IRESite: the database of experimentally verified IRES structures (www.iresite.org).
IRESite is an exhaustive, manually annotated non-redundant relational database focused on the IRES elements (Internal Ribosome Entry Site) and containing information not available in the primary public databases. IRES elements were originally found in eukaryotic viruses hijacking initiation of translation of their host. Later on, they were also discovered in 5'-untranslated regions of some eukaryotic mRNA molecules. Currently, IRESite presents up to 92 biologically relevant aspects of every experiment, e.g. the nature of an IRES element, its functionality/defectivity, origin, size, sequence, structure, its relative position with respect to surrounding protein coding regions, positive/negative controls used in the experiment, the reporter genes used to monitor IRES activity, the measured reporter protein yields/activities, and references to original publications as well as cross-references to other databases, and also comments from submitters and our curators. Furthermore, the site presents the known similarities to rRNA sequences as well as RNA-protein interactions. Special care is given to the annotation of promoter-like regions. The annotated data in IRESite are bound to mostly complete, full-length mRNA, and whenever possible, accompanied by original plasmid vector sequences. New data can be submitted through the publicly available web-based interface at http://www.iresite.org and are curated by a team of lab-experienced biologists.
Mokrejs
Martin
M
Charles University, Faculty of Science, Department of Genetics and Microbiology, Vinicna 5, Prague 2, 128 44, Czech Republic. mmokrejs@iresite.org
Vopálenský
Václav
V
Kolenaty
Ondrej
O
Masek
Tomás
T
Feketová
Zuzana
Z
Sekyrová
Petra
P
Skaloudová
Barbora
B
Kríz
Vítezslav
V
Pospísek
Martin
M
D020121:5' Untranslated Regions / Q000737:chemistry*; D030561:Databases, Nucleic Acid; D020407:Internet; D010442:Peptide Chain Initiation, Translational; D010448:Peptide Initiation Factors / Q000378:metabolism; D010957:Plasmids / Q000737:chemistry; D011401:Promoter Regions, Genetic; D012333:RNA, Messenger / Q000737:chemistry; D012367:RNA, Viral / Q000737:chemistry; D038621:Regulatory Sequences, Ribonucleic Acid; D014584:User-Computer Interface
D020121:5' Untranslated Regions; D010448:Peptide Initiation Factors; D012333:RNA, Messenger; D012367:RNA, Viral; D038621:Regulatory Sequences, Ribonucleic Acid