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Fusion gene ID: 33466 |
FusionGeneSummary for SF3B3_NUP88 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: SF3B3_NUP88 | Fusion gene ID: 33466 | Hgene | Tgene | Gene symbol | SF3B3 | NUP88 | Gene ID | 23450 | 4927 |
| Gene name | splicing factor 3b subunit 3 | nucleoporin 88 | |
| Synonyms | RSE1|SAP130|SF3b130|STAF130 | - | |
| Cytomap | 16q22.1 | 17p13.2 | |
| Type of gene | protein-coding | protein-coding | |
| Description | splicing factor 3B subunit 3SAP 130pre-mRNA splicing factor SF3b, 130 kDa subunitspliceosome-associated protein 130 | nuclear pore complex protein Nup88karyoporinnuclear pore complex protein 88nucleoporin 88kDanucleoporin Nup88 | |
| Modification date | 20180523 | 20180523 | |
| UniProtAcc | Q15393 | Q99567 | |
| Ensembl transtripts involved in fusion gene | ENST00000302516, | ENST00000573169, ENST00000573584, | |
| Fusion gene scores | * DoF score | 10 X 10 X 7=700 | 3 X 3 X 2=18 |
| # samples | 12 | 3 | |
| ** MAII score | log2(12/700*10)=-2.54432051622381 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: SF3B3 [Title/Abstract] AND NUP88 [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 |
| Hgene | SF3B3 | GO:0000398 | mRNA splicing, via spliceosome | 28781166 |
| Hgene | SF3B3 | GO:0042177 | negative regulation of protein catabolic process | 23951410 |
| 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 | BE706779 | SF3B3 | chr16 | 70582572 | - | NUP88 | chr17 | 5319833 | + |
| * 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 | ENST00000302516 | ENST00000573169 | SF3B3 | chr16 | 70582572 | - | NUP88 | chr17 | 5319833 | + |
| intron-intron | ENST00000302516 | ENST00000573584 | SF3B3 | chr16 | 70582572 | - | NUP88 | chr17 | 5319833 | + |
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FusionProtFeatures for SF3B3_NUP88 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| SF3B3 | NUP88 |
| Involved in pre-mRNA splicing as a component of thesplicing factor SF3B complex, a constituent of the spliceosome(PubMed:10490618, PubMed:10882114, PubMed:27720643,PubMed:28781166). SF3B complex is required for 'A' complexassembly formed by the stable binding of U2 snRNP to thebranchpoint sequence (BPS) in pre-mRNA. Sequence independentbinding of SF3A/SF3B complex upstream of the branch site isessential, it may anchor U2 snRNP to the pre-mRNA(PubMed:12234937). May also be involved in the assembly of the 'E'complex (PubMed:10882114). Belongs also to the minor U12-dependentspliceosome, which is involved in the splicing of rare class ofnuclear pre-mRNA intron (PubMed:15146077).{ECO:0000269|PubMed:10490618, ECO:0000269|PubMed:10882114,ECO:0000269|PubMed:12234937, ECO:0000269|PubMed:15146077,ECO:0000269|PubMed:27720643, ECO:0000269|PubMed:28781166}. | Essential component of nuclear pore complex. |
| 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 SF3B3_NUP88 |
| 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 SF3B3_NUP88 |
| 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 SF3B3_NUP88 |
| 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 SF3B3_NUP88 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Tgene | NUP88 | C0019693 | HIV Infections | 1 | CTD_human |
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