title: The rice word landscape--a detailed catalog of the rice motif content in the noncoding regions.
abstract: Among the different areas of molecular biology concerning the detailed study of different parts of the cell such as genomics, proteomics, or metabolomics, different new areas of study are emerging that 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 is to draw up and analyze a catalog of all statistically relevant putative functional octamer words or motifs found within first introns, promoters, the 5' and 3' 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 noncoding rice sequence sets. The diversity of motifs in rice was higher in Arabidopsis, implicating a higher mutation turnover. Although common motifs were found between the two species, motif pairs were missing, showing the difference between the regulatory machinery between rice and Arabidopsis.
authors: Institute of Plant Biology, Biological Research Center, Szeged, Hungary. csmatyi@brc.hu
authors: Mátyás
authors: M
authors: Cserháti
authors: Zoltán
authors: Z
authors: Turóczy
authors: Dénes
authors: D
authors: Dudits
authors: János
authors: J
authors: Györgyey
mesh_terms: D017360:Arabidopsis / Q000235:genetics; D019295:Computational Biology / Q000379:methods; D018744:DNA, Plant / Q000737:chemistry*; D030561:Databases, Nucleic Acid; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D059372:Nucleotide Motifs; D012275:Oryza / Q000235:genetics* / Q000378:metabolism; D017422:Sequence Analysis, DNA; D020506:Untranslated Regions
chemical_list: D018744:DNA, Plant; D020506:Untranslated Regions