA1chr2

24930064

+
intron-intronENST00000521023ENST00000348332PCGF3chr4

702588

-NCOA1chr2

24930064

+
intron-intronENST00000521023ENST00000395856PCGF3chr4

702588

-NCOA1chr2

24930064

+
intron-intronENST00000521023ENST00000405141PCGF3chr4

702588

-NCOA1chr2

24930064

+
intron-intronENST00000521023ENST00000407230PCGF3chr4

702588

-NCOA1chr2

24930064

+
intron-intronENST00000521023ENST00000469850PCGF3chr4

702588

-NCOA1chr2

24930064

+
intron-intronENST00000521023ENST00000538539PCGF3chr4

702588

-NCOA1chr2

24930064

+

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 PCGF3-NCOA1


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 PCGF3-NCOA1


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/:702588/:24930064)
- 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
.NCOA1

Q15788

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: Nuclear receptor coactivator that directly binds nuclear receptors and stimulates the transcriptional activities in a hormone-dependent fashion. Involved in the coactivation of different nuclear receptors, such as for steroids (PGR, GR and ER), retinoids (RXRs), thyroid hormone (TRs) and prostanoids (PPARs). Also involved in coactivation mediated by STAT3, STAT5A, STAT5B and STAT6 transcription factors. Displays histone acetyltransferase activity toward H3 and H4; the relevance of such activity remains however unclear. Plays a central role in creating multisubunit coactivator complexes that act via remodeling of chromatin, and possibly acts by participating in both chromatin remodeling and recruitment of general transcription factors. Required with NCOA2 to control energy balance between white and brown adipose tissues. Required for mediating steroid hormone response. Isoform 2 has a higher thyroid hormone-dependent transactivation activity than isoform 1 and isoform 3. {ECO:0000269|PubMed:10449719, ECO:0000269|PubMed:12954634, ECO:0000269|PubMed:7481822, ECO:0000269|PubMed:9223281, ECO:0000269|PubMed:9223431, ECO:0000269|PubMed:9296499, ECO:0000269|PubMed:9427757}.

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 PCGF3-NCOA1


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 PCGF3-NCOA1


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 PCGF3-NCOA1


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 PCGF3-NCOA1


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