Automated conserved non-coding sequence (CNS) discovery reveals differences in gene content and promoter evolution among grasses.

ABSTRACT: Conserved non-coding sequences (CNS) are islands of non-coding sequence that, like protein coding exons, show less divergence in sequence between related species than functionless DNA. Several CNSs have been demonstrated experimentally to function as cis-regulatory regions. However, the specific functions of most CNSs remain unknown. Previous searches for CNS in plants have either anchored on exons and only identified nearby sequences or required years of painstaking manual annotation. Here we present an open source tool that can accurately identify CNSs between any two related species with sequenced genomes, including both those immediately adjacent to exons and distal sequences separated by >12 kb of non-coding sequence. We have used this tool to characterize new motifs, associate CNSs w

SUBMITTER: Turco G 

PROVIDER: S-EPMC3708275 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature