FusionGDB Logo

Home

Download

Statistics

Examples

Help

Contact
Center for Computational Systems Medicine
leaf

Fusion Gene Summary

leaf

Fusion Gene ORF analysis

leaf

Fusion Genomic Features

leaf

Fusion Protein Features

leaf

Fusion Gene Sequence

leaf

Fusion Gene PPI analysis

leaf

Related Drugs

leaf

Related Diseases

Fusion gene:USP25-CAPN3 (FusionGDB2 ID:96630)

Fusion Gene Summary for USP25-CAPN3

check button Fusion gene summary
Fusion gene informationFusion gene name: USP25-CAPN3
Fusion gene ID: 96630
HgeneTgene
Gene symbol

USP25

CAPN3

Gene ID

29761

825

Gene nameubiquitin specific peptidase 25calpain 3
SynonymsUSP21CANP3|CANPL3|LGMD2|LGMD2A|LGMDD4|LGMDR1|nCL-1|p94
Cytomap

21q21.1

15q15.1

Type of geneprotein-codingprotein-coding
Descriptionubiquitin carboxyl-terminal hydrolase 25USP on chromosome 21deubiquitinating enzyme 25ubiquitin thioesterase 25ubiquitin thiolesterase 25ubiquitin-specific processing protease 25calpain-3calpain p94, large [catalytic] subunitcalpain, large polypeptide L3muscle-specific calcium-activated neutral protease 3 large subunitnew calpain 1
Modification date2020031320200328
UniProtAcc.

P20807

Ensembl transtripts involved in fusion geneENST00000351097, ENST00000285679, 
ENST00000285681, ENST00000400183, 
ENST00000547201, 		ENST00000356316, 
ENST00000318023, ENST00000357568, 
ENST00000349748, ENST00000397163, 
ENST00000397200, ENST00000337571, 
ENST00000569136, ENST00000561817, 
ENST00000397204, ENST00000562199, 
Fusion gene scores* DoF score13 X 10 X 9=11705 X 5 X 4=100
# samples 135
** MAII scorelog2(13/1170*10)=-3.16992500144231
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(5/100*10)=-1
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: USP25 [Title/Abstract] AND CAPN3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointUSP25(17203948)-CAPN3(42676681), # samples:2
Anticipated loss of major functional domain due to fusion event.USP25-CAPN3 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
USP25-CAPN3 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
HgeneUSP25

GO:0016579

protein deubiquitination

22590560

TgeneCAPN3

GO:0006508

proteolysis

9642272|18310072|19386580|20694146

TgeneCAPN3

GO:0033234

negative regulation of protein sumoylation

20694146

TgeneCAPN3

GO:0050790

regulation of catalytic activity

20694146

TgeneCAPN3

GO:0097264

self proteolysis

9642272

TgeneCAPN3

GO:1990092

calcium-dependent self proteolysis

12482600


check buttonFusion gene breakpoints across USP25 (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 CAPN3 (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
ChimerDB4LUSCTCGA-77-A5G3-01AUSP25chr21

17203948

+CAPN3chr15

42676681

+
ChimerDB4LUSCTCGA-77-A5G3-01AUSP25chr21

17203948

-CAPN3chr15

42676681

+


Top

Fusion Gene ORF analysis for USP25-CAPN3

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
intron-3CDSENST00000351097ENST00000356316USP25chr21

17203948

+CAPN3chr15

42676681

+
intron-3CDSENST00000351097ENST00000318023USP25chr21

17203948

+CAPN3chr15

42676681

+
intron-3CDSENST00000351097ENST00000357568USP25chr21

17203948

+CAPN3chr15

42676681

+
intron-3CDSENST00000351097ENST00000349748USP25chr21

17203948

+CAPN3chr15

42676681

+
intron-3CDSENST00000351097ENST00000397163USP25chr21

17203948

+CAPN3chr15

42676681

+
intron-intronENST00000351097ENST00000397200USP25chr21

17203948

+CAPN3chr15

42676681

+
intron-intronENST00000351097ENST00000337571USP25chr21

17203948

+CAPN3chr15

42676681

+
intron-intronENST00000351097ENST00000569136USP25chr21

17203948

+CAPN3chr15

42676681

+
intron-intronENST00000351097ENST00000561817USP25chr21

17203948

+CAPN3chr15

42676681

+
intron-intronENST00000351097ENST00000397204USP25chr21

17203948

+CAPN3chr15

42676681

+
intron-intronENST00000351097ENST00000562199USP25chr21

17203948

+CAPN3chr15

42676681

+
Frame-shiftENST00000285679ENST00000356316USP25chr21

17203948

+CAPN3chr15

42676681

+
Frame-shiftENST00000285679ENST00000318023USP25chr21

17203948

+CAPN3chr15

42676681

+
Frame-shiftENST00000285679ENST00000357568USP25chr21

17203948

+CAPN3chr15

42676681

+
Frame-shiftENST00000285679ENST00000349748USP25chr21

17203948

+CAPN3chr15

42676681

+
Frame-shiftENST00000285679ENST00000397163USP25chr21

17203948

+CAPN3chr15

42676681

+
5CDS-intronENST00000285679ENST00000397200USP25chr21

17203948

+CAPN3chr15

42676681

+
5CDS-intronENST00000285679ENST00000337571USP25chr21

17203948

+CAPN3chr15

42676681

+
5CDS-intronENST00000285679ENST00000569136USP25chr21

17203948

+CAPN3chr15

42676681

+
5CDS-intronENST00000285679ENST00000561817USP25chr21

17203948

+CAPN3chr15

42676681

+
5CDS-intronENST00000285679ENST00000397204USP25chr21

17203948

+CAPN3chr15

42676681

+
5CDS-intronENST00000285679ENST00000562199USP25chr21

17203948

+CAPN3chr15

42676681

+
Frame-shiftENST00000285681ENST00000356316USP25chr21

17203948

+CAPN3chr15

42676681

+
Frame-shiftENST00000285681ENST00000318023USP25chr21

17203948

+CAPN3chr15

42676681

+
Frame-shiftENST00000285681ENST00000357568USP25chr21

17203948

+CAPN3chr15

42676681

+
Frame-shiftENST00000285681ENST00000349748USP25chr21

17203948

+CAPN3chr15

42676681

+
Frame-shiftENST00000285681ENST00000397163USP25chr21

17203948

+CAPN3chr15

42676681

+
5CDS-intronENST00000285681ENST00000397200USP25chr21

17203948

+CAPN3chr15

42676681

+
5CDS-intronENST00000285681ENST00000337571USP25chr21

17203948

+CAPN3chr15

42676681

+
5CDS-intronENST00000285681ENST00000569136USP25chr21

17203948

+CAPN3chr15

42676681

+
5CDS-intronENST00000285681ENST00000561817USP25chr21

17203948

+CAPN3chr15

42676681

+
5CDS-intronENST00000285681ENST00000397204USP25chr21

17203948

+CAPN3chr15

42676681

+
5CDS-intronENST00000285681ENST00000562199USP25chr21

17203948

+CAPN3chr15

42676681

+
Frame-shiftENST00000400183ENST00000356316USP25chr21

17203948

+CAPN3chr15

42676681

+
Frame-shiftENST00000400183ENST00000318023USP25chr21

17203948

+CAPN3chr15

42676681

+
Frame-shiftENST00000400183ENST00000357568USP25chr21

17203948

+CAPN3chr15

42676681

+
Frame-shiftENST00000400183ENST00000349748USP25chr21

17203948

+CAPN3chr15

42676681

+
Frame-shiftENST00000400183ENST00000397163USP25chr21

17203948

+CAPN3chr15

42676681

+
5CDS-intronENST00000400183ENST00000397200USP25chr21

17203948

+CAPN3chr15

42676681

+
5CDS-intronENST00000400183ENST00000337571USP25chr21

17203948

+CAPN3chr15

42676681

+
5CDS-intronENST00000400183ENST00000569136USP25chr21

17203948

+CAPN3chr15

42676681

+
5CDS-intronENST00000400183ENST00000561817USP25chr21

17203948

+CAPN3chr15

42676681

+
5CDS-intronENST00000400183ENST00000397204USP25chr21

17203948

+CAPN3chr15

42676681

+
5CDS-intronENST00000400183ENST00000562199USP25chr21

17203948

+CAPN3chr15

42676681

+
intron-3CDSENST00000547201ENST00000356316USP25chr21

17203948

+CAPN3chr15

42676681

+
intron-3CDSENST00000547201ENST00000318023USP25chr21

17203948

+CAPN3chr15

42676681

+
intron-3CDSENST00000547201ENST00000357568USP25chr21

17203948

+CAPN3chr15

42676681

+
intron-3CDSENST00000547201ENST00000349748USP25chr21

17203948

+CAPN3chr15

42676681

+
intron-3CDSENST00000547201ENST00000397163USP25chr21

17203948

+CAPN3chr15

42676681

+
intron-intronENST00000547201ENST00000397200USP25chr21

17203948

+CAPN3chr15

42676681

+
intron-intronENST00000547201ENST00000337571USP25chr21

17203948

+CAPN3chr15

42676681

+
intron-intronENST00000547201ENST00000569136USP25chr21

17203948

+CAPN3chr15

42676681

+
intron-intronENST00000547201ENST00000561817USP25chr21

17203948

+CAPN3chr15

42676681

+
intron-intronENST00000547201ENST00000397204USP25chr21

17203948

+CAPN3chr15

42676681

+
intron-intronENST00000547201ENST00000562199USP25chr21

17203948

+CAPN3chr15

42676681

+

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

Top

Fusion Genomic Features for USP25-CAPN3


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)
USP25chr2117203948+CAPN3chr1542676680+5.57E-111
USP25chr2117203948+CAPN3chr1542676680+5.57E-111

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.

Top

Fusion Protein Features for USP25-CAPN3


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
.CAPN3

P20807

FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.FUNCTION: Calcium-regulated non-lysosomal thiol-protease. Proteolytically cleaves CTBP1 at 'His-409'. {ECO:0000269|PubMed:23707407}.

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


Top

Fusion Gene Sequence for USP25-CAPN3


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.

Top

Fusion Gene PPI Analysis for USP25-CAPN3


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


Top

Related Drugs for USP25-CAPN3


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

Top

Related Diseases for USP25-CAPN3


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneCAPN3C1869123Limb-girdle muscular dystrophy type 2A10CTD_human;GENOMICS_ENGLAND;UNIPROT