uORFdb


36305828	The new uORFdb: integrating literature, sequence, and variation data in a central hub for uORF research. [PMID: 36305828] Manske F, Ogoniak L, Jürgens L, Grundmann N, Makałowski W, Wethmar K. Abstract 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. Nucleic Acids Res. 2022:() \| 14 Citations (from Europe PMC, 2025-03-15)
24163100	uORFdb--a comprehensive literature database on eukaryotic uORF biology. [PMID: 24163100] Wethmar K, Barbosa-Silva A, Andrade-Navarro MA, Leutz A. Abstract 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. Nucleic Acids Res. 2014:42(Database issue) \| 58 Citations (from Europe PMC, 2025-03-15)

The new uORFdb: integrating literature, sequence, and variation data in a central hub for uORF research. [PMID: 36305828]

Manske F, Ogoniak L, Jürgens L, Grundmann N, Makałowski W, Wethmar K.

Abstract

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.

Nucleic Acids Res. 2022:() | 14 Citations (from Europe PMC, 2025-03-15)

uORFdb--a comprehensive literature database on eukaryotic uORF biology. [PMID: 24163100]

Wethmar K, Barbosa-Silva A, Andrade-Navarro MA, Leutz A.

Abstract

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.

Nucleic Acids Res. 2014:42(Database issue) | 58 Citations (from Europe PMC, 2025-03-15)

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
Country/Region:	Germany

Data type:	DNA Protein RNA
Data object:	Animal
Database category:	Gene genome and annotation Genotype phenotype and variation Health and medicine Literature
Major species:	Homo sapiens Drosophila melanogaster Mus musculus Danio rerio Rattus norvegicus Bos taurus Xenopus laevis Xenopus tropicalis Macaca mulatta Gallus gallus Pongo abelii Sus scrofa Pan troglodytes
Keywords:	translational control upstream open reading frame literature browser model

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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Database Commons a catalog of worldwide biological databases