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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:NONO-CLIP3 (FusionGDB2 ID:59608) |
Fusion Gene Summary for NONO-CLIP3 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: NONO-CLIP3 | Fusion gene ID: 59608 | Hgene | Tgene | Gene symbol | NONO | CLIP3 | Gene ID | 4841 | 25999 |
| Gene name | non-POU domain containing octamer binding | CAP-Gly domain containing linker protein 3 | |
| Synonyms | MRXS34|NMT55|NRB54|P54|P54NRB|PPP1R114 | CLIPR-59|CLIPR59|RSNL1 | |
| Cytomap | Xq13.1 | 19q13.12 | |
| Type of gene | protein-coding | protein-coding | |
| Description | non-POU domain-containing octamer-binding protein54 kDa nuclear RNA- and DNA-binding protein55 kDa nuclear proteinDNA-binding p52/p100 complex, 52 kDa subunitnon-POU domain-containing octamer (ATGCAAAT) binding proteinp54(nrb)protein phosphatase 1, | CAP-Gly domain-containing linker protein 3CLIP-170-related 59 kDa proteincytoplasmic linker protein 170-related 59 kDa proteinrestin-like 1 | |
| Modification date | 20200313 | 20200313 | |
| UniProtAcc | Q15233 | Q96DZ5 | |
| Ensembl transtripts involved in fusion gene | ENST00000490044, ENST00000276079, ENST00000373841, ENST00000373856, ENST00000535149, | ENST00000360535, ENST00000593074, | |
| Fusion gene scores | * DoF score | 8 X 8 X 2=128 | 5 X 6 X 2=60 |
| # samples | 8 | 5 | |
| ** MAII score | log2(8/128*10)=-0.678071905112638 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(5/60*10)=-0.263034405833794 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: NONO [Title/Abstract] AND CLIP3 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Most frequent breakpoint | NONO(70518574)-CLIP3(36523731), # 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 | NONO | GO:0002218 | activation of innate immune response | 28712728 |
| Hgene | NONO | GO:1903377 | negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway | 15790595 |
| Fusion gene breakpoints across NONO (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 CLIP3 (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 |
| ChiTaRS5.0 | N/A | DA731450 | NONO | chrX | 70518574 | + | CLIP3 | chr19 | 36523731 | - |
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Fusion Gene ORF analysis for NONO-CLIP3 |
| 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 |
| 3UTR-5UTR | ENST00000490044 | ENST00000360535 | NONO | chrX | 70518574 | + | CLIP3 | chr19 | 36523731 | - |
| 3UTR-intron | ENST00000490044 | ENST00000593074 | NONO | chrX | 70518574 | + | CLIP3 | chr19 | 36523731 | - |
| 5CDS-5UTR | ENST00000276079 | ENST00000360535 | NONO | chrX | 70518574 | + | CLIP3 | chr19 | 36523731 | - |
| 5CDS-5UTR | ENST00000373841 | ENST00000360535 | NONO | chrX | 70518574 | + | CLIP3 | chr19 | 36523731 | - |
| 5CDS-5UTR | ENST00000373856 | ENST00000360535 | NONO | chrX | 70518574 | + | CLIP3 | chr19 | 36523731 | - |
| 5CDS-5UTR | ENST00000535149 | ENST00000360535 | NONO | chrX | 70518574 | + | CLIP3 | chr19 | 36523731 | - |
| 5CDS-intron | ENST00000276079 | ENST00000593074 | NONO | chrX | 70518574 | + | CLIP3 | chr19 | 36523731 | - |
| 5CDS-intron | ENST00000373841 | ENST00000593074 | NONO | chrX | 70518574 | + | CLIP3 | chr19 | 36523731 | - |
| 5CDS-intron | ENST00000373856 | ENST00000593074 | NONO | chrX | 70518574 | + | CLIP3 | chr19 | 36523731 | - |
| 5CDS-intron | ENST00000535149 | ENST00000593074 | NONO | chrX | 70518574 | + | CLIP3 | chr19 | 36523731 | - |
| 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 NONO-CLIP3 |
| 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 NONO-CLIP3 |
| Four levels of functional features of fusion genes Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:70518574/:36523731) - 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 |
| NONO | CLIP3 |
| FUNCTION: DNA- and RNA binding protein, involved in several nuclear processes. Binds the conventional octamer sequence in double-stranded DNA. Also binds single-stranded DNA and RNA at a site independent of the duplex site. Involved in pre-mRNA splicing, probably as a heterodimer with SFPQ. Interacts with U5 snRNA, probably by binding to a purine-rich sequence located on the 3' side of U5 snRNA stem 1b. Together with PSPC1, required for the formation of nuclear paraspeckles. The SFPQ-NONO heteromer associated with MATR3 may play a role in nuclear retention of defective RNAs. The SFPQ-NONO heteromer may be involved in DNA unwinding by modulating the function of topoisomerase I/TOP1. 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. NONO is involved in transcriptional regulation. The SFPQ-NONO-NR5A1 complex binds to the CYP17 promoter and regulates basal and cAMP-dependent transcriptional activity. NONO binds to an enhancer element in long terminal repeats of endogenous intracisternal A particles (IAPs) and activates transcription. Regulates the circadian clock by repressing the transcriptional activator activity of the CLOCK-ARNTL/BMAL1 heterodimer. Important for the functional organization of GABAergic synapses. Plays a specific and important role in the regulation of synaptic RNAs and GPHN/gephyrin scaffold structure, through the regulation of GABRA2 transcript. 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:Q99K48, ECO:0000269|PubMed:10858305, ECO:0000269|PubMed:11525732, ECO:0000269|PubMed:11897684, ECO:0000269|PubMed:15590677, ECO:0000269|PubMed:22416126, ECO:0000269|PubMed:26571461, ECO:0000269|PubMed:28712728}. | FUNCTION: Functions as a cytoplasmic linker protein. Involved in TGN-endosome dynamics. May modulate the cellular compartmentalization of AKT kinase family and promote its cell membrane localization, thereby playing a role in glucose transport in adipocytes. {ECO:0000269|PubMed:19139280}. |
| 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 NONO-CLIP3 |
| 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 NONO-CLIP3 |
| 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 NONO-CLIP3 |
| 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 NONO-CLIP3 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
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