ARED-Plus: an updated and expanded database of AU-rich element-containing mRNAs and pre-mRNAs

Abstract

Here we present an updated version of the AU-Rich Element Database (ARED-Plus) that is freely available at http://brp.kfshrc.edu.sa/ared. AREs are conserved sequence elements that were first discovered in the 3'UTR of mammalian transcripts. Over the past years, we compiled a series of ARE databases that revealed the extent and wide distribution of ARE-containing genes. For this update, we adopted an optimized search algorithm with improved specificity and sensitivity in ARE selection. The designation of the different ARE clusters was simplified by directly correlating the number of the ARE cluster to the number of overlapping AUUUA pentamers. Additionally, the new database was expanded to include genes with intronic AREs (pre-mRNAs) and their characteristics since recent observations reported their abundance and biological significance. Several enhancements were incorporated such as customized column view, additional search options and live search functionalities. The new version includes links to AREsite and AREScore, two related ARE assessment algorithms for further evaluation of the ARE characteristics. ARED-Plus now contains an updated repertoire of AREs in the human transcriptome that may be useful in several research fields.

Figure 1.

Output table of a basic 3′UTR and intron ARE search. Typically, the output table contains the gene names, Ensembl gene IDs, genes definition, Ensembl transcript IDs, ARE-clusters and sequence, in the sequence pane a link to ARE SCORE is available, start and end location of the ARE in the transcript, a link to the ARE site and a details link to additional information such as GO annotations, RefSeq, UNIGENE and Entrez IDs. If the gene contains intronic AREs their number will be displayed along with a link that directs the user to them.