title: Compositional gradients in Gramineae genes.
abstract: In this study, we describe a property of Gramineae genes, and perhaps all monocot genes, that is not observed in eudicot genes. Along the direction of transcription, beginning at the junction of the 5'-UTR and the coding region, there are gradients in GC content, codon usage, and amino-acid usage. The magnitudes of these gradients are large enough to hinder the annotation of the rice genome and to confound the detection of protein homologies across the monocot-eudicot divide.
authors.affiliation: Hangzhou Genomics Institute, Institute of Bioinformatics of Zhejiang University, Key Laboratory of Bioinformatics of Zhejiang Province, Hangzhou 310007, China. gksw@u.washington.edu
authors.forename: Gane Ka-Shu
authors.initials: GK
authors.lastname: Wong
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.forename: Lin
authors.initials: L
authors.lastname: Tao
authors.forename: Jun
authors.initials: J
authors.lastname: Tan
authors.forename: JianGuo
authors.initials: J
authors.lastname: Zhang
authors.forename: Douglas A
authors.initials: DA
authors.lastname: Passey
authors.forename: Jun
authors.initials: J
authors.lastname: Yu
mesh_terms: D000596:Amino Acids / Q000235:genetics; D017360:Arabidopsis / Q000235:genetics; D003062:Codon / Q000235:genetics; D020862:GC Rich Sequence / Q000235:genetics; D017343:Genes, Plant / Q000235:genetics*; D005815:Genetic Code / Q000235:genetics; D018745:Genome, Plant; D007438:Introns / Q000235:genetics; D012275:Oryza / Q000235:genetics; D006109:Poaceae / Q000235:genetics*; D014026:Nicotiana / Q000235:genetics; D003313:Zea mays / Q000235:genetics
chemical_list: D000596:Amino Acids; D003062:Codon