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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:CLCN3-SFPQ (FusionGDB2 ID:HG1182TG6421) |
Fusion Gene Summary for CLCN3-SFPQ |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: CLCN3-SFPQ | Fusion gene ID: hg1182tg6421 | Hgene | Tgene | Gene symbol | CLCN3 | SFPQ | Gene ID | 1182 | 6421 |
| Gene name | chloride voltage-gated channel 3 | splicing factor proline and glutamine rich | |
| Synonyms | CLC3|ClC-3 | POMP100|PPP1R140|PSF | |
| Cytomap | ('CLCN3')('SFPQ') 4q33 | 1p34.3 | |
| Type of gene | protein-coding | protein-coding | |
| Description | H(+)/Cl(-) exchange transporter 3chloride channel 3chloride channel protein 3chloride channel, voltage-sensitive 3chloride transporter ClC-3 | splicing factor, proline- and glutamine-rich100 kDa DNA-pairing proteinDNA-binding p52/p100 complex, 100 kDa subunitPTB-associated splicing factorepididymis secretory sperm binding proteinpolypyrimidine tract binding protein associatedpolypyrimidine | |
| Modification date | 20200313 | 20200313 | |
| UniProtAcc | P51790 | P23246 | |
| Ensembl transtripts involved in fusion gene | ENST00000347613, ENST00000360642, ENST00000504131, ENST00000513761, ENST00000506924, | ||
| Fusion gene scores | * DoF score | 13 X 9 X 6=702 | 23 X 15 X 8=2760 |
| # samples | 16 | 26 | |
| ** MAII score | log2(16/702*10)=-2.1333991254172 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: CLCN3 [Title/Abstract] AND SFPQ [Title/Abstract] AND fusion [Title/Abstract] | ||
| Most frequent breakpoint | CLCN3(170542214)-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 | CLCN3 | GO:1902476 | chloride transmembrane transport | 11274166 |
| Tgene | SFPQ | GO:0000122 | negative regulation of transcription by RNA polymerase II | 16731528 |
| Tgene | SFPQ | GO:0002218 | activation of innate immune response | 28712728 |
| Tgene | SFPQ | GO:1902177 | positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway | 15790595 |
| 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. |
| Source | Disease | Sample | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| ChimerDB4 | STAD | TCGA-CD-8525-01A | CLCN3 | chr4 | 170542214 | + | SFPQ | chr1 | 35643637 | - |
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Fusion Gene ORF analysis for CLCN3-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 |
| 5UTR-5UTR | ENST00000347613 | ENST00000468598 | CLCN3 | chr4 | 170542214 | + | SFPQ | chr1 | 35643637 | - |
| 5UTR-5UTR | ENST00000360642 | ENST00000468598 | CLCN3 | chr4 | 170542214 | + | SFPQ | chr1 | 35643637 | - |
| 5UTR-5UTR | ENST00000504131 | ENST00000468598 | CLCN3 | chr4 | 170542214 | + | SFPQ | chr1 | 35643637 | - |
| 5UTR-5UTR | ENST00000513761 | ENST00000468598 | CLCN3 | chr4 | 170542214 | + | SFPQ | chr1 | 35643637 | - |
| 5UTR-intron | ENST00000347613 | ENST00000357214 | CLCN3 | chr4 | 170542214 | + | SFPQ | chr1 | 35643637 | - |
| 5UTR-intron | ENST00000360642 | ENST00000357214 | CLCN3 | chr4 | 170542214 | + | SFPQ | chr1 | 35643637 | - |
| 5UTR-intron | ENST00000504131 | ENST00000357214 | CLCN3 | chr4 | 170542214 | + | SFPQ | chr1 | 35643637 | - |
| 5UTR-intron | ENST00000513761 | ENST00000357214 | CLCN3 | chr4 | 170542214 | + | SFPQ | chr1 | 35643637 | - |
| intron-5UTR | ENST00000506924 | ENST00000468598 | CLCN3 | chr4 | 170542214 | + | SFPQ | chr1 | 35643637 | - |
| intron-intron | ENST00000506924 | ENST00000357214 | CLCN3 | chr4 | 170542214 | + | 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 CLCN3-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) |
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Fusion Protein Features for CLCN3-SFPQ |
| Four levels of functional features of fusion genes Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:170542214/: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 |
| CLCN3 | SFPQ |
| FUNCTION: [Isoform 1]: Strongly outwardly rectifying, electrogenic H(+)/Cl(-)exchanger which mediates the exchange of chloride ions against protons (By similarity). The CLC channel family contains both chloride channels and proton-coupled anion transporters that exchange chloride or another anion for protons (PubMed:29845874). The presence of conserved gating glutamate residues is typical for family members that function as antiporters (PubMed:29845874). {ECO:0000250|UniProtKB:P51791, ECO:0000303|PubMed:29845874}.; FUNCTION: [Isoform 2]: Strongly outwardly rectifying, electrogenic H(+)/Cl(-)exchanger which mediates the exchange of chloride ions against protons. {ECO:0000269|PubMed:11967229}. | 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 CLCN3-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 CLCN3-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 CLCN3-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 |
| Tgene | SFPQ | P23246 | DB09130 | Copper | Small molecule | Approved|Investigational | |
| Tgene | SFPQ | P23246 | DB09130 | Copper | Small molecule | Approved|Investigational |
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Related Diseases for CLCN3-SFPQ |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | CLCN3 | C0017638 | Glioma | 1 | CTD_human |
| Hgene | CLCN3 | C0024623 | Malignant neoplasm of stomach | 1 | CTD_human |
| Hgene | CLCN3 | C0038356 | Stomach Neoplasms | 1 | CTD_human |
| Hgene | CLCN3 | C0235874 | Disease Exacerbation | 1 | CTD_human |
| Hgene | CLCN3 | C0259783 | mixed gliomas | 1 | CTD_human |
| Hgene | CLCN3 | C0555198 | Malignant Glioma | 1 | CTD_human |
| Hgene | CLCN3 | C1708349 | Hereditary Diffuse Gastric Cancer | 1 | CTD_human |
| Hgene | CLCN3 | C2931822 | Nasopharyngeal carcinoma | 1 | CTD_human |
| Tgene | C4518356 | MiT family translocation renal cell carcinoma | 2 | ORPHANET | |
| Tgene | C0019693 | HIV Infections | 1 | CTD_human | |
| Tgene | C0037274 | Dermatologic disorders | 1 | CTD_human | |
| Tgene | C0274861 | Arsenic Poisoning, Inorganic | 1 | CTD_human | |
| Tgene | C0274862 | Nervous System, Organic Arsenic Poisoning | 1 | CTD_human | |
| Tgene | C0311375 | Arsenic Poisoning | 1 | CTD_human | |
| Tgene | C0751851 | Arsenic Encephalopathy | 1 | CTD_human | |
| Tgene | C0751852 | Arsenic Induced Polyneuropathy | 1 | CTD_human | |
| Tgene | C4505456 | HIV Coinfection | 1 | CTD_human |
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