Ribosome recruitment via an Internal Ribosome Entry Site (IRES) is an alternative way to initiate translation in eukaryotic cells. IRESs were originally discovered in some viruses but several cellular mRNAs have been proposed to contain IRES sequences as well. These sequences are very diverse and are present in a growing list of mRNAs. The Rfam
database is a comprehensive resource for internal ribosome entry sites and presents currently available general information as well as detailed data for each IRES. Several
subsets of data are classified according to the viral taxon (for viral IRESs), to the gene product function (for cellular IRESs), to the possible cellular regulation or to the transacting factor that mediates IRES function. Each Rfam IRES family is associated with a secondary structure model. In many cases
this model is based on a limited number of primary sequences. The aim of this study was to examine the reliability of the secondary structure models by considering a larger number of sequences. Therefore, a number of novel IRES 'homologues' were identified in a range of different vertebrates and using different bioinformatics tools secondary
structure was predicted or examined using these novel sequences. In general however, there was no support for the secondary structure models proposed in Rfam. |