A guideline for the annotation of UTR regulatory elements in the UTRsite collection

Gene expression regulatory elements are scattered in gene promoters and pre-mRNAs. In particular, RNA elements lying in untranslated regions (5? and 3?UTRs) are poorly studied because of their peculiar features (i.e., a combination of primary and secondary structure elements) which also pose remarkable computational challenges. Several years ago, we began collecting experimentally characterized UTR regulatory elements, developing the specialized database UTRsite. This paper describes the detailed guidelines to annotate cis-regulatory elements in 5? and 3? UnTranslated Regions (UTRs) by computational analyses, retracing all main steps used by UTRsite curators.