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Fusion gene ID: 34903 |
FusionGeneSummary for SMG5_PMF1 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: SMG5_PMF1 | Fusion gene ID: 34903 | Hgene | Tgene | Gene symbol | SMG5 | PMF1 | Gene ID | 23381 | 100527963 |
| Gene name | SMG5, nonsense mediated mRNA decay factor | PMF1-BGLAP readthrough | |
| Synonyms | EST1B|LPTS-RP1|LPTSRP1|SMG-5 | PMF1 | |
| Cytomap | 1q22 | 1q22 | |
| Type of gene | protein-coding | protein-coding | |
| Description | protein SMG5EST1 telomerase component homolog BEST1-like protein BEst1p-like protein BLPTS interacting proteinever shorter telomeres 1Bsmg-5 homolog, nonsense mediated mRNA decay factor | PMF1-BGLAP proteinpolyamine-modulated factor 1 | |
| Modification date | 20180523 | 20180519 | |
| UniProtAcc | Q9UPR3 | Q6P1K2 | |
| Ensembl transtripts involved in fusion gene | ENST00000361813, ENST00000368267, ENST00000489907, | ENST00000368279, ENST00000368273, ENST00000368277, ENST00000565805, ENST00000567140, | |
| Fusion gene scores | * DoF score | 5 X 4 X 4=80 | 3 X 3 X 3=27 |
| # samples | 5 | 3 | |
| ** MAII score | log2(5/80*10)=-0.678071905112638 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(3/27*10)=0.15200309344505 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | |
| Context | PubMed: SMG5 [Title/Abstract] AND PMF1 [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 |
| TCGA | RV | STAD | TCGA-BR-8373-01A | SMG5 | chr1 | 156235572 | - | PMF1 | chr1 | 156206079 | + |
| * 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 |
| 5CDS-intron | ENST00000361813 | ENST00000368279 | SMG5 | chr1 | 156235572 | - | PMF1 | chr1 | 156206079 | + |
| 5CDS-intron | ENST00000361813 | ENST00000368273 | SMG5 | chr1 | 156235572 | - | PMF1 | chr1 | 156206079 | + |
| 5CDS-intron | ENST00000361813 | ENST00000368277 | SMG5 | chr1 | 156235572 | - | PMF1 | chr1 | 156206079 | + |
| 5CDS-intron | ENST00000361813 | ENST00000565805 | SMG5 | chr1 | 156235572 | - | PMF1 | chr1 | 156206079 | + |
| 5CDS-intron | ENST00000361813 | ENST00000567140 | SMG5 | chr1 | 156235572 | - | PMF1 | chr1 | 156206079 | + |
| intron-intron | ENST00000368267 | ENST00000368279 | SMG5 | chr1 | 156235572 | - | PMF1 | chr1 | 156206079 | + |
| intron-intron | ENST00000368267 | ENST00000368273 | SMG5 | chr1 | 156235572 | - | PMF1 | chr1 | 156206079 | + |
| intron-intron | ENST00000368267 | ENST00000368277 | SMG5 | chr1 | 156235572 | - | PMF1 | chr1 | 156206079 | + |
| intron-intron | ENST00000368267 | ENST00000565805 | SMG5 | chr1 | 156235572 | - | PMF1 | chr1 | 156206079 | + |
| intron-intron | ENST00000368267 | ENST00000567140 | SMG5 | chr1 | 156235572 | - | PMF1 | chr1 | 156206079 | + |
| intron-intron | ENST00000489907 | ENST00000368279 | SMG5 | chr1 | 156235572 | - | PMF1 | chr1 | 156206079 | + |
| intron-intron | ENST00000489907 | ENST00000368273 | SMG5 | chr1 | 156235572 | - | PMF1 | chr1 | 156206079 | + |
| intron-intron | ENST00000489907 | ENST00000368277 | SMG5 | chr1 | 156235572 | - | PMF1 | chr1 | 156206079 | + |
| intron-intron | ENST00000489907 | ENST00000565805 | SMG5 | chr1 | 156235572 | - | PMF1 | chr1 | 156206079 | + |
| intron-intron | ENST00000489907 | ENST00000567140 | SMG5 | chr1 | 156235572 | - | PMF1 | chr1 | 156206079 | + |
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FusionProtFeatures for SMG5_PMF1 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| SMG5 | PMF1 |
| Plays a role in nonsense-mediated mRNA decay. Does nothave RNase activity by itself. Promotes dephosphorylation of UPF1.Together with SMG7 is thought to provide a link to the mRNAdegradation machinery involving exonucleolytic pathways, and toserve as an adapter for UPF1 to protein phosphatase 2A (PP2A),thereby triggering UPF1 dephosphorylation. Necessary for TERTactivity. {ECO:0000269|PubMed:17053788}. |
| 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 SMG5_PMF1 |
| 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 SMG5_PMF1 |
| 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 |
| SMG5 | TERT, HDAC8, STUB1, APP, UPF1, ZWINT, PHB, RBM8A, MOV10, NXF1, SMG6, BTRC, PCM1, CEP152, TP53, C6orf141 | PMF1 | NFE2L2, MIS12, DSN1, GDF9, KIAA1377, MED31, CRMP1, PTN, COPS6, GIT1, COPS7A, SUGT1, HSP90AA1, TCP10L, KDM1A, USHBP1, BUB1B, NSMCE1, NSL1, ZWINT, SGTB, SEC63, PGRMC2, ZRANB1, WDR45B, GNPAT, PPP1CC, ZMPSTE24, CMTM6, GFER, TALDO1, SPC24, SPC25, CASC5, NUF2, KIF21B, BICD2, RUFY2, GCC2, NDC80, ZC4H2, CEP89, FBXO28, RUFY1, TSNAX, ATG16L1, NRBF2, ALOX5, MLLT10, CENPC, RGPD8, STXBP4, MLF1, TRIM25, UBE2S |
| - 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 SMG5_PMF1 |
| 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 SMG5_PMF1 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
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