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Fusion gene ID: 30440 |
FusionGeneSummary for RAPGEF5_EDEM1 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: RAPGEF5_EDEM1 | Fusion gene ID: 30440 | Hgene | Tgene | Gene symbol | RAPGEF5 | EDEM1 | Gene ID | 9771 | 9695 |
| Gene name | Rap guanine nucleotide exchange factor 5 | ER degradation enhancing alpha-mannosidase like protein 1 | |
| Synonyms | GFR|MR-GEF|REPAC | EDEM | |
| Cytomap | 7p15.3 | 3p26.1 | |
| Type of gene | protein-coding | protein-coding | |
| Description | rap guanine nucleotide exchange factor 5M-Ras-regulated GEFM-Ras-regulated Rap GEFRap guanine nucleotide exchange factor (GEF) 5guanine nucleotide exchange factor for Rap1related to Epac | ER degradation-enhancing alpha-mannosidase-like protein 1ER degradation enhancer, mannosidase alpha-like 1ER degradation-enhancing alpha-mannosidase-like 1 | |
| Modification date | 20180519 | 20180522 | |
| UniProtAcc | Q92565 | Q92611 | |
| Ensembl transtripts involved in fusion gene | ENST00000344041, ENST00000475788, ENST00000405243, ENST00000401957, | ENST00000256497, ENST00000445686, | |
| Fusion gene scores | * DoF score | 11 X 11 X 6=726 | 3 X 3 X 1=9 |
| # samples | 11 | 3 | |
| ** MAII score | log2(11/726*10)=-2.72246602447109 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(3/9*10)=1.73696559416621 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | |
| Context | PubMed: RAPGEF5 [Title/Abstract] AND EDEM1 [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 | R93121 | RAPGEF5 | chr7 | 22352155 | - | EDEM1 | chr3 | 5241903 | + |
| * 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 | ENST00000344041 | ENST00000256497 | RAPGEF5 | chr7 | 22352155 | - | EDEM1 | chr3 | 5241903 | + |
| intron-intron | ENST00000344041 | ENST00000445686 | RAPGEF5 | chr7 | 22352155 | - | EDEM1 | chr3 | 5241903 | + |
| intron-intron | ENST00000475788 | ENST00000256497 | RAPGEF5 | chr7 | 22352155 | - | EDEM1 | chr3 | 5241903 | + |
| intron-intron | ENST00000475788 | ENST00000445686 | RAPGEF5 | chr7 | 22352155 | - | EDEM1 | chr3 | 5241903 | + |
| intron-intron | ENST00000405243 | ENST00000256497 | RAPGEF5 | chr7 | 22352155 | - | EDEM1 | chr3 | 5241903 | + |
| intron-intron | ENST00000405243 | ENST00000445686 | RAPGEF5 | chr7 | 22352155 | - | EDEM1 | chr3 | 5241903 | + |
| intron-intron | ENST00000401957 | ENST00000256497 | RAPGEF5 | chr7 | 22352155 | - | EDEM1 | chr3 | 5241903 | + |
| intron-intron | ENST00000401957 | ENST00000445686 | RAPGEF5 | chr7 | 22352155 | - | EDEM1 | chr3 | 5241903 | + |
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FusionProtFeatures for RAPGEF5_EDEM1 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| RAPGEF5 | EDEM1 |
| Guanine nucleotide exchange factor (GEF) for RAP1A,RAP2A and MRAS/M-Ras-GTP. Its association with MRAS inhibits Rap1activation. {ECO:0000269|PubMed:10777494,ECO:0000269|PubMed:10934204}. | Extracts misfolded glycoproteins, but not glycoproteinsundergoing productive folding, from the calnexin cycle. It isdirectly involved in endoplasmic reticulum-associated degradation(ERAD) and targets misfolded glycoproteins for degradation in anN-glycan-independent manner, probably by forming a complex withSEL1L. It has low mannosidase activity, catalyzing mannosetrimming from Man8GlcNAc2 to Man7GlcNAc2.{ECO:0000269|PubMed:12610306, ECO:0000269|PubMed:19524542,ECO:0000269|PubMed:19934218, ECO:0000269|PubMed:25092655}. |
| 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 RAPGEF5_EDEM1 |
| 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 RAPGEF5_EDEM1 |
| 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 RAPGEF5_EDEM1 |
| 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 RAPGEF5_EDEM1 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | RAPGEF5 | C0005586 | Bipolar Disorder | 1 | PSYGENET |
| Hgene | RAPGEF5 | C0033975 | Psychotic Disorders | 1 | PSYGENET |
| Hgene | RAPGEF5 | C0036341 | Schizophrenia | 1 | PSYGENET |
| Hgene | RAPGEF5 | C0041696 | Unipolar Depression | 1 | PSYGENET |
| Hgene | RAPGEF5 | C0236733 | Amphetamine-Related Disorders | 1 | CTD_human |
| Hgene | RAPGEF5 | C0349204 | Nonorganic psychosis | 1 | PSYGENET |
| Hgene | RAPGEF5 | C1269683 | Major Depressive Disorder | 1 | PSYGENET |
| Tgene | EDEM1 | C0041696 | Unipolar Depression | 1 | PSYGENET |
| Tgene | EDEM1 | C1269683 | Major Depressive Disorder | 1 | PSYGENET |
| Tgene | EDEM1 | C4277682 | Chemical and Drug Induced Liver Injury | 1 | CTD_human |
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