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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:PEX13-CHMP3 (FusionGDB2 ID:HG5194TG51652)

Fusion Gene Summary for PEX13-CHMP3

check button Fusion gene summary
Fusion gene informationFusion gene name: PEX13-CHMP3
Fusion gene ID: hg5194tg51652
HgeneTgene
Gene symbol

PEX13

CHMP3

Gene ID

5194

51652

Gene nameperoxisomal biogenesis factor 13charged multivesicular body protein 3
SynonymsNALD|PBD11A|PBD11B|ZWSCGI-149|NEDF|VPS24
Cytomap('PEX13')('CHMP3')

2p15

2p11.2

Type of geneprotein-codingprotein-coding
Descriptionperoxisome biogenesis factor 13peroxin-13peroxisomal membrane protein PEX13charged multivesicular body protein 325.1 proteinCHMP family, member 3chromatin-modifying protein 3neuroendocrine differentiation factorvacuolar protein sorting 24 homologvacuolar protein sorting-associated protein 24
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000472678, ENST00000295030, 
ENST00000401576, ENST00000414712, 
ENST00000444100, 
Fusion gene scores* DoF score1 X 2 X 1=25 X 3 X 3=45
# samples 26
** MAII scorelog2(2/2*10)=3.32192809488736log2(6/45*10)=0.415037499278844
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: PEX13 [Title/Abstract] AND CHMP3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPEX13(61244986)-CHMP3(86737602), # samples:2
Anticipated loss of major functional domain due to fusion event.PEX13-CHMP3 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
PEX13-CHMP3 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
TgeneCHMP3

GO:0039702

viral budding via host ESCRT complex

24878737

TgeneCHMP3

GO:0051258

protein polymerization

23051622



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
ChimerDB4LUSCTCGA-60-2715-01APEX13chr2

61244986

+CHMP3chr2

86737602

-
ChimerDB4LUSCTCGA-60-2715PEX13chr2

61244986

+CHMP3chr2

86737602

-
ChimerDB4LUSCTCGA-60-2715PEX13chr2

61245009

+CHMP3chr2

86737602

-


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Fusion Gene ORF analysis for PEX13-CHMP3

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-3CDSENST00000472678ENST00000263856PEX13chr2

61244986

+CHMP3chr2

86737602

-
3UTR-3CDSENST00000472678ENST00000263856PEX13chr2

61245009

+CHMP3chr2

86737602

-
3UTR-5UTRENST00000472678ENST00000494623PEX13chr2

61244986

+CHMP3chr2

86737602

-
3UTR-5UTRENST00000472678ENST00000494623PEX13chr2

61245009

+CHMP3chr2

86737602

-
3UTR-intronENST00000472678ENST00000409225PEX13chr2

61244986

+CHMP3chr2

86737602

-
3UTR-intronENST00000472678ENST00000409225PEX13chr2

61245009

+CHMP3chr2

86737602

-
3UTR-intronENST00000472678ENST00000409727PEX13chr2

61244986

+CHMP3chr2

86737602

-
3UTR-intronENST00000472678ENST00000409727PEX13chr2

61245009

+CHMP3chr2

86737602

-
3UTR-intronENST00000472678ENST00000439940PEX13chr2

61244986

+CHMP3chr2

86737602

-
3UTR-intronENST00000472678ENST00000439940PEX13chr2

61245009

+CHMP3chr2

86737602

-
5CDS-5UTRENST00000295030ENST00000494623PEX13chr2

61244986

+CHMP3chr2

86737602

-
5CDS-5UTRENST00000401576ENST00000494623PEX13chr2

61244986

+CHMP3chr2

86737602

-
5CDS-5UTRENST00000414712ENST00000494623PEX13chr2

61244986

+CHMP3chr2

86737602

-
5CDS-5UTRENST00000444100ENST00000494623PEX13chr2

61244986

+CHMP3chr2

86737602

-
5CDS-intronENST00000295030ENST00000409225PEX13chr2

61244986

+CHMP3chr2

86737602

-
5CDS-intronENST00000295030ENST00000409727PEX13chr2

61244986

+CHMP3chr2

86737602

-
5CDS-intronENST00000295030ENST00000439940PEX13chr2

61244986

+CHMP3chr2

86737602

-
5CDS-intronENST00000401576ENST00000409225PEX13chr2

61244986

+CHMP3chr2

86737602

-
5CDS-intronENST00000401576ENST00000409727PEX13chr2

61244986

+CHMP3chr2

86737602

-
5CDS-intronENST00000401576ENST00000439940PEX13chr2

61244986

+CHMP3chr2

86737602

-
5CDS-intronENST00000414712ENST00000409225PEX13chr2

61244986

+CHMP3chr2

86737602

-
5CDS-intronENST00000414712ENST00000409727PEX13chr2

61244986

+CHMP3chr2

86737602

-
5CDS-intronENST00000414712ENST00000439940PEX13chr2

61244986

+CHMP3chr2

86737602

-
5CDS-intronENST00000444100ENST00000409225PEX13chr2

61244986

+CHMP3chr2

86737602

-
5CDS-intronENST00000444100ENST00000409727PEX13chr2

61244986

+CHMP3chr2

86737602

-
5CDS-intronENST00000444100ENST00000439940PEX13chr2

61244986

+CHMP3chr2

86737602

-
Frame-shiftENST00000295030ENST00000263856PEX13chr2

61244986

+CHMP3chr2

86737602

-
Frame-shiftENST00000401576ENST00000263856PEX13chr2

61244986

+CHMP3chr2

86737602

-
Frame-shiftENST00000414712ENST00000263856PEX13chr2

61244986

+CHMP3chr2

86737602

-
Frame-shiftENST00000444100ENST00000263856PEX13chr2

61244986

+CHMP3chr2

86737602

-
intron-3CDSENST00000295030ENST00000263856PEX13chr2

61245009

+CHMP3chr2

86737602

-
intron-3CDSENST00000401576ENST00000263856PEX13chr2

61245009

+CHMP3chr2

86737602

-
intron-3CDSENST00000414712ENST00000263856PEX13chr2

61245009

+CHMP3chr2

86737602

-
intron-3CDSENST00000444100ENST00000263856PEX13chr2

61245009

+CHMP3chr2

86737602

-
intron-5UTRENST00000295030ENST00000494623PEX13chr2

61245009

+CHMP3chr2

86737602

-
intron-5UTRENST00000401576ENST00000494623PEX13chr2

61245009

+CHMP3chr2

86737602

-
intron-5UTRENST00000414712ENST00000494623PEX13chr2

61245009

+CHMP3chr2

86737602

-
intron-5UTRENST00000444100ENST00000494623PEX13chr2

61245009

+CHMP3chr2

86737602

-
intron-intronENST00000295030ENST00000409225PEX13chr2

61245009

+CHMP3chr2

86737602

-
intron-intronENST00000295030ENST00000409727PEX13chr2

61245009

+CHMP3chr2

86737602

-
intron-intronENST00000295030ENST00000439940PEX13chr2

61245009

+CHMP3chr2

86737602

-
intron-intronENST00000401576ENST00000409225PEX13chr2

61245009

+CHMP3chr2

86737602

-
intron-intronENST00000401576ENST00000409727PEX13chr2

61245009

+CHMP3chr2

86737602

-
intron-intronENST00000401576ENST00000439940PEX13chr2

61245009

+CHMP3chr2

86737602

-
intron-intronENST00000414712ENST00000409225PEX13chr2

61245009

+CHMP3chr2

86737602

-
intron-intronENST00000414712ENST00000409727PEX13chr2

61245009

+CHMP3chr2

86737602

-
intron-intronENST00000414712ENST00000439940PEX13chr2

61245009

+CHMP3chr2

86737602

-
intron-intronENST00000444100ENST00000409225PEX13chr2

61245009

+CHMP3chr2

86737602

-
intron-intronENST00000444100ENST00000409727PEX13chr2

61245009

+CHMP3chr2

86737602

-
intron-intronENST00000444100ENST00000439940PEX13chr2

61245009

+CHMP3chr2

86737602

-

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 PEX13-CHMP3


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 PEX13-CHMP3


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/:61244986/:86737602)
- 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 PEX13-CHMP3


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 PEX13-CHMP3


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 PEX13-CHMP3


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 PEX13-CHMP3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgenePEX13C3554001PEROXISOME BIOGENESIS DISORDER 11B6CTD_human;GENOMICS_ENGLAND;UNIPROT
HgenePEX13C3554000PEROXISOME BIOGENESIS DISORDER 11A (ZELLWEGER)5CTD_human;GENOMICS_ENGLAND
HgenePEX13C1832200Peroxisome biogenesis disorders4CTD_human;GENOMICS_ENGLAND
HgenePEX13C0043459Zellweger Syndrome2CTD_human
HgenePEX13C0751594Zellweger-Like Syndrome2CTD_human
HgenePEX13C3658299Zellweger Spectrum2CTD_human
HgenePEX13C0162309Adrenoleukodystrophy1CTD_human
HgenePEX13C1527231Adrenomyeloneuropathy1CTD_human