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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:RBM41-PPP3CA (FusionGDB2 ID:HG55285TG5530)

Fusion Gene Summary for RBM41-PPP3CA

check button Fusion gene summary
Fusion gene informationFusion gene name: RBM41-PPP3CA
Fusion gene ID: hg55285tg5530
HgeneTgene
Gene symbol

RBM41

PPP3CA

Gene ID

55285

5530

Gene nameRNA binding motif protein 41protein phosphatase 3 catalytic subunit alpha
Synonyms-ACCIID|CALN|CALNA|CALNA1|CCN1|CNA1|IECEE|IECEE1|PPP2B
Cytomap('RBM41')('PPP3CA')

Xq22.3

4q24

Type of geneprotein-codingprotein-coding
DescriptionRNA-binding protein 41serine/threonine-protein phosphatase 2B catalytic subunit alpha isoformCAM-PRP catalytic subunitcalcineurin A alphacalmodulin-dependent calcineurin A subunit alpha isoformprotein phosphatase 2B, catalytic subunit, alpha isoformprotein phosphatase 3 (
Modification date2020031320200315
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000203616, ENST00000372479, 
ENST00000372487, ENST00000471079, 
Fusion gene scores* DoF score6 X 6 X 2=7214 X 11 X 4=616
# samples 614
** MAII scorelog2(6/72*10)=-0.263034405833794
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(14/616*10)=-2.13750352374993
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: RBM41 [Title/Abstract] AND PPP3CA [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointRBM41(106313093)-PPP3CA(101945485), # 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
TgenePPP3CA

GO:0006470

protein dephosphorylation

18815128|19154138

TgenePPP3CA

GO:0033173

calcineurin-NFAT signaling cascade

19154138|22688515

TgenePPP3CA

GO:0035690

cellular response to drug

11005320

TgenePPP3CA

GO:0045944

positive regulation of transcription by RNA polymerase II

22688515

TgenePPP3CA

GO:0051592

response to calcium ion

18815128



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
ChiTaRS5.0N/ACB049205RBM41chrX

106313093

-PPP3CAchr4

101945485

+


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Fusion Gene ORF analysis for RBM41-PPP3CA

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-3UTRENST00000203616ENST00000323055RBM41chrX

106313093

-PPP3CAchr4

101945485

+
intron-3UTRENST00000203616ENST00000394854RBM41chrX

106313093

-PPP3CAchr4

101945485

+
intron-3UTRENST00000203616ENST00000512215RBM41chrX

106313093

-PPP3CAchr4

101945485

+
intron-3UTRENST00000372479ENST00000323055RBM41chrX

106313093

-PPP3CAchr4

101945485

+
intron-3UTRENST00000372479ENST00000394854RBM41chrX

106313093

-PPP3CAchr4

101945485

+
intron-3UTRENST00000372479ENST00000512215RBM41chrX

106313093

-PPP3CAchr4

101945485

+
intron-3UTRENST00000372487ENST00000323055RBM41chrX

106313093

-PPP3CAchr4

101945485

+
intron-3UTRENST00000372487ENST00000394854RBM41chrX

106313093

-PPP3CAchr4

101945485

+
intron-3UTRENST00000372487ENST00000512215RBM41chrX

106313093

-PPP3CAchr4

101945485

+
intron-3UTRENST00000471079ENST00000323055RBM41chrX

106313093

-PPP3CAchr4

101945485

+
intron-3UTRENST00000471079ENST00000394854RBM41chrX

106313093

-PPP3CAchr4

101945485

+
intron-3UTRENST00000471079ENST00000512215RBM41chrX

106313093

-PPP3CAchr4

101945485

+
intron-intronENST00000203616ENST00000394853RBM41chrX

106313093

-PPP3CAchr4

101945485

+
intron-intronENST00000203616ENST00000507176RBM41chrX

106313093

-PPP3CAchr4

101945485

+
intron-intronENST00000203616ENST00000510292RBM41chrX

106313093

-PPP3CAchr4

101945485

+
intron-intronENST00000203616ENST00000523694RBM41chrX

106313093

-PPP3CAchr4

101945485

+
intron-intronENST00000372479ENST00000394853RBM41chrX

106313093

-PPP3CAchr4

101945485

+
intron-intronENST00000372479ENST00000507176RBM41chrX

106313093

-PPP3CAchr4

101945485

+
intron-intronENST00000372479ENST00000510292RBM41chrX

106313093

-PPP3CAchr4

101945485

+
intron-intronENST00000372479ENST00000523694RBM41chrX

106313093

-PPP3CAchr4

101945485

+
intron-intronENST00000372487ENST00000394853RBM41chrX

106313093

-PPP3CAchr4

101945485

+
intron-intronENST00000372487ENST00000507176RBM41chrX

106313093

-PPP3CAchr4

101945485

+
intron-intronENST00000372487ENST00000510292RBM41chrX

106313093

-PPP3CAchr4

101945485

+
intron-intronENST00000372487ENST00000523694RBM41chrX

106313093

-PPP3CAchr4

101945485

+
intron-intronENST00000471079ENST00000394853RBM41chrX

106313093

-PPP3CAchr4

101945485

+
intron-intronENST00000471079ENST00000507176RBM41chrX

106313093

-PPP3CAchr4

101945485

+
intron-intronENST00000471079ENST00000510292RBM41chrX

106313093

-PPP3CAchr4

101945485

+
intron-intronENST00000471079ENST00000523694RBM41chrX

106313093

-PPP3CAchr4

101945485

+

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 RBM41-PPP3CA


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 RBM41-PPP3CA


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/:106313093/:101945485)
- 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 RBM41-PPP3CA


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 RBM41-PPP3CA


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 RBM41-PPP3CA


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 RBM41-PPP3CA


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneC4540199EPILEPTIC ENCEPHALOPATHY, INFANTILE OR EARLY CHILDHOOD, 12GENOMICS_ENGLAND;UNIPROT
TgeneC0019202Hepatolenticular Degeneration1CTD_human
TgeneC0030305Pancreatitis1CTD_human
TgeneC0033578Prostatic Neoplasms1CTD_human
TgeneC0039584Testicular Diseases1CTD_human
TgeneC0149721Left Ventricular Hypertrophy1CTD_human
TgeneC0152013Adenocarcinoma of lung (disorder)1CTD_human
TgeneC0376358Malignant neoplasm of prostate1CTD_human
TgeneC1527352Hepatic Form of Wilson Disease1CTD_human
TgeneC4721610Carcinoma, Ovarian Epithelial1CTD_human
TgeneC4748872ARTHROGRYPOSIS, CLEFT PALATE, CRANIOSYNOSTOSIS, AND IMPAIRED INTELLECTUAL DEVELOPMENT1UNIPROT