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Fusion gene ID: 20343 |
FusionGeneSummary for LSM4_RCC1 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: LSM4_RCC1 | Fusion gene ID: 20343 | Hgene | Tgene | Gene symbol | LSM4 | RCC1 | Gene ID | 25804 | 1104 |
| Gene name | LSM4 homolog, U6 small nuclear RNA and mRNA degradation associated | regulator of chromosome condensation 1 | |
| Synonyms | GRP|YER112W | CHC1|RCC1-I|SNHG3-RCC1 | |
| Cytomap | 19p13.11 | 1p35.3 | |
| Type of gene | protein-coding | protein-coding | |
| Description | U6 snRNA-associated Sm-like protein LSm4LSM4 U6 small nuclear RNA and mRNA degradation associatedLSM4 homolog, U6 small nuclear RNA associatedglycine-rich protein | regulator of chromosome condensationSNHG3-RCC1 readthroughcell cycle regulatory proteinguanine nucleotide-releasing protein | |
| Modification date | 20180523 | 20180522 | |
| UniProtAcc | Q9Y4Z0 | P18754 | |
| Ensembl transtripts involved in fusion gene | ENST00000593829, ENST00000252816, | ENST00000398958, ENST00000373833, ENST00000373832, ENST00000373831, ENST00000429051, | |
| Fusion gene scores | * DoF score | 6 X 3 X 5=90 | 5 X 5 X 5=125 |
| # samples | 6 | 6 | |
| ** MAII score | log2(6/90*10)=-0.584962500721156 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(6/125*10)=-1.05889368905357 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: LSM4 [Title/Abstract] AND RCC1 [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 | RCC1 | GO:0007052 | mitotic spindle organization | 15014043 |
| Tgene | RCC1 | GO:0007088 | regulation of mitotic nuclear division | 15014043 |
| Tgene | RCC1 | GO:0051290 | protein heterotetramerization | 11336674 |
| 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 | LD | UCS | TCGA-N9-A4Q3-01A | LSM4 | chr19 | 18433828 | - | RCC1 | chr1 | 28856370 | + |
| * 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-5UTR | ENST00000593829 | ENST00000398958 | LSM4 | chr19 | 18433828 | - | RCC1 | chr1 | 28856370 | + |
| 5CDS-5UTR | ENST00000593829 | ENST00000373833 | LSM4 | chr19 | 18433828 | - | RCC1 | chr1 | 28856370 | + |
| 5CDS-5UTR | ENST00000593829 | ENST00000373832 | LSM4 | chr19 | 18433828 | - | RCC1 | chr1 | 28856370 | + |
| 5CDS-5UTR | ENST00000593829 | ENST00000373831 | LSM4 | chr19 | 18433828 | - | RCC1 | chr1 | 28856370 | + |
| 5CDS-intron | ENST00000593829 | ENST00000429051 | LSM4 | chr19 | 18433828 | - | RCC1 | chr1 | 28856370 | + |
| 5CDS-5UTR | ENST00000252816 | ENST00000398958 | LSM4 | chr19 | 18433828 | - | RCC1 | chr1 | 28856370 | + |
| 5CDS-5UTR | ENST00000252816 | ENST00000373833 | LSM4 | chr19 | 18433828 | - | RCC1 | chr1 | 28856370 | + |
| 5CDS-5UTR | ENST00000252816 | ENST00000373832 | LSM4 | chr19 | 18433828 | - | RCC1 | chr1 | 28856370 | + |
| 5CDS-5UTR | ENST00000252816 | ENST00000373831 | LSM4 | chr19 | 18433828 | - | RCC1 | chr1 | 28856370 | + |
| 5CDS-intron | ENST00000252816 | ENST00000429051 | LSM4 | chr19 | 18433828 | - | RCC1 | chr1 | 28856370 | + |
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FusionProtFeatures for LSM4_RCC1 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| LSM4 | RCC1 |
| Binds specifically to the 3'-terminal U-tract of U6snRNA. | Guanine-nucleotide releasing factor that promotes theexchange of Ran-bound GDP by GTP, and thereby plays an importantrole in RAN-mediated functions in nuclear import and mitosis(PubMed:1944575, PubMed:17435751, PubMed:20668449,PubMed:22215983, PubMed:11336674). Contributes to the generationof high levels of chromosome-associated, GTP-bound RAN, which isimportant for mitotic spindle assembly and normal progress throughmitosis (PubMed:12194828, PubMed:17435751, PubMed:22215983). Viaits role in maintaining high levels of GTP-bound RAN in thenucleus, contributes to the release of cargo proteins fromimportins after nuclear import (PubMed:22215983). Involved in theregulation of onset of chromosome condensation in the S phase(PubMed:3678831). Binds both to the nucleosomes and double-stranded DNA (PubMed:17435751, PubMed:18762580).{ECO:0000269|PubMed:11336674, ECO:0000269|PubMed:12194828,ECO:0000269|PubMed:17435751, ECO:0000269|PubMed:18762580,ECO:0000269|PubMed:1944575, ECO:0000269|PubMed:20668449,ECO:0000269|PubMed:22215983, ECO:0000269|PubMed:3678831}. |
| 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 LSM4_RCC1 |
| 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 LSM4_RCC1 |
| 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 |
| LSM4 | SNRPE, XRN1, CALCOCO2, LSM1, LSM2, LSM3, LSM6, LSM7, LSM8, SMN1, USP15, USP4, PRPF4, SART3, MEPCE, RNU4ATAC, RNU6ATAC, TOP1, LSM5, DDX39B, PRPF18, VAC14, TCEA2, WDR44, PYROXD1, MTR, RMI2, GTF2B, RAD23A, SGTA, PPIB, PPIP5K1, HUWE1, SMU1, TOE1, SLC22A2, SMIM14, NMI, RHOXF2, COX5B, PLEKHA5, WWOX, PSTPIP1, IKZF1, ZBTB10, L3MBTL3, HNRNPR, KLC2, LRPPRC, PKN2, NAA38, SF3A3, SF3B3, SYNCRIP, ZMAT2, XPO1, SIN3B, PRPF3, SNRPN, ALYREF, RPL26L1, PPIH, OLA1, RPL32 | RCC1 | CSNK1A1, RAN, TAL1, KPNA3, RANBP3, XPO1, H2AFY, KPNA4, KPNB1, NTMT1, HIST1H3A, HIST2H2AC, HIST2H2BE, HIST1H4A, NUDT21, CHGB, SPRED1, USP4, TP53, CSAD, PKM, NGFR, DYNC1I1, PDHB, GNB2, SDF4, RPA1, FLAD1, DDAH2, APLP1, UNC119, HADHB, ZNF135, WIZ, TLE1, KMT2B, TRMT2A, ACTB, CCT7, BAG6, HOXD8, LRIF1, FAF1, TUBB3, CDK2AP2, HDGF, RANBP1, NCSTN, U2AF1, HNRNPM, SF3B6, RBM14, LUC7L3, ACIN1, HNRNPK, FN1, VCAM1, ITGA4, HMGA1, HDAC9, PTMA, ENO1, SHMT2, MOV10, NXF1, CUL7, OBSL1, SUZ12, RNF2, NUSAP1, RGPD3, RGPD8, RANBP2, RGPD5, RANGAP1, NAV1, DIS3, GLYR1, UBE2I, NUP153, NUP107, RBPJ, TEAD2, FOXA1, FOXB1, FOXE1, FOXH1, FOXI2, FOXP1, FOXQ1, OTUB1, PPM1G, DLGAP5, DNM1L, TRIM25, G3BP1 |
| - 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 LSM4_RCC1 |
| 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 LSM4_RCC1 |
| 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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