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Fusion gene ID: 35172 |
FusionGeneSummary for SNRNP40_COL6A5 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: SNRNP40_COL6A5 | Fusion gene ID: 35172 | Hgene | Tgene | Gene symbol | SNRNP40 | COL6A5 | Gene ID | 9410 | 256076 |
| Gene name | small nuclear ribonucleoprotein U5 subunit 40 | collagen type VI alpha 5 chain | |
| Synonyms | 40K|HPRP8BP|PRP8BP|PRPF8BP|SPF38|WDR57 | COL29A1|VWA4 | |
| Cytomap | 1p35.2 | 3q22.1 | |
| Type of gene | protein-coding | protein-coding | |
| Description | U5 small nuclear ribonucleoprotein 40 kDa protein38 kDa-splicing factorPrp8-binding proteinU5 snRNP 40 kDa proteinU5 snRNP-specific 40 kDa protein (hPrp8-binding)U5-40KU5-40kD proteinWD repeat domain 57 (U5 snRNP specific)WD repeat-containing prot | collagen alpha-5(VI) chaincollagen, type VI, alpha 5collagen, type XXIX, alpha 1von Willebrand factor A domain-containing protein 4 | |
| Modification date | 20180523 | 20180522 | |
| UniProtAcc | Q96DI7 | A8TX70 | |
| Ensembl transtripts involved in fusion gene | ENST00000263694, ENST00000489853, ENST00000373720, ENST00000446633, | ENST00000265379, ENST00000432398, | |
| Fusion gene scores | * DoF score | 6 X 3 X 5=90 | 2 X 2 X 2=8 |
| # samples | 5 | 2 | |
| ** MAII score | log2(5/90*10)=-0.84799690655495 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(2/8*10)=1.32192809488736 | |
| Context | PubMed: SNRNP40 [Title/Abstract] AND COL6A5 [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 | LD | CESC | TCGA-VS-A9UO-01A | SNRNP40 | chr1 | 31754221 | - | COL6A5 | chr3 | 130187639 | + |
| * 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 |
| Frame-shift | ENST00000263694 | ENST00000265379 | SNRNP40 | chr1 | 31754221 | - | COL6A5 | chr3 | 130187639 | + |
| Frame-shift | ENST00000263694 | ENST00000432398 | SNRNP40 | chr1 | 31754221 | - | COL6A5 | chr3 | 130187639 | + |
| 5UTR-3CDS | ENST00000489853 | ENST00000265379 | SNRNP40 | chr1 | 31754221 | - | COL6A5 | chr3 | 130187639 | + |
| 5UTR-3CDS | ENST00000489853 | ENST00000432398 | SNRNP40 | chr1 | 31754221 | - | COL6A5 | chr3 | 130187639 | + |
| intron-3CDS | ENST00000373720 | ENST00000265379 | SNRNP40 | chr1 | 31754221 | - | COL6A5 | chr3 | 130187639 | + |
| intron-3CDS | ENST00000373720 | ENST00000432398 | SNRNP40 | chr1 | 31754221 | - | COL6A5 | chr3 | 130187639 | + |
| Frame-shift | ENST00000446633 | ENST00000265379 | SNRNP40 | chr1 | 31754221 | - | COL6A5 | chr3 | 130187639 | + |
| Frame-shift | ENST00000446633 | ENST00000432398 | SNRNP40 | chr1 | 31754221 | - | COL6A5 | chr3 | 130187639 | + |
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FusionProtFeatures for SNRNP40_COL6A5 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| SNRNP40 | COL6A5 |
| Component of the U5 small nuclear ribonucleoprotein(snRNP) complex. The U5 snRNP is part of the spliceosome, amultiprotein complex that catalyzes the removal of introns frompre-messenger RNAs. {ECO:0000269|PubMed:9774689}. |
| 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 SNRNP40_COL6A5 |
| 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 SNRNP40_COL6A5 |
| 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 |
| SNRNP40 | PRPF8, SNRNP200, EFTUD2, CD2BP2, PRPF6, SNRPB2, PFDN2, MAGEA6, SF3B1, DDR1, USP39, PRPF4, CUL4A, CUL4B, WDR5, SRRM1, PML, RARA, ELAVL1, DHX16, RNU4ATAC, RNU6ATAC, APP, SNRPE, RALY, TBL1X, MDC1, EIF4A3, MAGOH, PRPF4B, RPA3, RPA2, RPA1, MOV10, NXF1, CUL7, OBSL1, SUZ12, DDX23, TSSC4, RSRC1, PRPF3, TFIP11, PAXBP1, PRPF31, SART1, ECD, SNRPD2, CCDC12, DHX38, SNRNP27, ZNHIT2, TXNL4A, AQR, SNRPD1, ISY1, RBM42, CHD3, CRNKL1, POLR3C, SREK1, XPO1, YWHAZ, USP37, SNW1, CDC5L, SNRPF, PPIE, AAR2, LMNA | COL6A5 | CYLD |
| - 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 SNRNP40_COL6A5 |
| 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 SNRNP40_COL6A5 |
| 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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