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Fusion gene ID: 41121 |
FusionGeneSummary for USP39_VAMP8 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: USP39_VAMP8 | Fusion gene ID: 41121 | Hgene | Tgene | Gene symbol | USP39 | VAMP8 | Gene ID | 10713 | 8673 |
| Gene name | ubiquitin specific peptidase 39 | vesicle associated membrane protein 8 | |
| Synonyms | 65K|CGI-21|HSPC332|SAD1|SNRNP65 | EDB|VAMP-8 | |
| Cytomap | 2p11.2 | 2p11.2 | |
| Type of gene | protein-coding | protein-coding | |
| Description | U4/U6.U5 tri-snRNP-associated protein 2SAD1 homologSnRNP assembly defective 1 homologU4/U6.U5 tri-snRNP-associated 65 kDa proteininactive ubiquitin-specific peptidase 39small nuclear ribonucleoprotein 65kDa (U4/U6.U5)ubiquitin specific protease 39 | vesicle-associated membrane protein 8vesicle-associated membrane protein 8 (endobrevin) | |
| Modification date | 20180522 | 20180522 | |
| UniProtAcc | Q53GS9 | Q9BV40 | |
| Ensembl transtripts involved in fusion gene | ENST00000459775, ENST00000450066, ENST00000409025, ENST00000409470, ENST00000323701, ENST00000409766, | ENST00000432071, ENST00000263864, ENST00000409760, | |
| Fusion gene scores | * DoF score | 9 X 8 X 7=504 | 3 X 2 X 3=18 |
| # samples | 10 | 3 | |
| ** MAII score | log2(10/504*10)=-2.33342373372519 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(3/18*10)=0.736965594166206 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | |
| Context | PubMed: USP39 [Title/Abstract] AND VAMP8 [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 |
| Tgene | VAMP8 | GO:0016240 | autophagosome membrane docking | 25686604 |
| Tgene | VAMP8 | GO:1903076 | regulation of protein localization to plasma membrane | 18570918 |
| Tgene | VAMP8 | GO:1903531 | negative regulation of secretion by cell | 12130530 |
| 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 |
| TCGA | RV | LIHC | TCGA-RC-A6M4-01A | USP39 | chr2 | 85852814 | + | VAMP8 | chr2 | 85808699 | + |
| * 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 |
| 3UTR-3CDS | ENST00000459775 | ENST00000432071 | USP39 | chr2 | 85852814 | + | VAMP8 | chr2 | 85808699 | + |
| 3UTR-3CDS | ENST00000459775 | ENST00000263864 | USP39 | chr2 | 85852814 | + | VAMP8 | chr2 | 85808699 | + |
| 3UTR-3CDS | ENST00000459775 | ENST00000409760 | USP39 | chr2 | 85852814 | + | VAMP8 | chr2 | 85808699 | + |
| Frame-shift | ENST00000450066 | ENST00000432071 | USP39 | chr2 | 85852814 | + | VAMP8 | chr2 | 85808699 | + |
| In-frame | ENST00000450066 | ENST00000263864 | USP39 | chr2 | 85852814 | + | VAMP8 | chr2 | 85808699 | + |
| Frame-shift | ENST00000450066 | ENST00000409760 | USP39 | chr2 | 85852814 | + | VAMP8 | chr2 | 85808699 | + |
| Frame-shift | ENST00000409025 | ENST00000432071 | USP39 | chr2 | 85852814 | + | VAMP8 | chr2 | 85808699 | + |
| In-frame | ENST00000409025 | ENST00000263864 | USP39 | chr2 | 85852814 | + | VAMP8 | chr2 | 85808699 | + |
| Frame-shift | ENST00000409025 | ENST00000409760 | USP39 | chr2 | 85852814 | + | VAMP8 | chr2 | 85808699 | + |
| Frame-shift | ENST00000409470 | ENST00000432071 | USP39 | chr2 | 85852814 | + | VAMP8 | chr2 | 85808699 | + |
| In-frame | ENST00000409470 | ENST00000263864 | USP39 | chr2 | 85852814 | + | VAMP8 | chr2 | 85808699 | + |
| Frame-shift | ENST00000409470 | ENST00000409760 | USP39 | chr2 | 85852814 | + | VAMP8 | chr2 | 85808699 | + |
| Frame-shift | ENST00000323701 | ENST00000432071 | USP39 | chr2 | 85852814 | + | VAMP8 | chr2 | 85808699 | + |
| In-frame | ENST00000323701 | ENST00000263864 | USP39 | chr2 | 85852814 | + | VAMP8 | chr2 | 85808699 | + |
| Frame-shift | ENST00000323701 | ENST00000409760 | USP39 | chr2 | 85852814 | + | VAMP8 | chr2 | 85808699 | + |
| Frame-shift | ENST00000409766 | ENST00000432071 | USP39 | chr2 | 85852814 | + | VAMP8 | chr2 | 85808699 | + |
| In-frame | ENST00000409766 | ENST00000263864 | USP39 | chr2 | 85852814 | + | VAMP8 | chr2 | 85808699 | + |
| Frame-shift | ENST00000409766 | ENST00000409760 | USP39 | chr2 | 85852814 | + | VAMP8 | chr2 | 85808699 | + |
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FusionProtFeatures for USP39_VAMP8 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| USP39 | VAMP8 |
| SNAREs, soluble N-ethylmaleimide-sensitive factor-attachment protein receptors, are essential proteins for fusion ofcellular membranes. SNAREs localized on opposing membranesassemble to form a trans-SNARE complex, an extended, parallel fouralpha-helical bundle that drives membrane fusion. VAMP8 is a SNAREinvolved in autophagy through the direct control of autophagosomemembrane fusion with the lysososome membrane via its interactionwith the STX17-SNAP29 binary t-SNARE complex (PubMed:23217709,PubMed:25686604). Also required for dense-granule secretion inplatelets (PubMed:12130530). Plays also a role in regulated enzymesecretion in pancreatic acinar cells (By similarity). Involved inthe abscission of the midbody during cell division, which leads tocompletely separate daughter cells (By similarity). Involved inthe homotypic fusion of early and late endosomes (By similarity).{ECO:0000250|UniProtKB:Q9WUF4, ECO:0000269|PubMed:12130530,ECO:0000269|PubMed:23217709, ECO:0000269|PubMed:25686604}. |
| 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 USP39_VAMP8 |
| 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 USP39_VAMP8 |
| 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 |
| USP39 | CD2BP2, PA2G4, TP53, PRPF4B, SART1, PRPF4, PRPF3, EFTUD2, ZRANB2, SNRNP40, DDX23, DHX38, PRPF8, USP12, TXNL4A, SNRNP27, SNRNP200, RRP8, PRPF6, PRPF31, LSM8, GAR1, TRMT10C, RNMTL1, COPRS, DDX24, NOC3L, TSR2, RPL22L1, MEPCE, SART3, CAND1, RNU4ATAC, RNU6ATAC, APP, SF3B6, SRSF11, SF3A1, SRSF3, SRSF5, SF3B1, RBM39, DHX9, SRSF7, HNRNPC, HNRNPU, NCSTN, SON, GTF3C1, SAFB, TPBG, TRIM55, ZC3H18, SRSF10, VTN, SUPT16H, CETN2, TRAF6, TRIM25, TRIM26, TRIM39, TRIM8, TRIM5, FN1, MMS19, SP1, SRPK1, WWOX, PTEN, SAE1, CUL7, OBSL1, CCDC8, ADARB1, CSNK1E, LGALS9, NSUN2, PCNA, APEH, ARF1, HSPA4, HSPH1, NCAPD3, PRPF19, RUVBL2, NTRK1, SCARNA22, SRPK2, CDC5L, NCL, EAPP, ZNHIT2 | VAMP8 | STX2, SNAP23, NAPA, STX4, STX6, VTI1A, STX7, STX8, STX1A, VAMP2, VAMP3, ATP6V1B1, FN1, VCAM1, YWHAE, MLH1, ITGA4, ATP4A, CDC25A, UBE2G2, USP8, STAMBP, STX12, STX3, STX19, CEP170, STX18, HAUS7, DTNBP1, TMEM17, STX11, SYPL1, MED21 |
| - 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 USP39_VAMP8 |
| 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 USP39_VAMP8 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Tgene | VAMP8 | C0024667 | Animal Mammary Neoplasms | 1 | CTD_human |
| Tgene | VAMP8 | C0024668 | Mammary Neoplasms, Experimental | 1 | CTD_human |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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