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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:BRCA1-PSME3 (FusionGDB2 ID:10155)

Fusion Gene Summary for BRCA1-PSME3

check button Fusion gene summary
Fusion gene informationFusion gene name: BRCA1-PSME3
Fusion gene ID: 10155
HgeneTgene
Gene symbol

BRCA1

PSME3

Gene ID

672

10197

Gene nameBRCA1 DNA repair associatedproteasome activator subunit 3
SynonymsBRCAI|BRCC1|BROVCA1|FANCS|IRIS|PNCA4|PPP1R53|PSCP|RNF53HEL-S-283|Ki|PA28-gamma|PA28G|PA28gamma|REG-GAMMA
Cytomap

17q21.31

17q21.31

Type of geneprotein-codingprotein-coding
Descriptionbreast cancer type 1 susceptibility proteinBRCA1/BRCA2-containing complex, subunit 1Fanconi anemia, complementation group SRING finger protein 53breast and ovarian cancer susceptibility protein 1breast cancer 1, early onsetearly onset breast cancer proteasome activator complex subunit 311S regulator complex gamma subunit11S regulator complex subunit gammaKi antigenKi nuclear autoantigenPA28 gamma variant 5REG gamma-3activator of multicatalytic protease subunit 3epididymis secretory protein L
Modification date2020032920200313
UniProtAcc

P38398

Q9GZU8

Ensembl transtripts involved in fusion geneENST00000309486, ENST00000346315, 
ENST00000468300, ENST00000491747, 
ENST00000493795, ENST00000351666, 
ENST00000352993, ENST00000354071, 
ENST00000357654, ENST00000471181, 
ENST00000586385, ENST00000591534, 
ENST00000591849, 		ENST00000545225, 
ENST00000590720, ENST00000541124, 
ENST00000293362, ENST00000441946, 
ENST00000592169, ENST00000592578, 
Fusion gene scores* DoF score9 X 8 X 7=5046 X 6 X 3=108
# samples 96
** MAII scorelog2(9/504*10)=-2.48542682717024
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(6/108*10)=-0.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: BRCA1 [Title/Abstract] AND PSME3 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointBRCA1(41277294)-PSME3(40990748), # 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
HgeneBRCA1

GO:0000724

double-strand break repair via homologous recombination

17349954

HgeneBRCA1

GO:0006301

postreplication repair

17349954

HgeneBRCA1

GO:0006302

double-strand break repair

22186889

HgeneBRCA1

GO:0008630

intrinsic apoptotic signaling pathway in response to DNA damage

14654789

HgeneBRCA1

GO:0016567

protein ubiquitination

17349954

HgeneBRCA1

GO:0031398

positive regulation of protein ubiquitination

15965487

HgeneBRCA1

GO:0035066

positive regulation of histone acetylation

20820192

HgeneBRCA1

GO:0043627

response to estrogen

8895509

HgeneBRCA1

GO:0045892

negative regulation of transcription, DNA-templated

16288014

HgeneBRCA1

GO:0045893

positive regulation of transcription, DNA-templated

20160719

HgeneBRCA1

GO:0045944

positive regulation of transcription by RNA polymerase II

16331276

HgeneBRCA1

GO:0051571

positive regulation of histone H3-K4 methylation

20820192

HgeneBRCA1

GO:0051573

negative regulation of histone H3-K9 methylation

20820192

HgeneBRCA1

GO:0051865

protein autoubiquitination

12890688|20351172

HgeneBRCA1

GO:0070512

positive regulation of histone H4-K20 methylation

20820192

HgeneBRCA1

GO:0071158

positive regulation of cell cycle arrest

21102443

HgeneBRCA1

GO:0071681

cellular response to indole-3-methanol

10868478

HgeneBRCA1

GO:0085020

protein K6-linked ubiquitination

12890688|20351172

HgeneBRCA1

GO:2000617

positive regulation of histone H3-K9 acetylation

20820192

HgeneBRCA1

GO:2000620

positive regulation of histone H4-K16 acetylation

20820192

TgenePSME3

GO:0061136

regulation of proteasomal protein catabolic process

18309296

TgenePSME3

GO:2001237

negative regulation of extrinsic apoptotic signaling pathway

18309296


check buttonFusion gene breakpoints across BRCA1 (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 PSME3 (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
ChimerDB4GBMTCGA-27-2523-01ABRCA1chr17

41277294

-PSME3chr17

40990748

+


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Fusion Gene ORF analysis for BRCA1-PSME3

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
5UTR-3CDSENST00000309486ENST00000545225BRCA1chr17

41277294

-PSME3chr17

40990748

+
5UTR-3CDSENST00000309486ENST00000590720BRCA1chr17

41277294

-PSME3chr17

40990748

+
5UTR-3CDSENST00000346315ENST00000545225BRCA1chr17

41277294

-PSME3chr17

40990748

+
5UTR-3CDSENST00000346315ENST00000590720BRCA1chr17

41277294

-PSME3chr17

40990748

+
5UTR-3CDSENST00000468300ENST00000545225BRCA1chr17

41277294

-PSME3chr17

40990748

+
5UTR-3CDSENST00000468300ENST00000590720BRCA1chr17

41277294

-PSME3chr17

40990748

+
5UTR-3CDSENST00000491747ENST00000545225BRCA1chr17

41277294

-PSME3chr17

40990748

+
5UTR-3CDSENST00000491747ENST00000590720BRCA1chr17

41277294

-PSME3chr17

40990748

+
5UTR-3CDSENST00000493795ENST00000545225BRCA1chr17

41277294

-PSME3chr17

40990748

+
5UTR-3CDSENST00000493795ENST00000590720BRCA1chr17

41277294

-PSME3chr17

40990748

+
5UTR-3UTRENST00000309486ENST00000541124BRCA1chr17

41277294

-PSME3chr17

40990748

+
5UTR-3UTRENST00000346315ENST00000541124BRCA1chr17

41277294

-PSME3chr17

40990748

+
5UTR-3UTRENST00000468300ENST00000541124BRCA1chr17

41277294

-PSME3chr17

40990748

+
5UTR-3UTRENST00000491747ENST00000541124BRCA1chr17

41277294

-PSME3chr17

40990748

+
5UTR-3UTRENST00000493795ENST00000541124BRCA1chr17

41277294

-PSME3chr17

40990748

+
5UTR-intronENST00000309486ENST00000293362BRCA1chr17

41277294

-PSME3chr17

40990748

+
5UTR-intronENST00000309486ENST00000441946BRCA1chr17

41277294

-PSME3chr17

40990748

+
5UTR-intronENST00000309486ENST00000592169BRCA1chr17

41277294

-PSME3chr17

40990748

+
5UTR-intronENST00000309486ENST00000592578BRCA1chr17

41277294

-PSME3chr17

40990748

+
5UTR-intronENST00000346315ENST00000293362BRCA1chr17

41277294

-PSME3chr17

40990748

+
5UTR-intronENST00000346315ENST00000441946BRCA1chr17

41277294

-PSME3chr17

40990748

+
5UTR-intronENST00000346315ENST00000592169BRCA1chr17

41277294

-PSME3chr17

40990748

+
5UTR-intronENST00000346315ENST00000592578BRCA1chr17

41277294

-PSME3chr17

40990748

+
5UTR-intronENST00000468300ENST00000293362BRCA1chr17

41277294

-PSME3chr17

40990748

+
5UTR-intronENST00000468300ENST00000441946BRCA1chr17

41277294

-PSME3chr17

40990748

+
5UTR-intronENST00000468300ENST00000592169BRCA1chr17

41277294

-PSME3chr17

40990748

+
5UTR-intronENST00000468300ENST00000592578BRCA1chr17

41277294

-PSME3chr17

40990748

+
5UTR-intronENST00000491747ENST00000293362BRCA1chr17

41277294

-PSME3chr17

40990748

+
5UTR-intronENST00000491747ENST00000441946BRCA1chr17

41277294

-PSME3chr17

40990748

+
5UTR-intronENST00000491747ENST00000592169BRCA1chr17

41277294

-PSME3chr17

40990748

+
5UTR-intronENST00000491747ENST00000592578BRCA1chr17

41277294

-PSME3chr17

40990748

+
5UTR-intronENST00000493795ENST00000293362BRCA1chr17

41277294

-PSME3chr17

40990748

+
5UTR-intronENST00000493795ENST00000441946BRCA1chr17

41277294

-PSME3chr17

40990748

+
5UTR-intronENST00000493795ENST00000592169BRCA1chr17

41277294

-PSME3chr17

40990748

+
5UTR-intronENST00000493795ENST00000592578BRCA1chr17

41277294

-PSME3chr17

40990748

+
intron-3CDSENST00000351666ENST00000545225BRCA1chr17

41277294

-PSME3chr17

40990748

+
intron-3CDSENST00000351666ENST00000590720BRCA1chr17

41277294

-PSME3chr17

40990748

+
intron-3CDSENST00000352993ENST00000545225BRCA1chr17

41277294

-PSME3chr17

40990748

+
intron-3CDSENST00000352993ENST00000590720BRCA1chr17

41277294

-PSME3chr17

40990748

+
intron-3CDSENST00000354071ENST00000545225BRCA1chr17

41277294

-PSME3chr17

40990748

+
intron-3CDSENST00000354071ENST00000590720BRCA1chr17

41277294

-PSME3chr17

40990748

+
intron-3CDSENST00000357654ENST00000545225BRCA1chr17

41277294

-PSME3chr17

40990748

+
intron-3CDSENST00000357654ENST00000590720BRCA1chr17

41277294

-PSME3chr17

40990748

+
intron-3CDSENST00000471181ENST00000545225BRCA1chr17

41277294

-PSME3chr17

40990748

+
intron-3CDSENST00000471181ENST00000590720BRCA1chr17

41277294

-PSME3chr17

40990748

+
intron-3CDSENST00000586385ENST00000545225BRCA1chr17

41277294

-PSME3chr17

40990748

+
intron-3CDSENST00000586385ENST00000590720BRCA1chr17

41277294

-PSME3chr17

40990748

+
intron-3CDSENST00000591534ENST00000545225BRCA1chr17

41277294

-PSME3chr17

40990748

+
intron-3CDSENST00000591534ENST00000590720BRCA1chr17

41277294

-PSME3chr17

40990748

+
intron-3CDSENST00000591849ENST00000545225BRCA1chr17

41277294

-PSME3chr17

40990748

+
intron-3CDSENST00000591849ENST00000590720BRCA1chr17

41277294

-PSME3chr17

40990748

+
intron-3UTRENST00000351666ENST00000541124BRCA1chr17

41277294

-PSME3chr17

40990748

+
intron-3UTRENST00000352993ENST00000541124BRCA1chr17

41277294

-PSME3chr17

40990748

+
intron-3UTRENST00000354071ENST00000541124BRCA1chr17

41277294

-PSME3chr17

40990748

+
intron-3UTRENST00000357654ENST00000541124BRCA1chr17

41277294

-PSME3chr17

40990748

+
intron-3UTRENST00000471181ENST00000541124BRCA1chr17

41277294

-PSME3chr17

40990748

+
intron-3UTRENST00000586385ENST00000541124BRCA1chr17

41277294

-PSME3chr17

40990748

+
intron-3UTRENST00000591534ENST00000541124BRCA1chr17

41277294

-PSME3chr17

40990748

+
intron-3UTRENST00000591849ENST00000541124BRCA1chr17

41277294

-PSME3chr17

40990748

+
intron-intronENST00000351666ENST00000293362BRCA1chr17

41277294

-PSME3chr17

40990748

+
intron-intronENST00000351666ENST00000441946BRCA1chr17

41277294

-PSME3chr17

40990748

+
intron-intronENST00000351666ENST00000592169BRCA1chr17

41277294

-PSME3chr17

40990748

+
intron-intronENST00000351666ENST00000592578BRCA1chr17

41277294

-PSME3chr17

40990748

+
intron-intronENST00000352993ENST00000293362BRCA1chr17

41277294

-PSME3chr17

40990748

+
intron-intronENST00000352993ENST00000441946BRCA1chr17

41277294

-PSME3chr17

40990748

+
intron-intronENST00000352993ENST00000592169BRCA1chr17

41277294

-PSME3chr17

40990748

+
intron-intronENST00000352993ENST00000592578BRCA1chr17

41277294

-PSME3chr17

40990748

+
intron-intronENST00000354071ENST00000293362BRCA1chr17

41277294

-PSME3chr17

40990748

+
intron-intronENST00000354071ENST00000441946BRCA1chr17

41277294

-PSME3chr17

40990748

+
intron-intronENST00000354071ENST00000592169BRCA1chr17

41277294

-PSME3chr17

40990748

+
intron-intronENST00000354071ENST00000592578BRCA1chr17

41277294

-PSME3chr17

40990748

+
intron-intronENST00000357654ENST00000293362BRCA1chr17

41277294

-PSME3chr17

40990748

+
intron-intronENST00000357654ENST00000441946BRCA1chr17

41277294

-PSME3chr17

40990748

+
intron-intronENST00000357654ENST00000592169BRCA1chr17

41277294

-PSME3chr17

40990748

+
intron-intronENST00000357654ENST00000592578BRCA1chr17

41277294

-PSME3chr17

40990748

+
intron-intronENST00000471181ENST00000293362BRCA1chr17

41277294

-PSME3chr17

40990748

+
intron-intronENST00000471181ENST00000441946BRCA1chr17

41277294

-PSME3chr17

40990748

+
intron-intronENST00000471181ENST00000592169BRCA1chr17

41277294

-PSME3chr17

40990748

+
intron-intronENST00000471181ENST00000592578BRCA1chr17

41277294

-PSME3chr17

40990748

+
intron-intronENST00000586385ENST00000293362BRCA1chr17

41277294

-PSME3chr17

40990748

+
intron-intronENST00000586385ENST00000441946BRCA1chr17

41277294

-PSME3chr17

40990748

+
intron-intronENST00000586385ENST00000592169BRCA1chr17

41277294

-PSME3chr17

40990748

+
intron-intronENST00000586385ENST00000592578BRCA1chr17

41277294

-PSME3chr17

40990748

+
intron-intronENST00000591534ENST00000293362BRCA1chr17

41277294

-PSME3chr17

40990748

+
intron-intronENST00000591534ENST00000441946BRCA1chr17

41277294

-PSME3chr17

40990748

+
intron-intronENST00000591534ENST00000592169BRCA1chr17

41277294

-PSME3chr17

40990748

+
intron-intronENST00000591534ENST00000592578BRCA1chr17

41277294

-PSME3chr17

40990748

+
intron-intronENST00000591849ENST00000293362BRCA1chr17

41277294

-PSME3chr17

40990748

+
intron-intronENST00000591849ENST00000441946BRCA1chr17

41277294

-PSME3chr17

40990748

+
intron-intronENST00000591849ENST00000592169BRCA1chr17

41277294

-PSME3chr17

40990748

+
intron-intronENST00000591849ENST00000592578BRCA1chr17

41277294

-PSME3chr17

40990748

+

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 BRCA1-PSME3


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)
BRCA1chr1741277293-PSME3chr1740990747+0.51976820.48023188
BRCA1chr1741277293-PSME3chr1740990747+0.51976820.48023188

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.
genomic feature of top 1%

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Fusion Protein Features for BRCA1-PSME3


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/:41277294/:40990748)
- 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
BRCA1

P38398

PSME3

Q9GZU8

FUNCTION: E3 ubiquitin-protein ligase that specifically mediates the formation of 'Lys-6'-linked polyubiquitin chains and plays a central role in DNA repair by facilitating cellular responses to DNA damage (PubMed:12890688, PubMed:14976165, PubMed:16818604, PubMed:17525340, PubMed:12887909, PubMed:10500182, PubMed:19261748). It is unclear whether it also mediates the formation of other types of polyubiquitin chains (PubMed:12890688). The BRCA1-BARD1 heterodimer coordinates a diverse range of cellular pathways such as DNA damage repair, ubiquitination and transcriptional regulation to maintain genomic stability (PubMed:12890688, PubMed:14976165, PubMed:20351172). Regulates centrosomal microtubule nucleation (PubMed:18056443). Required for appropriate cell cycle arrests after ionizing irradiation in both the S-phase and the G2 phase of the cell cycle (PubMed:10724175, PubMed:12183412, PubMed:11836499, PubMed:19261748). Required for FANCD2 targeting to sites of DNA damage (PubMed:12887909). Inhibits lipid synthesis by binding to inactive phosphorylated ACACA and preventing its dephosphorylation (PubMed:16326698). Contributes to homologous recombination repair (HRR) via its direct interaction with PALB2, fine-tunes recombinational repair partly through its modulatory role in the PALB2-dependent loading of BRCA2-RAD51 repair machinery at DNA breaks (PubMed:19369211). Component of the BRCA1-RBBP8 complex which regulates CHEK1 activation and controls cell cycle G2/M checkpoints on DNA damage via BRCA1-mediated ubiquitination of RBBP8 (PubMed:16818604). Acts as a transcriptional activator (PubMed:20160719). {ECO:0000269|PubMed:10500182, ECO:0000269|PubMed:10724175, ECO:0000269|PubMed:11836499, ECO:0000269|PubMed:12183412, ECO:0000269|PubMed:12887909, ECO:0000269|PubMed:12890688, ECO:0000269|PubMed:14976165, ECO:0000269|PubMed:16326698, ECO:0000269|PubMed:16818604, ECO:0000269|PubMed:17525340, ECO:0000269|PubMed:18056443, ECO:0000269|PubMed:19261748, ECO:0000269|PubMed:19369211, ECO:0000269|PubMed:20160719, ECO:0000269|PubMed:20351172}.FUNCTION: Promotes the association of the proteasome activator complex subunit PSME3 with the 20S proteasome and regulates its activity. Inhibits PSME3-mediated degradation of some proteasome substrates, probably by affecting their diffusion rate into the catalytic chamber of the proteasome. Also inhibits the interaction of PSME3 with COIL, inhibits accumulation of PSME3 in Cajal bodies and positively regulates the number of Cajal bodies in the nucleus. {ECO:0000269|PubMed:29934401}.

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 BRCA1-PSME3


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 BRCA1-PSME3


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 BRCA1-PSME3


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 BRCA1-PSME3


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