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Fusion gene ID: 21460 |
FusionGeneSummary for MED13L_PTPN23 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: MED13L_PTPN23 | Fusion gene ID: 21460 | Hgene | Tgene | Gene symbol | MED13L | PTPN23 | Gene ID | 23389 | 25930 |
| Gene name | mediator complex subunit 13 like | protein tyrosine phosphatase, non-receptor type 23 | |
| Synonyms | MRFACD|PROSIT240|THRAP2|TRAP240L | HD-PTP|HDPTP|PTP-TD14 | |
| Cytomap | 12q24.21 | 3p21.31 | |
| Type of gene | protein-coding | protein-coding | |
| Description | mediator of RNA polymerase II transcription subunit 13-likethyroid hormone receptor-associated protein 2thyroid hormone receptor-associated protein complex 240 kDa component-like | tyrosine-protein phosphatase non-receptor type 23his domain-containing protein tyrosine phosphataseprotein tyrosine phosphatase TD14 | |
| Modification date | 20180523 | 20180519 | |
| UniProtAcc | Q71F56 | Q9H3S7 | |
| Ensembl transtripts involved in fusion gene | ENST00000281928, ENST00000551197, | ENST00000431726, ENST00000265562, | |
| Fusion gene scores | * DoF score | 21 X 13 X 12=3276 | 4 X 4 X 1=16 |
| # samples | 23 | 4 | |
| ** MAII score | log2(23/3276*10)=-3.83222959069663 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(4/16*10)=1.32192809488736 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | |
| Context | PubMed: MED13L [Title/Abstract] AND PTPN23 [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 | BF357082 | MED13L | chr12 | 116667232 | + | PTPN23 | chr3 | 47439486 | - |
| * 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 | ENST00000281928 | ENST00000431726 | MED13L | chr12 | 116667232 | + | PTPN23 | chr3 | 47439486 | - |
| intron-intron | ENST00000281928 | ENST00000265562 | MED13L | chr12 | 116667232 | + | PTPN23 | chr3 | 47439486 | - |
| intron-intron | ENST00000551197 | ENST00000431726 | MED13L | chr12 | 116667232 | + | PTPN23 | chr3 | 47439486 | - |
| intron-intron | ENST00000551197 | ENST00000265562 | MED13L | chr12 | 116667232 | + | PTPN23 | chr3 | 47439486 | - |
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FusionProtFeatures for MED13L_PTPN23 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| MED13L | PTPN23 |
| 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. This subunit may specifically regulatetranscription of targets of the Wnt signaling pathway and SHHsignaling pathway. | Plays a role in sorting of endocytic ubiquitinatedcargos into multivesicular bodies (MVBs) via its interaction withthe ESCRT-I complex (endosomal sorting complex required fortransport I), and possibly also other ESCRT complexes. May act asa negative regulator of Ras-mediated mitogenic activity. Plays arole in ciliogenesis. {ECO:0000269|PubMed:18434552,ECO:0000269|PubMed:20393563, ECO:0000269|PubMed:21757351}. |
| 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 MED13L_PTPN23 |
| 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 MED13L_PTPN23 |
| 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 MED13L_PTPN23 |
| 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 MED13L_PTPN23 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | MED13L | C1837341 | Transposition of the Great Arteries, Dextro-Looped 1 | 1 | CTD_human;UNIPROT |
| Hgene | MED13L | C3714756 | Intellectual Disability | 1 | CTD_human |
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