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Fusion gene ID: 30422 |
FusionGeneSummary for RAPGEF1_MED27 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: RAPGEF1_MED27 | Fusion gene ID: 30422 | Hgene | Tgene | Gene symbol | RAPGEF1 | MED27 | Gene ID | 2889 | 9442 |
| Gene name | Rap guanine nucleotide exchange factor 1 | mediator complex subunit 27 | |
| Synonyms | C3G|GRF2 | CRAP34|CRSP34|CRSP8|MED3|TRAP37 | |
| Cytomap | 9q34.13 | 9q34.13 | |
| Type of gene | protein-coding | protein-coding | |
| Description | rap guanine nucleotide exchange factor 1CRK SH3-binding GNRPRap guanine nucleotide exchange factor (GEF) 1guanine nucleotide-releasing factor 2 (specific for crk proto-oncogene) | mediator of RNA polymerase II transcription subunit 27CRSP complex subunit 8cofactor required for Sp1 transcriptional activation, subunit 8, 34kDap37 TRAP/SMCC/PC2 subunittranscriptional coactivator CRSP34 | |
| Modification date | 20180522 | 20180519 | |
| UniProtAcc | Q13905 | Q6P2C8 | |
| Ensembl transtripts involved in fusion gene | ENST00000372189, ENST00000372195, ENST00000372190, ENST00000481260, | ENST00000357028, ENST00000292035, ENST00000474263, | |
| Fusion gene scores | * DoF score | 17 X 14 X 10=2380 | 4 X 6 X 6=144 |
| # samples | 21 | 8 | |
| ** MAII score | log2(21/2380*10)=-3.50250034052918 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(8/144*10)=-0.84799690655495 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: RAPGEF1 [Title/Abstract] AND MED27 [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 |
| Hgene | RAPGEF1 | GO:0038180 | nerve growth factor signaling pathway | 17724123 |
| Hgene | RAPGEF1 | GO:0043547 | positive regulation of GTPase activity | 10548487 |
| Hgene | RAPGEF1 | GO:0071320 | cellular response to cAMP | 21840392 |
| Hgene | RAPGEF1 | GO:1990090 | cellular response to nerve growth factor stimulus | 17724123 |
| Tgene | MED27 | GO:0006357 | regulation of transcription by RNA polymerase II | 9989412 |
| 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 | HNSC | TCGA-CV-A45W-01A | RAPGEF1 | chr9 | 134497183 | - | MED27 | chr9 | 134769379 | - |
| TCGA | LD | LGG | TCGA-DU-A5TT-01A | RAPGEF1 | chr9 | 134615157 | - | MED27 | chr9 | 134738527 | - |
| TCGA | LD | LUAD | TCGA-55-8620-01A | RAPGEF1 | chr9 | 134615157 | - | MED27 | chr9 | 134769379 | - |
| TCGA | RV | UCS | TCGA-NA-A4R1-01A | RAPGEF1 | chr9 | 134471685 | - | MED27 | chr9 | 134759486 | - |
| * 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 | ENST00000372189 | ENST00000357028 | RAPGEF1 | chr9 | 134497183 | - | MED27 | chr9 | 134769379 | - |
| 5CDS-intron | ENST00000372189 | ENST00000292035 | RAPGEF1 | chr9 | 134497183 | - | MED27 | chr9 | 134769379 | - |
| 5CDS-intron | ENST00000372189 | ENST00000474263 | RAPGEF1 | chr9 | 134497183 | - | MED27 | chr9 | 134769379 | - |
| 5CDS-intron | ENST00000372195 | ENST00000357028 | RAPGEF1 | chr9 | 134497183 | - | MED27 | chr9 | 134769379 | - |
| 5CDS-intron | ENST00000372195 | ENST00000292035 | RAPGEF1 | chr9 | 134497183 | - | MED27 | chr9 | 134769379 | - |
| 5CDS-intron | ENST00000372195 | ENST00000474263 | RAPGEF1 | chr9 | 134497183 | - | MED27 | chr9 | 134769379 | - |
| 5CDS-intron | ENST00000372190 | ENST00000357028 | RAPGEF1 | chr9 | 134497183 | - | MED27 | chr9 | 134769379 | - |
| 5CDS-intron | ENST00000372190 | ENST00000292035 | RAPGEF1 | chr9 | 134497183 | - | MED27 | chr9 | 134769379 | - |
| 5CDS-intron | ENST00000372190 | ENST00000474263 | RAPGEF1 | chr9 | 134497183 | - | MED27 | chr9 | 134769379 | - |
| intron-intron | ENST00000481260 | ENST00000357028 | RAPGEF1 | chr9 | 134497183 | - | MED27 | chr9 | 134769379 | - |
| intron-intron | ENST00000481260 | ENST00000292035 | RAPGEF1 | chr9 | 134497183 | - | MED27 | chr9 | 134769379 | - |
| intron-intron | ENST00000481260 | ENST00000474263 | RAPGEF1 | chr9 | 134497183 | - | MED27 | chr9 | 134769379 | - |
| intron-3CDS | ENST00000372189 | ENST00000357028 | RAPGEF1 | chr9 | 134615157 | - | MED27 | chr9 | 134738527 | - |
| intron-3CDS | ENST00000372189 | ENST00000292035 | RAPGEF1 | chr9 | 134615157 | - | MED27 | chr9 | 134738527 | - |
| intron-intron | ENST00000372189 | ENST00000474263 | RAPGEF1 | chr9 | 134615157 | - | MED27 | chr9 | 134738527 | - |
| In-frame | ENST00000372195 | ENST00000357028 | RAPGEF1 | chr9 | 134615157 | - | MED27 | chr9 | 134738527 | - |
| In-frame | ENST00000372195 | ENST00000292035 | RAPGEF1 | chr9 | 134615157 | - | MED27 | chr9 | 134738527 | - |
| 5CDS-intron | ENST00000372195 | ENST00000474263 | RAPGEF1 | chr9 | 134615157 | - | MED27 | chr9 | 134738527 | - |
| intron-3CDS | ENST00000372190 | ENST00000357028 | RAPGEF1 | chr9 | 134615157 | - | MED27 | chr9 | 134738527 | - |
| intron-3CDS | ENST00000372190 | ENST00000292035 | RAPGEF1 | chr9 | 134615157 | - | MED27 | chr9 | 134738527 | - |
| intron-intron | ENST00000372190 | ENST00000474263 | RAPGEF1 | chr9 | 134615157 | - | MED27 | chr9 | 134738527 | - |
| intron-3CDS | ENST00000481260 | ENST00000357028 | RAPGEF1 | chr9 | 134615157 | - | MED27 | chr9 | 134738527 | - |
| intron-3CDS | ENST00000481260 | ENST00000292035 | RAPGEF1 | chr9 | 134615157 | - | MED27 | chr9 | 134738527 | - |
| intron-intron | ENST00000481260 | ENST00000474263 | RAPGEF1 | chr9 | 134615157 | - | MED27 | chr9 | 134738527 | - |
| intron-intron | ENST00000372189 | ENST00000357028 | RAPGEF1 | chr9 | 134615157 | - | MED27 | chr9 | 134769379 | - |
| intron-intron | ENST00000372189 | ENST00000292035 | RAPGEF1 | chr9 | 134615157 | - | MED27 | chr9 | 134769379 | - |
| intron-intron | ENST00000372189 | ENST00000474263 | RAPGEF1 | chr9 | 134615157 | - | MED27 | chr9 | 134769379 | - |
| 5CDS-intron | ENST00000372195 | ENST00000357028 | RAPGEF1 | chr9 | 134615157 | - | MED27 | chr9 | 134769379 | - |
| 5CDS-intron | ENST00000372195 | ENST00000292035 | RAPGEF1 | chr9 | 134615157 | - | MED27 | chr9 | 134769379 | - |
| 5CDS-intron | ENST00000372195 | ENST00000474263 | RAPGEF1 | chr9 | 134615157 | - | MED27 | chr9 | 134769379 | - |
| intron-intron | ENST00000372190 | ENST00000357028 | RAPGEF1 | chr9 | 134615157 | - | MED27 | chr9 | 134769379 | - |
| intron-intron | ENST00000372190 | ENST00000292035 | RAPGEF1 | chr9 | 134615157 | - | MED27 | chr9 | 134769379 | - |
| intron-intron | ENST00000372190 | ENST00000474263 | RAPGEF1 | chr9 | 134615157 | - | MED27 | chr9 | 134769379 | - |
| intron-intron | ENST00000481260 | ENST00000357028 | RAPGEF1 | chr9 | 134615157 | - | MED27 | chr9 | 134769379 | - |
| intron-intron | ENST00000481260 | ENST00000292035 | RAPGEF1 | chr9 | 134615157 | - | MED27 | chr9 | 134769379 | - |
| intron-intron | ENST00000481260 | ENST00000474263 | RAPGEF1 | chr9 | 134615157 | - | MED27 | chr9 | 134769379 | - |
| Frame-shift | ENST00000372189 | ENST00000357028 | RAPGEF1 | chr9 | 134471685 | - | MED27 | chr9 | 134759486 | - |
| Frame-shift | ENST00000372189 | ENST00000292035 | RAPGEF1 | chr9 | 134471685 | - | MED27 | chr9 | 134759486 | - |
| 5CDS-intron | ENST00000372189 | ENST00000474263 | RAPGEF1 | chr9 | 134471685 | - | MED27 | chr9 | 134759486 | - |
| Frame-shift | ENST00000372195 | ENST00000357028 | RAPGEF1 | chr9 | 134471685 | - | MED27 | chr9 | 134759486 | - |
| Frame-shift | ENST00000372195 | ENST00000292035 | RAPGEF1 | chr9 | 134471685 | - | MED27 | chr9 | 134759486 | - |
| 5CDS-intron | ENST00000372195 | ENST00000474263 | RAPGEF1 | chr9 | 134471685 | - | MED27 | chr9 | 134759486 | - |
| Frame-shift | ENST00000372190 | ENST00000357028 | RAPGEF1 | chr9 | 134471685 | - | MED27 | chr9 | 134759486 | - |
| Frame-shift | ENST00000372190 | ENST00000292035 | RAPGEF1 | chr9 | 134471685 | - | MED27 | chr9 | 134759486 | - |
| 5CDS-intron | ENST00000372190 | ENST00000474263 | RAPGEF1 | chr9 | 134471685 | - | MED27 | chr9 | 134759486 | - |
| intron-3CDS | ENST00000481260 | ENST00000357028 | RAPGEF1 | chr9 | 134471685 | - | MED27 | chr9 | 134759486 | - |
| intron-3CDS | ENST00000481260 | ENST00000292035 | RAPGEF1 | chr9 | 134471685 | - | MED27 | chr9 | 134759486 | - |
| intron-intron | ENST00000481260 | ENST00000474263 | RAPGEF1 | chr9 | 134471685 | - | MED27 | chr9 | 134759486 | - |
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FusionProtFeatures for RAPGEF1_MED27 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| RAPGEF1 | MED27 |
| Guanine nucleotide-releasing protein that binds to SH3domain of CRK and GRB2/ASH. Transduces signals from CRK toactivate RAS. Plays a role in the establishment of basalendothelial barrier function. Plays a role in nerve growth factor(NGF)-induced sustained activation of Rap1 and neurite outgrowth.{ECO:0000269|PubMed:17724123, ECO:0000269|PubMed:21840392,ECO:0000269|PubMed:7806500}. | Component of the Mediator complex, a coactivatorinvolved in the regulated transcription of nearly all RNApolymerase II-dependent genes. Mediator functions as a bridge toconvey information from gene-specific regulatory proteins to thebasal RNA polymerase II transcription machinery. Mediator isrecruited to promoters by direct interactions with regulatoryproteins and serves as a scaffold for the assembly of a functionalpreinitiation complex with RNA polymerase II and the generaltranscription factors. {ECO:0000269|PubMed:10882111,ECO:0000269|PubMed:9989412}. |
| 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 RAPGEF1_MED27 |
| 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. |
| >In-frame_RAPGEF1_ENST00000372195_chr9_134615157_-_MED27_ENST00000357028_chr9_134738527_-_91aa MSGGLGLRRSPEMSGKIEKAGDRPCHHCPAPLSAAPDAGCRGPILHDLVKKLHKAVPGPVPALREVSAGRPSPDMEGFPNPRSLPXHLPA >In-frame_RAPGEF1_ENST00000372195_chr9_134615157_-_MED27_ENST00000292035_chr9_134738527_-_91aa MSGGLGLRRSPEMSGKIEKAGDRPCHHCPAPLSAAPDAGCRGPILHDLVKKLHKAVPGPVPALREVSAGRPSPDMEGFPNPRSLPXHLPA |
| * Fusion transcript sequences (only coding sequence (CDS) region). |
| >In-frame_RAPGEF1_ENST00000372195_chr9_134615157_-_MED27_ENST00000357028_chr9_134738527_-_274nt ATGAGCGGCGGCCTCGGCCTCCGGCGCAGCCCGGAAATGTCCGGCAAGATCGAGAAAGCAGGTGACAGACCATGCCACCACTGCCCTGCT CCACTATCAGCTGCCCCAGATGCCGGATGTCGTGGTCCGATCCTTCATGACCTGGTTAAGAAGTTACATAAAGCTGTTCCAGGCCCCGTG CCAGCGCTGCGGGAAGTTTCTGCAGGACGGCCTTCCCCCGACATGGAGGGATTTCCGAACCCTCGAAGCCTTCCATGACACCTGCCGGCA >In-frame_RAPGEF1_ENST00000372195_chr9_134615157_-_MED27_ENST00000292035_chr9_134738527_-_274nt ATGAGCGGCGGCCTCGGCCTCCGGCGCAGCCCGGAAATGTCCGGCAAGATCGAGAAAGCAGGTGACAGACCATGCCACCACTGCCCTGCT CCACTATCAGCTGCCCCAGATGCCGGATGTCGTGGTCCGATCCTTCATGACCTGGTTAAGAAGTTACATAAAGCTGTTCCAGGCCCCGTG CCAGCGCTGCGGGAAGTTTCTGCAGGACGGCCTTCCCCCGACATGGAGGGATTTCCGAACCCTCGAAGCCTTCCATGACACCTGCCGGCA |
| * Fusion transcript sequences (Full-length transcript). |
| >In-frame_RAPGEF1_ENST00000372195_chr9_134615157_-_MED27_ENST00000357028_chr9_134738527_-_949nt CGCTGCGCTGCGGCCGGCTCGCGGGCCGGGGGAGCGGCGGCGGGCGCGCGGGAGGCGGAGCGGCGGCGGCGGGCGCGGCGGGAGCGGCTG GGCCCGGGCGGGCTGGAGCGCGGTCGCCGAGCGCAGGGCCGCGGCCGCGCGGAGCCCGCCATGCCGGCGCGGGTCTGAGGCGTGGCGAGC CAGGGCCGAGGCGAGCGGCGGGCGCGCCGCCCCTGTCGCCCCGCGGCGGCCCGGCCCGGGCCCGATGAGCGGCGGCCTCGGCCTCCGGCG CAGCCCGGAAATGTCCGGCAAGATCGAGAAAGCAGGTGACAGACCATGCCACCACTGCCCTGCTCCACTATCAGCTGCCCCAGATGCCGG ATGTCGTGGTCCGATCCTTCATGACCTGGTTAAGAAGTTACATAAAGCTGTTCCAGGCCCCGTGCCAGCGCTGCGGGAAGTTTCTGCAGG ACGGCCTTCCCCCGACATGGAGGGATTTCCGAACCCTCGAAGCCTTCCATGACACCTGCCGGCAGTAGCCCCCACGCTGGCCCCAGCCTC AGACCCCACCCAGCACCTTCCCAGACACGCAGGAAGCCCACAGAAGGCTCAGCTGGTTCCTCACTGCCCAGATGTGTACAGCTGCTCCTC CCTTTCATAAAGCAGCGCCATGTGTGCAGAGGCCACTCTTGAAGAGCAGACTCCCTCTGTGGCTGATGGGACTAATTATTCCCACTAGCC AGCGGACTGAAGGCAAAGAAGACCTTTCTAGAACCTGGTAGAAGGAAGCTGTGCAGCATGCTCCTCGTCCATGTGTGTCGGCAGTGCTGG TGTCTGTCGTCTCCGCGAGCTGTTACTGGAATGAGCCCTTGTGTTCATGGGTATCGTCATGCGGGGTTCTTGTGTTTTGTGGGGCTTGGG >In-frame_RAPGEF1_ENST00000372195_chr9_134615157_-_MED27_ENST00000292035_chr9_134738527_-_949nt CGCTGCGCTGCGGCCGGCTCGCGGGCCGGGGGAGCGGCGGCGGGCGCGCGGGAGGCGGAGCGGCGGCGGCGGGCGCGGCGGGAGCGGCTG GGCCCGGGCGGGCTGGAGCGCGGTCGCCGAGCGCAGGGCCGCGGCCGCGCGGAGCCCGCCATGCCGGCGCGGGTCTGAGGCGTGGCGAGC CAGGGCCGAGGCGAGCGGCGGGCGCGCCGCCCCTGTCGCCCCGCGGCGGCCCGGCCCGGGCCCGATGAGCGGCGGCCTCGGCCTCCGGCG CAGCCCGGAAATGTCCGGCAAGATCGAGAAAGCAGGTGACAGACCATGCCACCACTGCCCTGCTCCACTATCAGCTGCCCCAGATGCCGG ATGTCGTGGTCCGATCCTTCATGACCTGGTTAAGAAGTTACATAAAGCTGTTCCAGGCCCCGTGCCAGCGCTGCGGGAAGTTTCTGCAGG ACGGCCTTCCCCCGACATGGAGGGATTTCCGAACCCTCGAAGCCTTCCATGACACCTGCCGGCAGTAGCCCCCACGCTGGCCCCAGCCTC AGACCCCACCCAGCACCTTCCCAGACACGCAGGAAGCCCACAGAAGGCTCAGCTGGTTCCTCACTGCCCAGATGTGTACAGCTGCTCCTC CCTTTCATAAAGCAGCGCCATGTGTGCAGAGGCCACTCTTGAAGAGCAGACTCCCTCTGTGGCTGATGGGACTAATTATTCCCACTAGCC AGCGGACTGAAGGCAAAGAAGACCTTTCTAGAACCTGGTAGAAGGAAGCTGTGCAGCATGCTCCTCGTCCATGTGTGTCGGCAGTGCTGG TGTCTGTCGTCTCCGCGAGCTGTTACTGGAATGAGCCCTTGTGTTCATGGGTATCGTCATGCGGGGTTCTTGTGTTTTGTGGGGCTTGGG |
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FusionGenePPI for RAPGEF1_MED27 |
| 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 |
| RAPGEF1 | BCAR1, HCK, CRKL, NEDD9, GRB2, CRK, SHC1, CBL, ATXN1, MBIP, RPS15, SLC20A1, MOV10, NXF1, ABL1, EGFR, SPATS2L, RAP1A, RAP2B | MED27 | MED10, MED9, MED29, MED19, MED28, MED26, MED30, MED22, MED1, MED12, MED18, ZC3H13, TRIP4, OBFC1, QKI, TADA2A, MED14, MED4, FBXW7, EPAS1, POLR2C, ARFGAP1, AFP, RBPJ, SOX5, CDK8, CDK19, ESR1, MED7, CCNC, MED16, MED17, MED11, MED13, MED13L, MED15, MED20, MED24, MED6, MED8, MED23, MED21 |
| - 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 RAPGEF1_MED27 |
| 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 RAPGEF1_MED27 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
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