The Rice Word Landscape: A Detailed Catalogue of the Rice Motif Content in the Non-coding Regions

Among the different areas of molecular biology concerning the detailed study of different parts of the cell, such as genomics, proteomics, and metabolomics, different new areas of study are emerging which entail the analysis of different parts of the genome, such as the prediction of genes or different kinds of transcription factor binding sites (TFBSs). The goal of this study was to construct and analyze a catalogue of all statistically relevant putative functional octamer words or motifs (which we have termed the “motifome” of a given organism) found within first introns, promoters, the 5′ and 3′ untranslated regions (UTRs), and the entire genome of japonica rice, and compare them to results attained from a previous analysis performed on the Arabidopsis genome. We found a number of novel motifs in different sets of non-coding rice sequence sets. The diversity of motifs in rice was higher in Arabidopsis , implicating a higher mutation turnover. While common motifs were found between the two species, motif pairs were missing, showing the difference between the regulatory machinery between rice and Arabidopsis .