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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:MCM9-USP4 (FusionGDB2 ID:52269) |
Fusion Gene Summary for MCM9-USP4 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: MCM9-USP4 | Fusion gene ID: 52269 | Hgene | Tgene | Gene symbol | MCM9 | USP4 | Gene ID | 254394 | 7375 |
| Gene name | minichromosome maintenance 9 homologous recombination repair factor | ubiquitin specific peptidase 4 | |
| Synonyms | C6orf61|MCMDC1|ODG4|dJ329L24.1|dJ329L24.3 | UNP|Unph | |
| Cytomap | 6q22.31 | 3p21.31 | |
| Type of gene | protein-coding | protein-coding | |
| Description | DNA helicase MCM9DNA replication licensing factor MCM9mini-chromosome maintenance deficient domain-containing protein 1minichromosome maintenance complex component 9 | ubiquitin carboxyl-terminal hydrolase 4deubiquitinating enzyme 4ubiquitin carboxyl-terminal esterase 4ubiquitin specific peptidase 4 (proto-oncogene)ubiquitin specific protease 4 (proto-oncogene)ubiquitin thioesterase 4ubiquitin thiolesterase 4ubiq | |
| Modification date | 20200313 | 20200313 | |
| UniProtAcc | Q9NXL9 | Q9H9J4 | |
| Ensembl transtripts involved in fusion gene | ENST00000316068, ENST00000316316, ENST00000505485, | ENST00000265560, ENST00000351842, ENST00000415188, ENST00000416417, ENST00000488520, | |
| Fusion gene scores | * DoF score | 7 X 9 X 3=189 | 9 X 10 X 5=450 |
| # samples | 8 | 9 | |
| ** MAII score | log2(8/189*10)=-1.24031432933371 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(9/450*10)=-2.32192809488736 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: MCM9 [Title/Abstract] AND USP4 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Most frequent breakpoint | MCM9(119135552)-USP4(49315576), # 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 | MCM9 | GO:0000724 | double-strand break repair via homologous recombination | 22771115 |
| Hgene | MCM9 | GO:0006974 | cellular response to DNA damage stimulus | 22771115 |
| Tgene | USP4 | GO:0016579 | protein deubiquitination | 16316627|16339847|16472766 |
| Tgene | USP4 | GO:0031647 | regulation of protein stability | 16472766 |
| Tgene | USP4 | GO:0034394 | protein localization to cell surface | 16339847 |
| Fusion gene breakpoints across MCM9 (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 USP4 (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 | AA531180 | MCM9 | chr6 | 119135552 | - | USP4 | chr3 | 49315576 | + |
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Fusion Gene ORF analysis for MCM9-USP4 |
| 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 |
| intron-3UTR | ENST00000316068 | ENST00000265560 | MCM9 | chr6 | 119135552 | - | USP4 | chr3 | 49315576 | + |
| intron-3UTR | ENST00000316068 | ENST00000351842 | MCM9 | chr6 | 119135552 | - | USP4 | chr3 | 49315576 | + |
| intron-3UTR | ENST00000316316 | ENST00000265560 | MCM9 | chr6 | 119135552 | - | USP4 | chr3 | 49315576 | + |
| intron-3UTR | ENST00000316316 | ENST00000351842 | MCM9 | chr6 | 119135552 | - | USP4 | chr3 | 49315576 | + |
| intron-3UTR | ENST00000505485 | ENST00000265560 | MCM9 | chr6 | 119135552 | - | USP4 | chr3 | 49315576 | + |
| intron-3UTR | ENST00000505485 | ENST00000351842 | MCM9 | chr6 | 119135552 | - | USP4 | chr3 | 49315576 | + |
| intron-intron | ENST00000316068 | ENST00000415188 | MCM9 | chr6 | 119135552 | - | USP4 | chr3 | 49315576 | + |
| intron-intron | ENST00000316068 | ENST00000416417 | MCM9 | chr6 | 119135552 | - | USP4 | chr3 | 49315576 | + |
| intron-intron | ENST00000316068 | ENST00000488520 | MCM9 | chr6 | 119135552 | - | USP4 | chr3 | 49315576 | + |
| intron-intron | ENST00000316316 | ENST00000415188 | MCM9 | chr6 | 119135552 | - | USP4 | chr3 | 49315576 | + |
| intron-intron | ENST00000316316 | ENST00000416417 | MCM9 | chr6 | 119135552 | - | USP4 | chr3 | 49315576 | + |
| intron-intron | ENST00000316316 | ENST00000488520 | MCM9 | chr6 | 119135552 | - | USP4 | chr3 | 49315576 | + |
| intron-intron | ENST00000505485 | ENST00000415188 | MCM9 | chr6 | 119135552 | - | USP4 | chr3 | 49315576 | + |
| intron-intron | ENST00000505485 | ENST00000416417 | MCM9 | chr6 | 119135552 | - | USP4 | chr3 | 49315576 | + |
| intron-intron | ENST00000505485 | ENST00000488520 | MCM9 | chr6 | 119135552 | - | USP4 | chr3 | 49315576 | + |
| 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 MCM9-USP4 |
| 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 MCM9-USP4 |
| Four levels of functional features of fusion genes Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:119135552/:49315576) - 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 |
| MCM9 | USP4 |
| FUNCTION: Component of the MCM8-MCM9 complex, a complex involved in the repair of double-stranded DNA breaks (DBSs) and DNA interstrand cross-links (ICLs) by homologous recombination (HR) (PubMed:23401855). Required for DNA resection by the MRE11-RAD50-NBN/NBS1 (MRN) complex by recruiting the MRN complex to the repair site and by promoting the complex nuclease activity (PubMed:26215093). Probably by regulating the localization of the MRN complex, indirectly regulates the recruitment of downstream effector RAD51 to DNA damage sites including DBSs and ICLs (PubMed:23401855). Acts as a helicase in DNA mismatch repair (MMR) following DNA replication errors to unwind the mismatch containing DNA strand (PubMed:26300262). In addition, recruits MLH1, a component of the MMR complex, to chromatin (PubMed:26300262). The MCM8-MCM9 complex is dispensable for DNA replication and S phase progression (PubMed:23401855). Probably by regulating HR, plays a key role during gametogenesis (By similarity). {ECO:0000250|UniProtKB:Q2KHI9, ECO:0000269|PubMed:23401855, ECO:0000269|PubMed:26215093, ECO:0000269|PubMed:26300262}. | FUNCTION: Deubiquitinating enzyme which may play an important role during spermatogenesis. {ECO:0000250}. |
| 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 MCM9-USP4 |
| 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 MCM9-USP4 |
| 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 MCM9-USP4 |
| 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 MCM9-USP4 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
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