Identification of putative regulatory upstream ORFs in the yeast genome using heuristics and evolutionary conservation

Marija Cvijović¹^,3 , Daniel Dalevi² , Elizabeth Bilsland¹^,4 , Graham JL Kemp² and Per Sunnerhagen¹

¹Department of Cell and Molecular Biology, Lundberg Laboratory, Göteborg University, PO Box 462 SE-405 30 Göteborg, Sweden

²Department of Computer Science and Engineering, Chalmers University of Technology, SE-412 96 Göteborg, Sweden

³Max-Planck Institute for Molecular Genetics, Ihnestraße 63, D-14195 Berlin, Germany

⁴Biochemistry Department, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK

author email corresponding author email

BMC Bioinformatics 2007, 8:295doi:10.1186/1471-2105-8-295


Published:	8 August 2007

Additional files

Additional file 1:

uORFs in the dataset by Pesole et al. [18] of verified 5'-UTRs, which we have verified to be conserved. Numbering of uORFs is 5' to 3'.

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Additional file 2:

The 252 genes with conserved uORFs and with a maximal confidence factor score (0.98). Information given for each gene from left to right: Systematic name of gene, length of intergenic region in nucleotides, length of uORF in codons, position in nucleotides of uORF relative to ATG of main ORF. The first uORF listed is always the most distant from the main ATG. Genes appear in the list in no particular order.

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Additional file 3:

uORFs identified in verified 5'-UTRs by Zhang and Dietrich [19]. Numbering of uORFs is 5' to 3'.

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Additional file 4:

uORFs predicted to be functional by Zhang and Dietrich [17]. Numbering of uORFs 5' to 3'.

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Additional file 5:

Attribute values of the expert system and their certainty factor

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