|
||||||
|
 | |
| |
| |
| |
| |
|
Fusion gene ID: 21459 |
FusionGeneSummary for MED13L_PRIM1 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: MED13L_PRIM1 | Fusion gene ID: 21459 | Hgene | Tgene | Gene symbol | MED13L | PRIM1 | Gene ID | 23389 | 5557 |
| Gene name | mediator complex subunit 13 like | DNA primase subunit 1 | |
| Synonyms | MRFACD|PROSIT240|THRAP2|TRAP240L | p49 | |
| Cytomap | 12q24.21 | 12q13.3 | |
| 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 | DNA primase small subunitDNA primase 1DNA primase 49 kDa subunitDNA primase subunit 48primase (DNA) subunit 1primase p49 subunitprimase polypeptide 1, 49kDaprimase, DNA, polypeptide 1 (49kDa) | |
| Modification date | 20180523 | 20180523 | |
| UniProtAcc | Q71F56 | P49642 | |
| Ensembl transtripts involved in fusion gene | ENST00000281928, ENST00000551197, | ENST00000338193, ENST00000552408, | |
| Fusion gene scores | * DoF score | 21 X 13 X 12=3276 | 7 X 6 X 7=294 |
| # samples | 23 | 8 | |
| ** MAII score | log2(23/3276*10)=-3.83222959069663 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(8/294*10)=-1.877744249949 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: MED13L [Title/Abstract] AND PRIM1 [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 | BRCA | TCGA-AR-A1AV-01A | MED13L | chr12 | 116675273 | - | PRIM1 | chr12 | 57133147 | - |
| * 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 |
| In-frame | ENST00000281928 | ENST00000338193 | MED13L | chr12 | 116675273 | - | PRIM1 | chr12 | 57133147 | - |
| 5CDS-intron | ENST00000281928 | ENST00000552408 | MED13L | chr12 | 116675273 | - | PRIM1 | chr12 | 57133147 | - |
| 5UTR-3CDS | ENST00000551197 | ENST00000338193 | MED13L | chr12 | 116675273 | - | PRIM1 | chr12 | 57133147 | - |
| 5UTR-intron | ENST00000551197 | ENST00000552408 | MED13L | chr12 | 116675273 | - | PRIM1 | chr12 | 57133147 | - |
Top |
FusionProtFeatures for MED13L_PRIM1 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| MED13L | PRIM1 |
| 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. | DNA primase is the polymerase that synthesizes small RNAprimers for the Okazaki fragments made during discontinuous DNAreplication. |
| 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 |
| Hgene | >MED13L | chr12:116675273 | chr12:57133147 | ENST00000281928 | - | 2 | 31 | 1566_1610 | 103 | 2211 | Compositional bias | Note=Ser-rich |
| Hgene | >MED13L | chr12:116675273 | chr12:57133147 | ENST00000281928 | - | 2 | 31 | 1225_1229 | 103 | 2211 | Motif | Note=LXXLL motif 2 |
| Hgene | >MED13L | chr12:116675273 | chr12:57133147 | ENST00000281928 | - | 2 | 31 | 669_673 | 103 | 2211 | Motif | Note=LXXLL motif 1 |
| Hgene | >MED13L | chr12:116675273 | chr12:57133147 | ENST00000281928 | - | 2 | 31 | 1380_1401 | 103 | 2211 | Region | Note=Leucine-zipper |
| Tgene | PRIM1 | chr12:116675273 | chr12:57133147 | ENST00000338193 | - | 8 | 13 | 121_131 | 327 | 421 | Motif | Note=Zinc knuckle motif |
Top |
FusionGeneSequence for MED13L_PRIM1 |
| 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_MED13L_ENST00000281928_chr12_116675273_-_PRIM1_ENST00000338193_chr12_57133147_-_197aa MTAAANWVANGASLEDCHSNLFSLAELTGIKWRRYNFGGHGDCGPIISAPAQDDPILLSFIRCLQANLLCVWRRDVKPDCKELWIFWWGD EPNLVGVIHHELQGRISVPIDLQKVDQFDPFTVPTISFICRELDAISTNEEEKEENEAESDVKHRTRDYKKTSLAPYVKVFEHFLENLDK |
| * Fusion transcript sequences (only coding sequence (CDS) region). |
| >In-frame_MED13L_ENST00000281928_chr12_116675273_-_PRIM1_ENST00000338193_chr12_57133147_-_591nt ATGACTGCGGCAGCGAACTGGGTGGCGAACGGGGCGAGCCTGGAGGATTGTCACTCCAACCTCTTTTCGCTGGCTGAACTCACGGGAATC AAATGGCGTAGGTACAATTTTGGAGGGCATGGGGACTGTGGACCCATAATTTCAGCCCCAGCCCAAGATGATCCAATTCTGTTAAGTTTC ATCCGCTGTCTGCAAGCTAACCTGCTTTGTGTATGGCGTCGTGATGTCAAACCAGATTGCAAAGAGTTATGGATATTCTGGTGGGGAGAT GAACCCAACCTAGTGGGTGTAATACATCATGAACTGCAGGGTCGCATATCTGTGCCTATTGATTTGCAGAAAGTGGACCAGTTTGATCCA TTTACTGTTCCGACCATAAGCTTCATCTGCCGTGAATTGGATGCCATTTCCACTAATGAAGAGGAAAAAGAGGAGAATGAAGCTGAATCT GATGTCAAACATAGAACCAGAGATTATAAGAAGACCAGTCTAGCACCTTATGTGAAAGTTTTTGAACATTTTCTTGAAAATCTGGATAAA |
| * Fusion transcript sequences (Full-length transcript). |
| >In-frame_MED13L_ENST00000281928_chr12_116675273_-_PRIM1_ENST00000338193_chr12_57133147_-_891nt CCCCCCCGCCAGCCCGGGCCCGCTGCCCCCGGCGCGGCGTCGCCGCGGCGCCTCCCGCCTGCCCGCCGGCCCTCGCGCCCTCCCCCGGCG GCGGCGGCGGCCCGGCCGCCCCGCGCTCCCCGGCGAGGCGCCGCCGCCCGGCCCGGCCTCGCCTCGGACGCCTCGCTCCGACATGCCCCG CTCTGGCGGCCGGGCTCGCGGAGGATCATGACTGCGGCAGCGAACTGGGTGGCGAACGGGGCGAGCCTGGAGGATTGTCACTCCAACCTC TTTTCGCTGGCTGAACTCACGGGAATCAAATGGCGTAGGTACAATTTTGGAGGGCATGGGGACTGTGGACCCATAATTTCAGCCCCAGCC CAAGATGATCCAATTCTGTTAAGTTTCATCCGCTGTCTGCAAGCTAACCTGCTTTGTGTATGGCGTCGTGATGTCAAACCAGATTGCAAA GAGTTATGGATATTCTGGTGGGGAGATGAACCCAACCTAGTGGGTGTAATACATCATGAACTGCAGGGTCGCATATCTGTGCCTATTGAT TTGCAGAAAGTGGACCAGTTTGATCCATTTACTGTTCCGACCATAAGCTTCATCTGCCGTGAATTGGATGCCATTTCCACTAATGAAGAG GAAAAAGAGGAGAATGAAGCTGAATCTGATGTCAAACATAGAACCAGAGATTATAAGAAGACCAGTCTAGCACCTTATGTGAAAGTTTTT GAACATTTTCTTGAAAATCTGGATAAATCCCGAAAAGGAGAACTTCTTAAGAAGAGTGATTTACAAAAAGATTTCTGAAGACAGAGCTCC |
Top |
FusionGenePPI for MED13L_PRIM1 |
| 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 |
| MED13L | MED10, MED9, MED29, MED19, MED28, MED26, FBXW7, MED1, CDK8, CDK19, MED7, CCNC, HIF1A, MED12, MED16, MED27, MED6, MED4, MED23, SORT1, SYNCRIP, SGTB, MED21, MED18, TRIM25 | PRIM1 | XRCC5, RAE1, RPA1, RPA2, RPA3, COPS6, POLA1, PRIM2, POLA2, POLE, MDC1, MMS19, FAM96B, CIAO1, MOV10, NXF1, EGFR, KLHL20, OBFC1, LIPH, CCAR1, DUSP9, NLGN4Y, RNF31, DCAF10, NCAPH2, C6orf141, AK9 |
| - 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 |
Top |
RelatedDrugs for MED13L_PRIM1 |
| 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 |
Top |
RelatedDiseases for MED13L_PRIM1 |
| 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 |
Copyright 2018-Present -The University of Texas Health Science Center at Houston (UTHealth)
|