A large number of novel coding small open reading frames in the intergenic regions of the Arabidopsis thaliana genome are transcribed and/or under purifying selection.

ABSTRACT: Large-scale cDNA sequencing projects and tiling array studies have revealed the presence of many unannotated genes. For protein coding genes, small coding sequences may not be identified by gene finders because of the conservative nature of prediction algorithms. In this study, we identified small open reading frames (sORFs) with high coding potential by a simple gene finding method (Coding Index, CI) based on the nucleotide composition bias found in most coding sequences. Applying this method to 18 Arabidopsis thaliana and 84 yeast sORF genes with evidence of expression at the protein level gives 100% accurate prediction. In the A. thaliana genome, we identified 7159 sORFs that are likely coding sequences (coding sORFs) with the CI measure at the 1% false-positive rate. To determine if th

SUBMITTER: Hanada K 

PROVIDER: S-EPMC1855179 | biostudies-literature | 2007 May

REPOSITORIES: biostudies-literature