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 | Fusion Gene Summary |
| Fusion Gene ORF analysis |
| Fusion Genomic Features |
| Fusion Protein Features |
| Fusion Gene Sequence |
| Fusion Gene PPI analysis |
| Related Drugs |
| Related Diseases |
Fusion gene:PPP3CA-SFPQ (FusionGDB2 ID:68131) |
Fusion Gene Summary for PPP3CA-SFPQ |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: PPP3CA-SFPQ | Fusion gene ID: 68131 | Hgene | Tgene | Gene symbol | PPP3CA | SFPQ | Gene ID | 5530 | 654780 |
| Gene name | protein phosphatase 3 catalytic subunit alpha | splicing factor proline/glutamine-rich | |
| Synonyms | ACCIID|CALN|CALNA|CALNA1|CCN1|CNA1|IECEE|IECEE1|PPP2B | SFPQ | |
| Cytomap | 4q24 | 16q24.1 | |
| Type of gene | protein-coding | ncRNA | |
| Description | serine/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 date | 20200315 | 20200303 | |
| UniProtAcc | . | P23246 | |
| Ensembl transtripts involved in fusion gene | ENST00000323055, ENST00000394853, ENST00000394854, ENST00000512215, ENST00000523694, ENST00000507176, ENST00000510292, | ENST00000468598, ENST00000357214, | |
| Fusion gene scores | * DoF score | 25 X 13 X 8=2600 | 23 X 15 X 8=2760 |
| # samples | 23 | 26 | |
| ** MAII score | log2(23/2600*10)=-3.49880585697144 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(26/2760*10)=-3.40808473863708 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: PPP3CA [Title/Abstract] AND SFPQ [Title/Abstract] AND fusion [Title/Abstract] | ||
| Most frequent breakpoint | PPP3CA(102267896)-SFPQ(35643637), # 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) |
| Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Partner | Gene | GO ID | GO term | PubMed ID |
| Hgene | PPP3CA | GO:0006470 | protein dephosphorylation | 18815128|19154138 |
| Hgene | PPP3CA | GO:0033173 | calcineurin-NFAT signaling cascade | 19154138|22688515 |
| Hgene | PPP3CA | GO:0035690 | cellular response to drug | 11005320 |
| Hgene | PPP3CA | GO:0045944 | positive regulation of transcription by RNA polymerase II | 22688515 |
| Hgene | PPP3CA | GO:0051592 | response to calcium ion | 18815128 |
| Fusion gene breakpoints across PPP3CA (5'-gene) * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
| Fusion gene breakpoints across SFPQ (3'-gene) * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
| 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. |
| Source | Disease | Sample | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| ChimerDB4 | STAD | TCGA-CG-5721-01A | PPP3CA | chr4 | 102267896 | - | SFPQ | chr1 | 35643637 | - |
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Fusion Gene ORF analysis for PPP3CA-SFPQ |
| 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. |
| ORF | Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| 5CDS-5UTR | ENST00000323055 | ENST00000468598 | PPP3CA | chr4 | 102267896 | - | SFPQ | chr1 | 35643637 | - |
| 5CDS-5UTR | ENST00000394853 | ENST00000468598 | PPP3CA | chr4 | 102267896 | - | SFPQ | chr1 | 35643637 | - |
| 5CDS-5UTR | ENST00000394854 | ENST00000468598 | PPP3CA | chr4 | 102267896 | - | SFPQ | chr1 | 35643637 | - |
| 5CDS-5UTR | ENST00000512215 | ENST00000468598 | PPP3CA | chr4 | 102267896 | - | SFPQ | chr1 | 35643637 | - |
| 5CDS-5UTR | ENST00000523694 | ENST00000468598 | PPP3CA | chr4 | 102267896 | - | SFPQ | chr1 | 35643637 | - |
| 5CDS-intron | ENST00000323055 | ENST00000357214 | PPP3CA | chr4 | 102267896 | - | SFPQ | chr1 | 35643637 | - |
| 5CDS-intron | ENST00000394853 | ENST00000357214 | PPP3CA | chr4 | 102267896 | - | SFPQ | chr1 | 35643637 | - |
| 5CDS-intron | ENST00000394854 | ENST00000357214 | PPP3CA | chr4 | 102267896 | - | SFPQ | chr1 | 35643637 | - |
| 5CDS-intron | ENST00000512215 | ENST00000357214 | PPP3CA | chr4 | 102267896 | - | SFPQ | chr1 | 35643637 | - |
| 5CDS-intron | ENST00000523694 | ENST00000357214 | PPP3CA | chr4 | 102267896 | - | SFPQ | chr1 | 35643637 | - |
| 5UTR-5UTR | ENST00000507176 | ENST00000468598 | PPP3CA | chr4 | 102267896 | - | SFPQ | chr1 | 35643637 | - |
| 5UTR-intron | ENST00000507176 | ENST00000357214 | PPP3CA | chr4 | 102267896 | - | SFPQ | chr1 | 35643637 | - |
| intron-5UTR | ENST00000510292 | ENST00000468598 | PPP3CA | chr4 | 102267896 | - | SFPQ | chr1 | 35643637 | - |
| intron-intron | ENST00000510292 | ENST00000357214 | PPP3CA | chr4 | 102267896 | - | SFPQ | chr1 | 35643637 | - |
| ORFfinder result based on the fusion transcript sequence of in-frame fusion genes. |
| Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | Seq length (transcript) | BP loci (transcript) | Predicted start (transcript) | Predicted stop (transcript) | Seq length (amino acids) |
| DeepORF 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. |
| Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | No-coding score | Coding score |
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Fusion Genomic Features for PPP3CA-SFPQ |
| FusionAI 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. |
| Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | 1-p | p (fusion gene breakpoint) |
| Distribution 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. |
| Distribution 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. |
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Fusion Protein Features for PPP3CA-SFPQ |
| Four levels of functional features of fusion genes Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:102267896/:35643637) - 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. |
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| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| . | SFPQ |
| 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: DNA- and RNA binding protein, involved in several nuclear processes. Essential pre-mRNA splicing factor required early in spliceosome formation and for splicing catalytic step II, probably as a heteromer with NONO. Binds to pre-mRNA in spliceosome C complex, and specifically binds to intronic polypyrimidine tracts. Involved in regulation of signal-induced alternative splicing. During splicing of PTPRC/CD45, a phosphorylated form is sequestered by THRAP3 from the pre-mRNA in resting T-cells; T-cell activation and subsequent reduced phosphorylation is proposed to lead to release from THRAP3 allowing binding to pre-mRNA splicing regulatotry elements which represses exon inclusion. Interacts with U5 snRNA, probably by binding to a purine-rich sequence located on the 3' side of U5 snRNA stem 1b. May be involved in a pre-mRNA coupled splicing and polyadenylation process as component of a snRNP-free complex with SNRPA/U1A. The SFPQ-NONO heteromer associated with MATR3 may play a role in nuclear retention of defective RNAs. SFPQ may be involved in homologous DNA pairing; in vitro, promotes the invasion of ssDNA between a duplex DNA and produces a D-loop formation. The SFPQ-NONO heteromer may be involved in DNA unwinding by modulating the function of topoisomerase I/TOP1; in vitro, stimulates dissociation of TOP1 from DNA after cleavage and enhances its jumping between separate DNA helices. The SFPQ-NONO heteromer binds DNA (PubMed:25765647). The SFPQ-NONO heteromer may be involved in DNA non-homologous end joining (NHEJ) required for double-strand break repair and V(D)J recombination and may stabilize paired DNA ends; in vitro, the complex strongly stimulates DNA end joining, binds directly to the DNA substrates and cooperates with the Ku70/G22P1-Ku80/XRCC5 (Ku) dimer to establish a functional preligation complex. SFPQ is involved in transcriptional regulation. Functions as transcriptional activator (PubMed:25765647). Transcriptional repression is mediated by an interaction of SFPQ with SIN3A and subsequent recruitment of histone deacetylases (HDACs). The SFPQ-NONO-NR5A1 complex binds to the CYP17 promoter and regulates basal and cAMP-dependent transcriptional activity. SFPQ isoform Long binds to the DNA binding domains (DBD) of nuclear hormone receptors, like RXRA and probably THRA, and acts as transcriptional corepressor in absence of hormone ligands. Binds the DNA sequence 5'-CTGAGTC-3' in the insulin-like growth factor response element (IGFRE) and inhibits IGF-I-stimulated transcriptional activity. Regulates the circadian clock by repressing the transcriptional activator activity of the CLOCK-ARNTL/BMAL1 heterodimer. Required for the transcriptional repression of circadian target genes, such as PER1, mediated by the large PER complex through histone deacetylation (By similarity). Required for the assembly of nuclear speckles (PubMed:25765647). Plays a role in the regulation of DNA virus-mediated innate immune response by assembling into the HDP-RNP complex, a complex that serves as a platform for IRF3 phosphorylation and subsequent innate immune response activation through the cGAS-STING pathway (PubMed:28712728). {ECO:0000250|UniProtKB:Q8VIJ6, ECO:0000269|PubMed:10847580, ECO:0000269|PubMed:10858305, ECO:0000269|PubMed:10931916, ECO:0000269|PubMed:11259580, ECO:0000269|PubMed:11525732, ECO:0000269|PubMed:11897684, ECO:0000269|PubMed:15590677, ECO:0000269|PubMed:20932480, ECO:0000269|PubMed:25765647, ECO:0000269|PubMed:28712728, ECO:0000269|PubMed:8045264, ECO:0000269|PubMed:8449401}. |
| Retention 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 * 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. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
| - In-frame and not-retained protein feature among the 13 regional features. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
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Fusion Gene Sequence for PPP3CA-SFPQ |
| 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 PPP3CA-SFPQ |
| Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in |
| Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160) |
| Hgene | Hgene's interactors | Tgene | Tgene's interactors |
| - Retained PPIs in in-frame fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Still interaction with |
| - Lost PPIs in in-frame fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
| - Retained PPIs, but lost function due to frame-shift fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
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Related Drugs for PPP3CA-SFPQ |
| Drugs targeting genes involved in this fusion gene. (DrugBank Version 5.1.8 2021-05-08) |
| Partner | Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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Related Diseases for PPP3CA-SFPQ |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
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