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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:NPAS3-AKAP6 (FusionGDB2 ID:59834)

Fusion Gene Summary for NPAS3-AKAP6

check button Fusion gene summary
Fusion gene informationFusion gene name: NPAS3-AKAP6
Fusion gene ID: 59834
HgeneTgene
Gene symbol

NPAS3

AKAP6

Gene ID

64067

9472

Gene nameneuronal PAS domain protein 3A-kinase anchoring protein 6
SynonymsMOP6|PASD6|bHLHe12ADAP100|ADAP6|AKAP100|PRKA6|mAKAP
Cytomap

14q13.1

14q12

Type of geneprotein-codingprotein-coding
Descriptionneuronal 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 PAS3A-kinase anchor protein 6A kinase (PRKA) anchor protein 6A-kinase anchor protein 100 kDaAKAP 100AKAP-6protein kinase A anchoring protein 6
Modification date2020031320200313
UniProtAcc

Q8IXF0

Q13023

Ensembl transtripts involved in fusion geneENST00000341321, ENST00000346562, 
ENST00000356141, ENST00000357798, 
ENST00000548645, ENST00000551492, 
ENST00000547068, ENST00000550662, 
ENST00000551008, 		ENST00000554449, 
ENST00000557272, ENST00000557354, 
ENST00000280979, 
Fusion gene scores* DoF score10 X 9 X 4=36012 X 10 X 7=840
# samples 1313
** MAII scorelog2(13/360*10)=-1.46948528330122
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(13/840*10)=-2.69187770463767
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: NPAS3 [Title/Abstract] AND AKAP6 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointNPAS3(33525200)-AKAP6(33290608), # samples:1
NPAS3(33408572)-AKAP6(33147517), # samples:1
Anticipated loss of major functional domain due to fusion event.NPAS3-AKAP6 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
NPAS3-AKAP6 seems lost the major protein functional domain in Hgene partner, which is a transcription factor due to the frame-shifted ORF.
NPAS3-AKAP6 seems lost the major protein functional domain in Tgene partner, which is a essential gene 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
TgeneAKAP6

GO:0060306

regulation of membrane repolarization

11299204

TgeneAKAP6

GO:0071320

cellular response to cAMP

11299204

TgeneAKAP6

GO:1901381

positive regulation of potassium ion transmembrane transport

11299204

TgeneAKAP6

GO:1902261

positive regulation of delayed rectifier potassium channel activity

11299204


check buttonFusion gene breakpoints across NPAS3 (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 AKAP6 (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
ChimerDB4LUADTCGA-55-7913-01BNPAS3chr14

33408572

-AKAP6chr14

33147517

+
ChimerDB4OVTCGA-25-1326-01ANPAS3chr14

33525200

-AKAP6chr14

33290608

+


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Fusion Gene ORF analysis for NPAS3-AKAP6

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-intronENST00000341321ENST00000554449NPAS3chr14

33408572

-AKAP6chr14

33147517

+
5CDS-intronENST00000341321ENST00000554449NPAS3chr14

33525200

-AKAP6chr14

33290608

+
5CDS-intronENST00000341321ENST00000557272NPAS3chr14

33525200

-AKAP6chr14

33290608

+
5CDS-intronENST00000341321ENST00000557354NPAS3chr14

33525200

-AKAP6chr14

33290608

+
5CDS-intronENST00000346562ENST00000554449NPAS3chr14

33408572

-AKAP6chr14

33147517

+
5CDS-intronENST00000356141ENST00000554449NPAS3chr14

33408572

-AKAP6chr14

33147517

+
5CDS-intronENST00000356141ENST00000554449NPAS3chr14

33525200

-AKAP6chr14

33290608

+
5CDS-intronENST00000356141ENST00000557272NPAS3chr14

33525200

-AKAP6chr14

33290608

+
5CDS-intronENST00000356141ENST00000557354NPAS3chr14

33525200

-AKAP6chr14

33290608

+
5CDS-intronENST00000357798ENST00000554449NPAS3chr14

33408572

-AKAP6chr14

33147517

+
5CDS-intronENST00000548645ENST00000554449NPAS3chr14

33408572

-AKAP6chr14

33147517

+
5CDS-intronENST00000551492ENST00000554449NPAS3chr14

33525200

-AKAP6chr14

33290608

+
5CDS-intronENST00000551492ENST00000557272NPAS3chr14

33525200

-AKAP6chr14

33290608

+
5CDS-intronENST00000551492ENST00000557354NPAS3chr14

33525200

-AKAP6chr14

33290608

+
Frame-shiftENST00000341321ENST00000280979NPAS3chr14

33408572

-AKAP6chr14

33147517

+
Frame-shiftENST00000341321ENST00000280979NPAS3chr14

33525200

-AKAP6chr14

33290608

+
Frame-shiftENST00000341321ENST00000557272NPAS3chr14

33408572

-AKAP6chr14

33147517

+
Frame-shiftENST00000341321ENST00000557354NPAS3chr14

33408572

-AKAP6chr14

33147517

+
Frame-shiftENST00000346562ENST00000280979NPAS3chr14

33408572

-AKAP6chr14

33147517

+
Frame-shiftENST00000346562ENST00000557272NPAS3chr14

33408572

-AKAP6chr14

33147517

+
Frame-shiftENST00000346562ENST00000557354NPAS3chr14

33408572

-AKAP6chr14

33147517

+
Frame-shiftENST00000356141ENST00000280979NPAS3chr14

33408572

-AKAP6chr14

33147517

+
Frame-shiftENST00000356141ENST00000280979NPAS3chr14

33525200

-AKAP6chr14

33290608

+
Frame-shiftENST00000356141ENST00000557272NPAS3chr14

33408572

-AKAP6chr14

33147517

+
Frame-shiftENST00000356141ENST00000557354NPAS3chr14

33408572

-AKAP6chr14

33147517

+
Frame-shiftENST00000357798ENST00000280979NPAS3chr14

33408572

-AKAP6chr14

33147517

+
Frame-shiftENST00000357798ENST00000557272NPAS3chr14

33408572

-AKAP6chr14

33147517

+
Frame-shiftENST00000357798ENST00000557354NPAS3chr14

33408572

-AKAP6chr14

33147517

+
Frame-shiftENST00000548645ENST00000280979NPAS3chr14

33408572

-AKAP6chr14

33147517

+
Frame-shiftENST00000548645ENST00000557272NPAS3chr14

33408572

-AKAP6chr14

33147517

+
Frame-shiftENST00000548645ENST00000557354NPAS3chr14

33408572

-AKAP6chr14

33147517

+
Frame-shiftENST00000551492ENST00000280979NPAS3chr14

33525200

-AKAP6chr14

33290608

+
intron-3CDSENST00000346562ENST00000280979NPAS3chr14

33525200

-AKAP6chr14

33290608

+
intron-3CDSENST00000357798ENST00000280979NPAS3chr14

33525200

-AKAP6chr14

33290608

+
intron-3CDSENST00000547068ENST00000280979NPAS3chr14

33408572

-AKAP6chr14

33147517

+
intron-3CDSENST00000547068ENST00000280979NPAS3chr14

33525200

-AKAP6chr14

33290608

+
intron-3CDSENST00000547068ENST00000557272NPAS3chr14

33408572

-AKAP6chr14

33147517

+
intron-3CDSENST00000547068ENST00000557354NPAS3chr14

33408572

-AKAP6chr14

33147517

+
intron-3CDSENST00000548645ENST00000280979NPAS3chr14

33525200

-AKAP6chr14

33290608

+
intron-3CDSENST00000550662ENST00000280979NPAS3chr14

33408572

-AKAP6chr14

33147517

+
intron-3CDSENST00000550662ENST00000280979NPAS3chr14

33525200

-AKAP6chr14

33290608

+
intron-3CDSENST00000550662ENST00000557272NPAS3chr14

33408572

-AKAP6chr14

33147517

+
intron-3CDSENST00000550662ENST00000557354NPAS3chr14

33408572

-AKAP6chr14

33147517

+
intron-3CDSENST00000551008ENST00000280979NPAS3chr14

33408572

-AKAP6chr14

33147517

+
intron-3CDSENST00000551008ENST00000280979NPAS3chr14

33525200

-AKAP6chr14

33290608

+
intron-3CDSENST00000551008ENST00000557272NPAS3chr14

33408572

-AKAP6chr14

33147517

+
intron-3CDSENST00000551008ENST00000557354NPAS3chr14

33408572

-AKAP6chr14

33147517

+
intron-3CDSENST00000551492ENST00000280979NPAS3chr14

33408572

-AKAP6chr14

33147517

+
intron-3CDSENST00000551492ENST00000557272NPAS3chr14

33408572

-AKAP6chr14

33147517

+
intron-3CDSENST00000551492ENST00000557354NPAS3chr14

33408572

-AKAP6chr14

33147517

+
intron-intronENST00000346562ENST00000554449NPAS3chr14

33525200

-AKAP6chr14

33290608

+
intron-intronENST00000346562ENST00000557272NPAS3chr14

33525200

-AKAP6chr14

33290608

+
intron-intronENST00000346562ENST00000557354NPAS3chr14

33525200

-AKAP6chr14

33290608

+
intron-intronENST00000357798ENST00000554449NPAS3chr14

33525200

-AKAP6chr14

33290608

+
intron-intronENST00000357798ENST00000557272NPAS3chr14

33525200

-AKAP6chr14

33290608

+
intron-intronENST00000357798ENST00000557354NPAS3chr14

33525200

-AKAP6chr14

33290608

+
intron-intronENST00000547068ENST00000554449NPAS3chr14

33408572

-AKAP6chr14

33147517

+
intron-intronENST00000547068ENST00000554449NPAS3chr14

33525200

-AKAP6chr14

33290608

+
intron-intronENST00000547068ENST00000557272NPAS3chr14

33525200

-AKAP6chr14

33290608

+
intron-intronENST00000547068ENST00000557354NPAS3chr14

33525200

-AKAP6chr14

33290608

+
intron-intronENST00000548645ENST00000554449NPAS3chr14

33525200

-AKAP6chr14

33290608

+
intron-intronENST00000548645ENST00000557272NPAS3chr14

33525200

-AKAP6chr14

33290608

+
intron-intronENST00000548645ENST00000557354NPAS3chr14

33525200

-AKAP6chr14

33290608

+
intron-intronENST00000550662ENST00000554449NPAS3chr14

33408572

-AKAP6chr14

33147517

+
intron-intronENST00000550662ENST00000554449NPAS3chr14

33525200

-AKAP6chr14

33290608

+
intron-intronENST00000550662ENST00000557272NPAS3chr14

33525200

-AKAP6chr14

33290608

+
intron-intronENST00000550662ENST00000557354NPAS3chr14

33525200

-AKAP6chr14

33290608

+
intron-intronENST00000551008ENST00000554449NPAS3chr14

33408572

-AKAP6chr14

33147517

+
intron-intronENST00000551008ENST00000554449NPAS3chr14

33525200

-AKAP6chr14

33290608

+
intron-intronENST00000551008ENST00000557272NPAS3chr14

33525200

-AKAP6chr14

33290608

+
intron-intronENST00000551008ENST00000557354NPAS3chr14

33525200

-AKAP6chr14

33290608

+
intron-intronENST00000551492ENST00000554449NPAS3chr14

33408572

-AKAP6chr14

33147517

+

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 NPAS3-AKAP6


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 NPAS3-AKAP6


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/:33525200/:33290608)
- 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
NPAS3

Q8IXF0

AKAP6

Q13023

FUNCTION: May play a broad role in neurogenesis. May control regulatory pathways relevant to schizophrenia and to psychotic illness (By similarity). {ECO:0000250}.FUNCTION: Binds to type II regulatory subunits of protein kinase A and anchors/targets them to the nuclear membrane or sarcoplasmic reticulum. May act as an adapter for assembling multiprotein complexes.

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 NPAS3-AKAP6


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 NPAS3-AKAP6


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 NPAS3-AKAP6


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 NPAS3-AKAP6


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