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Fusion gene ID: 20040 |
FusionGeneSummary for LPP_LSM1 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: LPP_LSM1 | Fusion gene ID: 20040 | Hgene | Tgene | Gene symbol | LPP | LSM1 | Gene ID | 4026 | 27257 |
| Gene name | LIM domain containing preferred translocation partner in lipoma | LSM1 homolog, mRNA degradation associated | |
| Synonyms | - | CASM|YJL124C | |
| Cytomap | 3q27.3-q28 | 8p11.23 | |
| Type of gene | protein-coding | protein-coding | |
| Description | lipoma-preferred partnerLIM proteinlipoma preferred partner | U6 snRNA-associated Sm-like protein LSm1LSM1 homolog, U6 small nuclear RNA associatedLSM1 mRNA degradation associatedLSM1, U6 small nuclear RNA associatedLSM1-like protein U6 small nuclear RNA associatedcancer-associated Sm proteincancer-associated | |
| Modification date | 20180519 | 20180523 | |
| UniProtAcc | Q93052 | O15116 | |
| Ensembl transtripts involved in fusion gene | ENST00000448637, ENST00000312675, ENST00000543006, ENST00000471917, | ENST00000311351, ENST00000520755, ENST00000522515, | |
| Fusion gene scores | * DoF score | 29 X 22 X 11=7018 | 5 X 2 X 3=30 |
| # samples | 37 | 5 | |
| ** MAII score | log2(37/7018*10)=-4.24546277188585 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(5/30*10)=0.736965594166206 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | |
| Context | PubMed: LPP [Title/Abstract] AND LSM1 [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 | AA501557 | LPP | chr3 | 188138333 | - | LSM1 | chr8 | 38020935 | + |
| * 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-3UTR | ENST00000448637 | ENST00000311351 | LPP | chr3 | 188138333 | - | LSM1 | chr8 | 38020935 | + |
| intron-3UTR | ENST00000448637 | ENST00000520755 | LPP | chr3 | 188138333 | - | LSM1 | chr8 | 38020935 | + |
| intron-5UTR | ENST00000448637 | ENST00000522515 | LPP | chr3 | 188138333 | - | LSM1 | chr8 | 38020935 | + |
| intron-3UTR | ENST00000312675 | ENST00000311351 | LPP | chr3 | 188138333 | - | LSM1 | chr8 | 38020935 | + |
| intron-3UTR | ENST00000312675 | ENST00000520755 | LPP | chr3 | 188138333 | - | LSM1 | chr8 | 38020935 | + |
| intron-5UTR | ENST00000312675 | ENST00000522515 | LPP | chr3 | 188138333 | - | LSM1 | chr8 | 38020935 | + |
| intron-3UTR | ENST00000543006 | ENST00000311351 | LPP | chr3 | 188138333 | - | LSM1 | chr8 | 38020935 | + |
| intron-3UTR | ENST00000543006 | ENST00000520755 | LPP | chr3 | 188138333 | - | LSM1 | chr8 | 38020935 | + |
| intron-5UTR | ENST00000543006 | ENST00000522515 | LPP | chr3 | 188138333 | - | LSM1 | chr8 | 38020935 | + |
| intron-3UTR | ENST00000471917 | ENST00000311351 | LPP | chr3 | 188138333 | - | LSM1 | chr8 | 38020935 | + |
| intron-3UTR | ENST00000471917 | ENST00000520755 | LPP | chr3 | 188138333 | - | LSM1 | chr8 | 38020935 | + |
| intron-5UTR | ENST00000471917 | ENST00000522515 | LPP | chr3 | 188138333 | - | LSM1 | chr8 | 38020935 | + |
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FusionProtFeatures for LPP_LSM1 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| LPP | LSM1 |
| May play a structural role at sites of cell adhesion inmaintaining cell shape and motility. In addition to thesestructural functions, it may also be implicated in signalingevents and activation of gene transcription. May be involved insignal transduction from cell adhesion sites to the nucleusallowing successful integration of signals arising from solublefactors and cell-cell adhesion sites. Also suggested to serve as ascaffold protein upon which distinct protein complexes areassembled in the cytoplasm and in the nucleus.{ECO:0000269|PubMed:10637295, ECO:0000269|Ref.2}. | Plays a role in the degradation of histone mRNAs, theonly eukaryotic mRNAs that are not polyadenylated(PubMed:18172165). Probably also part of an LSm subunits-containing complex involved in the general process of mRNAdegradation (By similarity). {ECO:0000250|UniProtKB:P47017,ECO:0000269|PubMed:18172165}. |
| 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 LPP_LSM1 |
| 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 LPP_LSM1 |
| 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 LPP_LSM1 |
| 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 LPP_LSM1 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | LPP | C3495559 | Juvenile arthritis | 1 | CTD_human |
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