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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:AFF3-NPAS2 (FusionGDB2 ID:HG3899TG4862)

Fusion Gene Summary for AFF3-NPAS2

check button Fusion gene summary
Fusion gene informationFusion gene name: AFF3-NPAS2
Fusion gene ID: hg3899tg4862
HgeneTgene
Gene symbol

AFF3

NPAS2

Gene ID

3899

4862

Gene nameAF4/FMR2 family member 3neuronal PAS domain protein 2
SynonymsLAF4|MLLT2-likeMOP4|PASD4|bHLHe9
Cytomap('AFF3')('NPAS2')

2q11.2

2q11.2

Type of geneprotein-codingprotein-coding
DescriptionAF4/FMR2 family member 3MLLT2-related proteinlymphoid nuclear protein 4lymphoid nuclear protein related to AF4protein LAF-4neuronal PAS domain-containing protein 2PAS domain-containing protein 4basic-helix-loop-helix-PAS protein MOP4class E basic helix-loop-helix protein 9member of PAS protein 4member of PAS superfamily 4neuronal PAS2
Modification date2020031320200313
UniProtAcc

P51826

.
Ensembl transtripts involved in fusion geneENST00000317233, ENST00000356421, 
ENST00000409236, ENST00000409579, 
ENST00000483600, 
Fusion gene scores* DoF score17 X 13 X 7=15479 X 9 X 5=405
# samples 179
** MAII scorelog2(17/1547*10)=-3.18586654531133
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(9/405*10)=-2.16992500144231
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: AFF3 [Title/Abstract] AND NPAS2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointAFF3(100623094)-NPAS2(101604541), # samples:3
Anticipated loss of major functional domain due to fusion event.AFF3-NPAS2 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF.
AFF3-NPAS2 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
AFF3-NPAS2 seems lost the major protein functional domain in Tgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
AFF3-NPAS2 seems lost the major protein functional domain in Tgene partner, which is a epigenetic factor due to the frame-shifted ORF.
AFF3-NPAS2 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
AFF3-NPAS2 seems lost the major protein functional domain in Tgene partner, which is a transcription factor due to the frame-shifted ORF.
AFF3-NPAS2 seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor 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)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
TgeneNPAS2

GO:0045893

positive regulation of transcription, DNA-templated

11441146

TgeneNPAS2

GO:0051775

response to redox state

11441146



check button Fusion gene information
* 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
ChimerDB4LUADTCGA-97-8174-01AAFF3chr2

100623094

-NPAS2chr2

101604541

+


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Fusion Gene ORF analysis for AFF3-NPAS2

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
5CDS-intronENST00000317233ENST00000486017AFF3chr2

100623094

-NPAS2chr2

101604541

+
5CDS-intronENST00000356421ENST00000486017AFF3chr2

100623094

-NPAS2chr2

101604541

+
5CDS-intronENST00000409236ENST00000486017AFF3chr2

100623094

-NPAS2chr2

101604541

+
5CDS-intronENST00000409579ENST00000486017AFF3chr2

100623094

-NPAS2chr2

101604541

+
Frame-shiftENST00000317233ENST00000335681AFF3chr2

100623094

-NPAS2chr2

101604541

+
Frame-shiftENST00000317233ENST00000542504AFF3chr2

100623094

-NPAS2chr2

101604541

+
Frame-shiftENST00000356421ENST00000335681AFF3chr2

100623094

-NPAS2chr2

101604541

+
Frame-shiftENST00000356421ENST00000542504AFF3chr2

100623094

-NPAS2chr2

101604541

+
Frame-shiftENST00000409236ENST00000335681AFF3chr2

100623094

-NPAS2chr2

101604541

+
Frame-shiftENST00000409236ENST00000542504AFF3chr2

100623094

-NPAS2chr2

101604541

+
Frame-shiftENST00000409579ENST00000335681AFF3chr2

100623094

-NPAS2chr2

101604541

+
Frame-shiftENST00000409579ENST00000542504AFF3chr2

100623094

-NPAS2chr2

101604541

+
intron-3CDSENST00000483600ENST00000335681AFF3chr2

100623094

-NPAS2chr2

101604541

+
intron-3CDSENST00000483600ENST00000542504AFF3chr2

100623094

-NPAS2chr2

101604541

+
intron-intronENST00000483600ENST00000486017AFF3chr2

100623094

-NPAS2chr2

101604541

+

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 AFF3-NPAS2


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)
AFF3chr2100623093-NPAS2chr2101604540+2.67E-070.99999976
AFF3chr2100623093-NPAS2chr2101604540+2.67E-070.99999976


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.
genomic feature of top 1%

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Fusion Protein Features for AFF3-NPAS2


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/:100623094/:101604541)
- 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
AFF3

P51826

.
FUNCTION: Putative transcription activator that may function in lymphoid development and oncogenesis. Binds, in vitro, to double-stranded DNA.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}.

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 AFF3-NPAS2


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 AFF3-NPAS2


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 AFF3-NPAS2


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 AFF3-NPAS2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneAFF3C0003873Rheumatoid Arthritis2CTD_human
HgeneAFF3C0013146Drug abuse1CTD_human
HgeneAFF3C0013170Drug habituation1CTD_human
HgeneAFF3C0013222Drug Use Disorders1CTD_human
HgeneAFF3C0029231Organic Mental Disorders, Substance-Induced1CTD_human
HgeneAFF3C0036572Seizures1GENOMICS_ENGLAND
HgeneAFF3C0038580Substance Dependence1CTD_human
HgeneAFF3C0038586Substance Use Disorders1CTD_human
HgeneAFF3C0236969Substance-Related Disorders1CTD_human
HgeneAFF3C0740858Substance abuse problem1CTD_human
HgeneAFF3C1510472Drug Dependence1CTD_human
HgeneAFF3C3714756Intellectual Disability1GENOMICS_ENGLAND
HgeneAFF3C4316881Prescription Drug Abuse1CTD_human
TgeneC0005586Bipolar Disorder5PSYGENET
TgeneC0085159Seasonal Affective Disorder4PSYGENET
TgeneC0011581Depressive disorder2PSYGENET
TgeneC0004352Autistic Disorder1CTD_human
TgeneC0011570Mental Depression1PSYGENET
TgeneC0023893Liver Cirrhosis, Experimental1CTD_human
TgeneC0036337Schizoaffective Disorder1PSYGENET
TgeneC0036341Schizophrenia1PSYGENET