title: Genome-wide analysis of rice (Oryza sativa L. subsp. japonica) TATA box and Y Patch promoter elements.
abstract: The TATA box is one of the best characterized transcription factor binding sites. However, it is not a ubiquitous element of core promoters, and other sequence motifs such as Y Patches seem to play a major role in plants. Here, we present a first genome-wide computational analysis of the TATA box and Y Patch distribution in rice (Oryza sativa L. subsp. japonica) promoter sequences. Utilizing a probabilistic sequence model, we ascertain that only approximately 19% of rice genes possess the TATA box, but approximately 50% contain one or more Y Patches in their core promoters. By computational processing of identified elements, we generated extended TATA box and Y Patch nucleotide frequency matrices capable of predicting these motifs in plants with a high degree of confidence.
authors.affiliation: Department of Genetics, Faculty of Natural Sciences, Comenius University, Mlynská dolina B-1, 842 15 Bratislava, Slovakia. civan@fns.uniba.sk
authors.forename: P
authors.initials: P
authors.lastname: Civán
authors.forename: M
authors.initials: M
authors.lastname: Svec
mesh_terms: D018745:Genome, Plant; D012275:Oryza / Q000235:genetics*; D011401:Promoter Regions, Genetic / Q000235:genetics*; D012045:Regulatory Sequences, Nucleic Acid / Q000235:genetics*; D016385:TATA Box / Q000235:genetics*