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Fusion gene ID: 41636 |
FusionGeneSummary for VPS54_RBPMS2 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: VPS54_RBPMS2 | Fusion gene ID: 41636 | Hgene | Tgene | Gene symbol | VPS54 | RBPMS2 | Gene ID | 51542 | 348093 |
| Gene name | VPS54, GARP complex subunit | RNA binding protein, mRNA processing factor 2 | |
| Synonyms | HCC8|PPP1R164|SLP-8p|VPS54L|WR|hVps54L | - | |
| Cytomap | 2p15-p14 | 15q22.31 | |
| Type of gene | protein-coding | protein-coding | |
| Description | vacuolar protein sorting-associated protein 54hepatocellular carcinoma protein 8protein phosphatase 1, regulatory subunit 164tumor antigen HOM-HCC-8tumor antigen SLP-8pvacuolar protein sorting 54 homolog | RNA-binding protein with multiple splicing 2RNA binding protein with multiple splicing 2 | |
| Modification date | 20180523 | 20180523 | |
| UniProtAcc | Q9P1Q0 | Q6ZRY4 | |
| Ensembl transtripts involved in fusion gene | ENST00000409558, ENST00000272322, ENST00000354504, | ENST00000560606, ENST00000300069, | |
| Fusion gene scores | * DoF score | 3 X 4 X 3=36 | 7 X 6 X 4=168 |
| # samples | 5 | 8 | |
| ** MAII score | log2(5/36*10)=0.473931188332412 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | log2(8/168*10)=-1.0703893278914 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: VPS54 [Title/Abstract] AND RBPMS2 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Functional or gene categories assigned by FusionGDB annotation | |||
| * 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 |
| Fusion gene information from three resources (ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018)) * 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. |
| Data type | Source | Cancer type | Sample | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| ChiTaRS3.1 | AI637777 | VPS54 | chr2 | 64245646 | + | RBPMS2 | chr15 | 65064925 | + | ||
| ChiTaRS3.1 | AW139503 | VPS54 | chr2 | 64245646 | + | RBPMS2 | chr15 | 65064925 | + |
| * LD: Li Ding group's fusion gene list RV: Roel Verhaak group's fusion gene list ChiTaRs fusion database |
| 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-intron | ENST00000409558 | ENST00000560606 | VPS54 | chr2 | 64245646 | + | RBPMS2 | chr15 | 65064925 | + |
| intron-intron | ENST00000409558 | ENST00000300069 | VPS54 | chr2 | 64245646 | + | RBPMS2 | chr15 | 65064925 | + |
| intron-intron | ENST00000272322 | ENST00000560606 | VPS54 | chr2 | 64245646 | + | RBPMS2 | chr15 | 65064925 | + |
| intron-intron | ENST00000272322 | ENST00000300069 | VPS54 | chr2 | 64245646 | + | RBPMS2 | chr15 | 65064925 | + |
| intron-intron | ENST00000354504 | ENST00000560606 | VPS54 | chr2 | 64245646 | + | RBPMS2 | chr15 | 65064925 | + |
| intron-intron | ENST00000354504 | ENST00000300069 | VPS54 | chr2 | 64245646 | + | RBPMS2 | chr15 | 65064925 | + |
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FusionProtFeatures for VPS54_RBPMS2 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| VPS54 | RBPMS2 |
| Acts as component of the GARP complex that is involvedin retrograde transport from early and late endosomes to thetrans-Golgi network (TGN). The GARP complex is required for themaintenance of the cycling of mannose 6-phosphate receptorsbetween the TGN and endosomes, this cycling is necessary forproper lysosomal sorting of acid hydrolases such as CTSD(PubMed:18367545). Within the GARP complex, required to tether thecomplex to the TGN. Not involved in endocytic recycling(PubMed:25799061). {ECO:0000269|PubMed:18367545,ECO:0000269|PubMed:25799061}. | Contributes to the regulation of smooth muscle celldifferentiation and proliferation in the gastrointestinal system.Binds NOG mRNA. Mediates an increase of NOG mRNA levels, andthereby contributes to the negative regulation of the BMPsignaling pathway. This promotes reversible dedifferentiation ofsmooth muscle cells and promotes smooth muscle cell proliferation.{ECO:0000250|UniProtKB:Q9W6I1}. |
| 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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FusionGeneSequence for VPS54_RBPMS2 |
| For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. (nt: nucleotides, aa: amino acids) |
| * Fusion amino acid sequences. |
| * Fusion transcript sequences (only coding sequence (CDS) region). |
| * Fusion transcript sequences (Full-length transcript). |
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FusionGenePPI for VPS54_RBPMS2 |
| 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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RelatedDrugs for VPS54_RBPMS2 |
| Drugs targeting genes involved in this fusion gene. (DrugBank Version 5.1.0 2018-04-02) |
| Partner | Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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RelatedDiseases for VPS54_RBPMS2 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | VPS54 | C0027746 | Nerve Degeneration | 1 | CTD_human |
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