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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:STX16-NPEPL1-NEDD4L (FusionGDB2 ID:HG100534593TG23327)

Fusion Gene Summary for STX16-NPEPL1-NEDD4L

check button Fusion gene summary
Fusion gene informationFusion gene name: STX16-NPEPL1-NEDD4L
Fusion gene ID: hg100534593tg23327
HgeneTgene
Gene symbol

STX16-NPEPL1

NEDD4L

Gene ID

100534593

23327

Gene nameSTX16-NPEPL1 readthrough (NMD candidate)NEDD4 like E3 ubiquitin protein ligase
Synonyms-NEDD4-2|NEDD4.2|PVNH7|RSP5|hNEDD4-2
Cytomap('STX16-NPEPL1')('NEDD4L')

20q13.32

18q21.31

Type of genencRNAprotein-coding
DescriptionSTX16-NPEPL1 readthrough (non-protein coding)E3 ubiquitin-protein ligase NEDD4-likeHECT-type E3 ubiquitin transferase NED4Lneural precursor cell expressed, developmentally down-regulated 4-like, E3 ubiquitin protein ligaseubiquitin-protein ligase Rsp5
Modification date2020031320200329
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000530122, 
Fusion gene scores* DoF score5 X 5 X 1=2527 X 28 X 6=4536
# samples 532
** MAII scorelog2(5/25*10)=1
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(32/4536*10)=-3.82527683005487
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: STX16-NPEPL1 [Title/Abstract] AND NEDD4L [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointSTX16-NPEPL1(57236433)-NEDD4L(56065315), # 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
TgeneNEDD4L

GO:0003254

regulation of membrane depolarization

15217910

TgeneNEDD4L

GO:0006511

ubiquitin-dependent protein catabolic process

21463633

TgeneNEDD4L

GO:0010038

response to metal ion

11244092

TgeneNEDD4L

GO:0016567

protein ubiquitination

15217910|25631046

TgeneNEDD4L

GO:0034765

regulation of ion transmembrane transport

17289006

TgeneNEDD4L

GO:0042391

regulation of membrane potential

17289006

TgeneNEDD4L

GO:0043161

proteasome-mediated ubiquitin-dependent protein catabolic process

21463633

TgeneNEDD4L

GO:0060306

regulation of membrane repolarization

21463633

TgeneNEDD4L

GO:0070936

protein K48-linked ubiquitination

21463633

TgeneNEDD4L

GO:1901016

regulation of potassium ion transmembrane transporter activity

17289006

TgeneNEDD4L

GO:1901017

negative regulation of potassium ion transmembrane transporter activity

21463633

TgeneNEDD4L

GO:1901380

negative regulation of potassium ion transmembrane transport

21463633

TgeneNEDD4L

GO:1902306

negative regulation of sodium ion transmembrane transport

15217910

TgeneNEDD4L

GO:1903861

positive regulation of dendrite extension

23999003

TgeneNEDD4L

GO:2000009

negative regulation of protein localization to cell surface

21463633

TgeneNEDD4L

GO:2000650

negative regulation of sodium ion transmembrane transporter activity

15217910



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


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Fusion Gene ORF analysis for STX16-NPEPL1-NEDD4L

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

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 STX16-NPEPL1-NEDD4L


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)


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Fusion Protein Features for STX16-NPEPL1-NEDD4L


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/:57236433/:56065315)
- 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
..
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: 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 STX16-NPEPL1-NEDD4L


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 STX16-NPEPL1-NEDD4L


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 STX16-NPEPL1-NEDD4L


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 STX16-NPEPL1-NEDD4L


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC0020538Hypertensive disease2CTD_human
TgeneC4310669PERIVENTRICULAR NODULAR HETEROTOPIA 72GENOMICS_ENGLAND;UNIPROT
TgeneC0008925Cleft Palate1CTD_human;GENOMICS_ENGLAND
TgeneC0014175Endometriosis1CTD_human
TgeneC0039075Syndactyly1CTD_human
TgeneC0265553Polysyndactyly1CTD_human
TgeneC0269102Endometrioma1CTD_human
TgeneC0543888Epileptic encephalopathy1GENOMICS_ENGLAND
TgeneC1837218Cleft palate, isolated1CTD_human
TgeneC1848213Periventricular Heterotopia, X-Linked1CTD_human
TgeneC1868720Periventricular Nodular Heterotopia1CTD_human;ORPHANET
TgeneC4551969Bilateral Periventricular Nodular Heterotopia1CTD_human