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Fusion Protein:USP36-EXOSC9 |
Fusion Gene and Fusion Protein Summary |
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Fusion partner gene information | Fusion gene name: USP36-EXOSC9 | FusionPDB ID: 97430 | FusionGDB2.0 ID: 97430 | Hgene | Tgene | Gene symbol | USP36 | EXOSC9 | Gene ID | 57602 | 5393 |
Gene name | ubiquitin specific peptidase 36 | exosome component 9 | |
Synonyms | DUB1 | PCH1D|PM/Scl-75|PMSCL1|RRP45|Rrp45p|p5|p6 | |
Cytomap | 17q25.3 | 4q27 | |
Type of gene | protein-coding | protein-coding | |
Description | ubiquitin carboxyl-terminal hydrolase 36deubiquitinating enzyme 36ubiquitin specific protease 36ubiquitin thioesterase 36ubiquitin-specific-processing protease 36 | exosome complex component RRP45P75 polymyositis-scleroderma overlap syndrome associated autoantigenPMSCL autoantigen, 75kDautoantigen PM/Scl 1exosome complex exonuclease RRP45polymyositis/scleroderma autoantigen 1, 75kDa | |
Modification date | 20200313 | 20200320 | |
UniProtAcc | . | Q06265 Main function of 5'-partner protein: FUNCTION: Non-catalytic component of the RNA exosome complex which has 3'->5' exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. In the nucleus, the RNA exosome complex is involved in proper maturation of stable RNA species such as rRNA, snRNA and snoRNA, in the elimination of RNA processing by-products and non-coding 'pervasive' transcripts, such as antisense RNA species and promoter-upstream transcripts (PROMPTs), and of mRNAs with processing defects, thereby limiting or excluding their export to the cytoplasm. The RNA exosome may be involved in Ig class switch recombination (CSR) and/or Ig variable region somatic hypermutation (SHM) by targeting AICDA deamination activity to transcribed dsDNA substrates. In the cytoplasm, the RNA exosome complex is involved in general mRNA turnover and specifically degrades inherently unstable mRNAs containing AU-rich elements (AREs) within their 3' untranslated regions, and in RNA surveillance pathways, preventing translation of aberrant mRNAs. It seems to be involved in degradation of histone mRNA. The catalytic inactive RNA exosome core complex of 9 subunits (Exo-9) is proposed to play a pivotal role in the binding and presentation of RNA for ribonucleolysis, and to serve as a scaffold for the association with catalytic subunits and accessory proteins or complexes. EXOSC9 binds to ARE-containing RNAs. {ECO:0000269|PubMed:11782436, ECO:0000269|PubMed:16455498, ECO:0000269|PubMed:16912217, ECO:0000269|PubMed:17545563}. | |
Ensembl transtripts involved in fusion gene | ENST ids | ENST00000312010, ENST00000449938, ENST00000542802, ENST00000588467, ENST00000589424, ENST00000590546, | ENST00000379663, ENST00000509980, ENST00000512454, ENST00000243498, |
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0) | * DoF score | 5 X 7 X 4=140 | 8 X 8 X 4=256 |
# samples | 7 | 8 | |
** MAII score | log2(7/140*10)=-1 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(8/256*10)=-1.67807190511264 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
Fusion gene context | PubMed: USP36 [Title/Abstract] AND EXOSC9 [Title/Abstract] AND fusion [Title/Abstract] | ||
Fusion neoantigen context | PubMed: USP36 [Title/Abstract] AND EXOSC9 [Title/Abstract] AND neoantigen [Title/Abstract] | ||
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0) | USP36(76814748)-EXOSC9(122737523), # samples:2 | ||
Anticipated loss of major functional domain due to fusion event. | USP36-EXOSC9 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF. USP36-EXOSC9 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF. USP36-EXOSC9 seems lost the major protein functional domain in Hgene partner, which is a epigenetic factor due to the frame-shifted ORF. USP36-EXOSC9 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF. USP36-EXOSC9 seems lost the major protein functional domain in Tgene partner, which is a cell metabolism gene due to the frame-shifted ORF. USP36-EXOSC9 seems lost the major protein functional domain in Tgene partner, which is a epigenetic factor due to the frame-shifted ORF. USP36-EXOSC9 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF. |
* DoF score (Degree of Frequency) = # partners X # break points X # cancer types ** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10) |
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Partner | Gene | GO ID | GO term | PubMed ID |
Hgene | USP36 | GO:0007000 | nucleolus organization | 19208757 |
Hgene | USP36 | GO:0016579 | protein deubiquitination | 14715245|19208757|25775507 |
Hgene | USP36 | GO:2000232 | regulation of rRNA processing | 19208757 |
![]() Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr17:76814748/chr4:122737523) - 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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![]() * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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![]() * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
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Fusion Amino Acid Sequences |
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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) |
ENST00000312010 | USP36 | chr17 | 76814748 | - | ENST00000243498 | EXOSC9 | chr4 | 122737523 | + | 1565 | 1348 | 325 | 1359 | 344 |
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Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | No-coding score | Coding score |
ENST00000312010 | ENST00000243498 | USP36 | chr17 | 76814748 | - | EXOSC9 | chr4 | 122737523 | + | 0.005763262 | 0.9942367 |
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Get the fusion protein sequences from here. |
Fusion protein sequence information is available in the fasta format. >FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP |
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Fusion Protein Breakpoint Sequences for USP36-EXOSC9 |
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Hgene | Hchr | Hbp | Tgene | Tchr | Tbp | Length(fusion protein) | BP in fusion protein | Peptide |
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Potential FusionNeoAntigen Information of USP36-EXOSC9 in HLA I |
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![]() * We used NetMHCpan v4.1 (%rank<0.5) and deepHLApan v1.1 (immunogenic score>0.5) |
Fusion gene | Hchr | Hbp | Tgene | Tchr | Tbp | HLA I | FusionNeoAntigen peptide | Binding score | Immunogenic score | Neoantigen start (at BP 13) | Neoantigen end (at BP 13) |
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Potential FusionNeoAntigen Information of USP36-EXOSC9 in HLA II |
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![]() * We used NetMHCIIpan v4.1 (%rank<0.5). |
Fusion gene | Hchr | Hbp | Tgene | Tchr | Tbp | HLA II | FusionNeoAntigen peptide | Neoantigen start (at BP 13) | Neoantigen end (at BP 13) |
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Fusion breakpoint peptide structures of USP36-EXOSC9 |
![]() * The minimum length of the amino acid sequence in RoseTTAFold is 14AA. Here, we predicted the 14AA fusion protein breakpoint sequence not the fusion neoantigen peptide, which is shorter than 14 AA. |
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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of USP36-EXOSC9 |
![]() * We used Glide to predict the interaction between HLAs and neoantigens. |
HLA allele | PDB ID | File name | BPseq | Docking score | Glide score |
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Vaccine Design for the FusionNeoAntigens of USP36-EXOSC9 |
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Fusion gene | Hchr | Hbp | Tchr | Tbp | Start in +/-13AA | End in +/-13AA | FusionNeoAntigen peptide sequence | FusionNeoAntigen RNA sequence |
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Fusion gene | Hchr | Hbp | Tchr | Tbp | Start in +/-13AA | End in +/-13AA | FusionNeoAntigen peptide | FusionNEoAntigen RNA sequence |
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Information of the samples that have these potential fusion neoantigens of USP36-EXOSC9 |
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Cancer type | Fusion gene | Hchr | Hbp | Henst | Tchr | Tbp | Tenst | Sample |
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Potential target of CAR-T therapy development for USP36-EXOSC9 |
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![]() * Minus value of BPloci means that the break point is located before the CDS. |
- In-frame and retained 'Transmembrane'. |
Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
![]() * We used DeepLoc 1.0. The order of the X-axis of the barplot is as follows: Entry_ID, Localization, Type, Nucleus, Cytoplasm, Extracellular, Mitochondrion, Cell_membrane, Endoplasmic_reticulum, Plastid, Golgi.apparatus, Lysosome.Vacuole, Peroxisome. Y-axis is the output score of DeepLoc. Clicking the image will open a new tab with a large image. |
Hgene | Hchr | Hbp | Henst | Tgene | Tchr | Tbp | Tenst | DeepLoc result |
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Related Drugs to USP36-EXOSC9 |
![]() (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
Hgene | Tgene | Drug | Source | PMID |
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Related Diseases to USP36-EXOSC9 |
![]() (Manual curation of PubMed, 04-30-2022 + MyCancerGenome) |
Hgene | Tgene | Disease | Source | PMID |
![]() (DisGeNet 4.0) |
Partner | Gene | Disease ID | Disease name | # pubmeds | Source |