| URL: | https://www.bioinformatics.uni-muenster.de/tools/uorfdb |
| Full name: | upstream open reading frames database |
| Description: | Database of upstream open reading frames that enables users to directly access sequence information from 13 species, graphical displays, literature, and genetic variation data from cancer patients. Links to external resources (UCSC Genome Browser, dbSNP, ClinVar) facilitate in-depth analysis of individual uORFs. |
| Year founded: | 2014 |
| Last update: | 2022-10-28 |
| Version: | v2.0 |
| Accessibility: |
Accessible
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| Country/Region: | Germany |
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| University/Institution: | University Hospital Münster |
| Address: | Albert-Schweitzer-Campus 1 (A1); 48149 Münster |
| City: | Münster |
| Province/State: | North Rhine-Westphalia |
| Country/Region: | Germany |
| Contact name (PI/Team): | Klaus Wethmar |
| Contact email (PI/Helpdesk): | klaus.wethmar@ukmuenster.de |
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The new uORFdb: integrating literature, sequence, and variation data in a central hub for uORF research. [PMID: 36305828]
Upstream open reading frames (uORFs) are initiated by AUG or near-cognate start codons and have been identified in the transcript leader sequences of the majority of eukaryotic transcripts. Functionally, uORFs are implicated in downstream translational regulation of the main protein coding sequence and may serve as a source of non-canonical peptides. Genetic defects in uORF sequences have been linked to the development of various diseases, including cancer. To simplify uORF-related research, the initial release of uORFdb in 2014 provided a comprehensive and manually curated collection of uORF-related literature. Here, we present an updated sequence-based version of uORFdb, accessible at https://www.bioinformatics.uni-muenster.de/tools/uorfdb. The new uORFdb enables users to directly access sequence information, graphical displays, and genetic variation data for over 2.4 million human uORFs. It also includes sequence data of >4.2 million uORFs in 12 additional species. Multiple uORFs can be displayed in transcript- and reading-frame-specific models to visualize the translational context. A variety of filters, sequence-related information, and links to external resources (UCSC Genome Browser, dbSNP, ClinVar) facilitate immediate in-depth analysis of individual uORFs. The database also contains uORF-related somatic variation data obtained from whole-genome sequencing (WGS) analyses of 677 cancer samples collected by the TCGA consortium. |
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uORFdb--a comprehensive literature database on eukaryotic uORF biology. [PMID: 24163100]
Approximately half of all human transcripts contain at least one upstream translational initiation site that precedes the main coding sequence (CDS) and gives rise to an upstream open reading frame (uORF). We generated uORFdb, publicly available at http://cbdm.mdc-berlin.de/tools/uorfdb, to serve as a comprehensive literature database on eukaryotic uORF biology. Upstream ORFs affect downstream translation by interfering with the unrestrained progression of ribosomes across the transcript leader sequence. Although the first uORF-related translational activity was observed >30 years ago, and an increasing number of studies link defective uORF-mediated translational control to the development of human diseases, the features that determine uORF-mediated regulation of downstream translation are not well understood. The uORFdb was manually curated from all uORF-related literature listed at the PubMed database. It categorizes individual publications by a variety of denominators including taxon, gene and type of study. Furthermore, the database can be filtered for multiple structural and functional uORF-related properties to allow convenient and targeted access to the complex field of eukaryotic uORF biology. |