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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:NCOA1-NPAS3 (FusionGDB2 ID:57690)

Fusion Gene Summary for NCOA1-NPAS3

check button Fusion gene summary
Fusion gene informationFusion gene name: NCOA1-NPAS3
Fusion gene ID: 57690
HgeneTgene
Gene symbol

NCOA1

NPAS3

Gene ID

8648

64067

Gene namenuclear receptor coactivator 1neuronal PAS domain protein 3
SynonymsF-SRC-1|KAT13A|RIP160|SRC1|bHLHe42|bHLHe74MOP6|PASD6|bHLHe12
Cytomap

2p23.3

14q13.1

Type of geneprotein-codingprotein-coding
Descriptionnuclear receptor coactivator 1Hin-2 proteinclass E basic helix-loop-helix protein 74renal carcinoma antigen NY-REN-52steroid receptor coactivator-1neuronal PAS domain-containing protein 3PAS domain-containing protein 6basic-helix-loop-helix-PAS protein MOP6class E basic helix-loop-helix protein 12member of PAS protein 6neuronal PAS3
Modification date2020031320200313
UniProtAcc

Q15788

Q8IXF0

Ensembl transtripts involved in fusion geneENST00000288599, ENST00000348332, 
ENST00000395856, ENST00000405141, 
ENST00000406961, ENST00000407230, 
ENST00000469850, ENST00000538539, 
ENST00000341321, ENST00000346562, 
ENST00000356141, ENST00000357798, 
ENST00000547068, ENST00000548645, 
ENST00000550662, ENST00000551008, 
ENST00000551492, 
Fusion gene scores* DoF score16 X 13 X 8=166414 X 16 X 7=1568
# samples 1716
** MAII scorelog2(17/1664*10)=-3.29104878200339
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(16/1568*10)=-3.29278174922785
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: NCOA1 [Title/Abstract] AND NPAS3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointNCOA1(24991403)-NPAS3(33987817), # 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
HgeneNCOA1

GO:0000435

positive regulation of transcription from RNA polymerase II promoter by galactose

10207113

HgeneNCOA1

GO:0006351

transcription, DNA-templated

9223431

HgeneNCOA1

GO:0045893

positive regulation of transcription, DNA-templated

11891224|15367689

HgeneNCOA1

GO:0045944

positive regulation of transcription by RNA polymerase II

15919756


check buttonFusion gene breakpoints across NCOA1 (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 NPAS3 (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/AU40396NCOA1chr2

24991403

+NPAS3chr14

33987817

-


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Fusion Gene ORF analysis for NCOA1-NPAS3

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-intronENST00000288599ENST00000341321NCOA1chr2

24991403

+NPAS3chr14

33987817

-
3UTR-intronENST00000288599ENST00000346562NCOA1chr2

24991403

+NPAS3chr14

33987817

-
3UTR-intronENST00000288599ENST00000356141NCOA1chr2

24991403

+NPAS3chr14

33987817

-
3UTR-intronENST00000288599ENST00000357798NCOA1chr2

24991403

+NPAS3chr14

33987817

-
3UTR-intronENST00000288599ENST00000547068NCOA1chr2

24991403

+NPAS3chr14

33987817

-
3UTR-intronENST00000288599ENST00000548645NCOA1chr2

24991403

+NPAS3chr14

33987817

-
3UTR-intronENST00000288599ENST00000550662NCOA1chr2

24991403

+NPAS3chr14

33987817

-
3UTR-intronENST00000288599ENST00000551008NCOA1chr2

24991403

+NPAS3chr14

33987817

-
3UTR-intronENST00000288599ENST00000551492NCOA1chr2

24991403

+NPAS3chr14

33987817

-
3UTR-intronENST00000348332ENST00000341321NCOA1chr2

24991403

+NPAS3chr14

33987817

-
3UTR-intronENST00000348332ENST00000346562NCOA1chr2

24991403

+NPAS3chr14

33987817

-
3UTR-intronENST00000348332ENST00000356141NCOA1chr2

24991403

+NPAS3chr14

33987817

-
3UTR-intronENST00000348332ENST00000357798NCOA1chr2

24991403

+NPAS3chr14

33987817

-
3UTR-intronENST00000348332ENST00000547068NCOA1chr2

24991403

+NPAS3chr14

33987817

-
3UTR-intronENST00000348332ENST00000548645NCOA1chr2

24991403

+NPAS3chr14

33987817

-
3UTR-intronENST00000348332ENST00000550662NCOA1chr2

24991403

+NPAS3chr14

33987817

-
3UTR-intronENST00000348332ENST00000551008NCOA1chr2

24991403

+NPAS3chr14

33987817

-
3UTR-intronENST00000348332ENST00000551492NCOA1chr2

24991403

+NPAS3chr14

33987817

-
3UTR-intronENST00000395856ENST00000341321NCOA1chr2

24991403

+NPAS3chr14

33987817

-
3UTR-intronENST00000395856ENST00000346562NCOA1chr2

24991403

+NPAS3chr14

33987817

-
3UTR-intronENST00000395856ENST00000356141NCOA1chr2

24991403

+NPAS3chr14

33987817

-
3UTR-intronENST00000395856ENST00000357798NCOA1chr2

24991403

+NPAS3chr14

33987817

-
3UTR-intronENST00000395856ENST00000547068NCOA1chr2

24991403

+NPAS3chr14

33987817

-
3UTR-intronENST00000395856ENST00000548645NCOA1chr2

24991403

+NPAS3chr14

33987817

-
3UTR-intronENST00000395856ENST00000550662NCOA1chr2

24991403

+NPAS3chr14

33987817

-
3UTR-intronENST00000395856ENST00000551008NCOA1chr2

24991403

+NPAS3chr14

33987817

-
3UTR-intronENST00000395856ENST00000551492NCOA1chr2

24991403

+NPAS3chr14

33987817

-
3UTR-intronENST00000405141ENST00000341321NCOA1chr2

24991403

+NPAS3chr14

33987817

-
3UTR-intronENST00000405141ENST00000346562NCOA1chr2

24991403

+NPAS3chr14

33987817

-
3UTR-intronENST00000405141ENST00000356141NCOA1chr2

24991403

+NPAS3chr14

33987817

-
3UTR-intronENST00000405141ENST00000357798NCOA1chr2

24991403

+NPAS3chr14

33987817

-
3UTR-intronENST00000405141ENST00000547068NCOA1chr2

24991403

+NPAS3chr14

33987817

-
3UTR-intronENST00000405141ENST00000548645NCOA1chr2

24991403

+NPAS3chr14

33987817

-
3UTR-intronENST00000405141ENST00000550662NCOA1chr2

24991403

+NPAS3chr14

33987817

-
3UTR-intronENST00000405141ENST00000551008NCOA1chr2

24991403

+NPAS3chr14

33987817

-
3UTR-intronENST00000405141ENST00000551492NCOA1chr2

24991403

+NPAS3chr14

33987817

-
3UTR-intronENST00000406961ENST00000341321NCOA1chr2

24991403

+NPAS3chr14

33987817

-
3UTR-intronENST00000406961ENST00000346562NCOA1chr2

24991403

+NPAS3chr14

33987817

-
3UTR-intronENST00000406961ENST00000356141NCOA1chr2

24991403

+NPAS3chr14

33987817

-
3UTR-intronENST00000406961ENST00000357798NCOA1chr2

24991403

+NPAS3chr14

33987817

-
3UTR-intronENST00000406961ENST00000547068NCOA1chr2

24991403

+NPAS3chr14

33987817

-
3UTR-intronENST00000406961ENST00000548645NCOA1chr2

24991403

+NPAS3chr14

33987817

-
3UTR-intronENST00000406961ENST00000550662NCOA1chr2

24991403

+NPAS3chr14

33987817

-
3UTR-intronENST00000406961ENST00000551008NCOA1chr2

24991403

+NPAS3chr14

33987817

-
3UTR-intronENST00000406961ENST00000551492NCOA1chr2

24991403

+NPAS3chr14

33987817

-
3UTR-intronENST00000407230ENST00000341321NCOA1chr2

24991403

+NPAS3chr14

33987817

-
3UTR-intronENST00000407230ENST00000346562NCOA1chr2

24991403

+NPAS3chr14

33987817

-
3UTR-intronENST00000407230ENST00000356141NCOA1chr2

24991403

+NPAS3chr14

33987817

-
3UTR-intronENST00000407230ENST00000357798NCOA1chr2

24991403

+NPAS3chr14

33987817

-
3UTR-intronENST00000407230ENST00000547068NCOA1chr2

24991403

+NPAS3chr14

33987817

-
3UTR-intronENST00000407230ENST00000548645NCOA1chr2

24991403

+NPAS3chr14

33987817

-
3UTR-intronENST00000407230ENST00000550662NCOA1chr2

24991403

+NPAS3chr14

33987817

-
3UTR-intronENST00000407230ENST00000551008NCOA1chr2

24991403

+NPAS3chr14

33987817

-
3UTR-intronENST00000407230ENST00000551492NCOA1chr2

24991403

+NPAS3chr14

33987817

-
intron-intronENST00000469850ENST00000341321NCOA1chr2

24991403

+NPAS3chr14

33987817

-
intron-intronENST00000469850ENST00000346562NCOA1chr2

24991403

+NPAS3chr14

33987817

-
intron-intronENST00000469850ENST00000356141NCOA1chr2

24991403

+NPAS3chr14

33987817

-
intron-intronENST00000469850ENST00000357798NCOA1chr2

24991403

+NPAS3chr14

33987817

-
intron-intronENST00000469850ENST00000547068NCOA1chr2

24991403

+NPAS3chr14

33987817

-
intron-intronENST00000469850ENST00000548645NCOA1chr2

24991403

+NPAS3chr14

33987817

-
intron-intronENST00000469850ENST00000550662NCOA1chr2

24991403

+NPAS3chr14

33987817

-
intron-intronENST00000469850ENST00000551008NCOA1chr2

24991403

+NPAS3chr14

33987817

-
intron-intronENST00000469850ENST00000551492NCOA1chr2

24991403

+NPAS3chr14

33987817

-
intron-intronENST00000538539ENST00000341321NCOA1chr2

24991403

+NPAS3chr14

33987817

-
intron-intronENST00000538539ENST00000346562NCOA1chr2

24991403

+NPAS3chr14

33987817

-
intron-intronENST00000538539ENST00000356141NCOA1chr2

24991403

+NPAS3chr14

33987817

-
intron-intronENST00000538539ENST00000357798NCOA1chr2

24991403

+NPAS3chr14

33987817

-
intron-intronENST00000538539ENST00000547068NCOA1chr2

24991403

+NPAS3chr14

33987817

-
intron-intronENST00000538539ENST00000548645NCOA1chr2

24991403

+NPAS3chr14

33987817

-
intron-intronENST00000538539ENST00000550662NCOA1chr2

24991403

+NPAS3chr14

33987817

-
intron-intronENST00000538539ENST00000551008NCOA1chr2

24991403

+NPAS3chr14

33987817

-
intron-intronENST00000538539ENST00000551492NCOA1chr2

24991403

+NPAS3chr14

33987817

-

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 NCOA1-NPAS3


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 NCOA1-NPAS3


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/:24991403/:33987817)
- 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

NPAS3

Q8IXF0

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}.FUNCTION: May play a broad role in neurogenesis. May control regulatory pathways relevant to schizophrenia and to psychotic illness (By similarity). {ECO:0000250}.

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 NCOA1-NPAS3


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 NCOA1-NPAS3


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 NCOA1-NPAS3


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 NCOA1-NPAS3


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