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Open Access Research article

Conserved upstream open reading frames in higher plants

Michael K Tran1, Carolyn J Schultz2 and Ute Baumann1*

Author Affiliations

1 Australian Centre for Plant Functional Genomics PMB 1 Glen Osmond SA 5064, Australia

2 School of Agriculture, Food, and Wine, University of Adelaide, Waite Campus, Glen Osmond, SA 5064, Australia

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BMC Genomics 2008, 9:361  doi:10.1186/1471-2164-9-361

Published: 31 July 2008



Upstream open reading frames (uORFs) can down-regulate the translation of the main open reading frame (mORF) through two broad mechanisms: ribosomal stalling and reducing reinitiation efficiency. In distantly related plants, such as rice and Arabidopsis, it has been found that conserved uORFs are rare in these transcriptomes with approximately 100 loci. It is unclear how prevalent conserved uORFs are in closely related plants.


We used a homology-based approach to identify conserved uORFs in five cereals (monocots) that could potentially regulate translation. Our approach used a modified reciprocal best hit method to identify putative orthologous sequences that were then analysed by a comparative R-nomics program called uORFSCAN to find conserved uORFs.


This research identified new genes that may be controlled at the level of translation by conserved uORFs. We report that conserved uORFs are rare (<150 loci contain them) in cereal transcriptomes, are generally short (less than 100 nt), highly conserved (50% median amino acid sequence similarity), position independent in their 5'-UTRs, and their start codon context and the usage of rare codons for translation does not appear to be important.