Ribosomal crosslinking data
Internal Ribosome Entry Sites (IRES) are cis-acting RNA sequences able to mediate internal entry of the 40S ribosomal subunit on some eukaryotic and viral messenger RNAs upstream of a translation initiation codon. These sequences are very diverse and are present in a growing list of mRNAs. Novel IRES sequences continue to be added to public databases every year and the list of unknown IRESes is certainly still very large. The IRES database is a comprehensive WWW ressource for internal ribosome entry sites and presents currently available general informations as well as detailed data for each IRES. It is a searchable, periodically updated collection of IRES RNA sequences. Sequences are presented in FASTA form and hotlinked to NCBI GenBank files. Several subsets of data are classified according to the viral taxon (for viral IRESes), to the gene product function (for cellular IRESes), to the possible cellular regulation or to the trans-acting factor that mediates IRES function. This database is accessible at http://ifr31w3.toulouse.inserm.fr/IRESdatabase/.
IRESite is a searchable collection of data concerning the Internal Ribosome Entry Segments (IRES) both of viral and cellular origin. IRESs are the RNA regions which are mostly defined functionally by their ability to attract a eukaryotic ribosomal translation initiation complex independently of presence of the commonly utilized 5 -terminal 7mG cap structure and thus to promote translation initiation even at the internal part of the RNA molecule.
IRESite can provide a broad set of information referring to particular IRES - briefly: primary sequence data, functional data, RNA structure and possible ribosomal RNA complementarity data, RNA:protein interaction data, links to primary databases, information about the relevant experiments and more. Most of the data are not available in the primary databases and are manually extracted from literature sources by IRESite curators. New data can also be submitted through the publicly available IRESite web interface after creating a personal account, however their release needs the curators approval.
Brief graphical overview of the database is present at http://www.iresite.org/docs/iresite.pdf
Funding was provided by the Czech Science Foundation (Grant No. 204/03/1487), by Charles University (Grant No. 251/2004/B-BIO/PrF) and by the Czech Ministry of Education (Grant No. MSM 0021620813).