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

Table 1 Evolutionary conservation of uORFs highlighted by Vilela and McCarthy [3]. Genes with conserved uORFs are shown in bold.

Gene	uORF conservation¹	If predicted not to be functional, reason for this	Evidence about functional role
*CLN3*	yes (1/1; 4/6)		[26]
*GCN4*	yes (4/4; 7/7)		[6]
INO2	no (0/1; 0/6)	uORF too long
PPR1	no (0/1; 0/6)	uORF too close to main AUG
SCO1	no (0/1; 0/5)	uORF too close to main AUG	[32]²
*CPA1*	yes (1/1; 5/5)		[4]
*HAP4*	yes (2/2; 4/4)		[43]³
LEU4	no (0/1; 0/7)	uORF too close to main AUG
*TIF4631*	yes (4/6; 4/6)		[31]³
*YAP1*	yes (1/1; 3/5)		[27]
*YAP2*	yes (2/2; 3/3)		[27]
CBS1	no (0/1; 0/5)	uORF too close to main AUG	[32]²
DCD1	no (0/1; 0/7)	uORF too close to main AUG
*HOL1*	yes (1/1; 4/4)		[29]
*PET111*	yes (3/4; 3/4)		[30]⁴
SCH9	no (0/1; 0/6)	uORF too long (55 codons)

The STA1-3 genes mentioned by Vilela and McCarthy are not present in the standard S288c genome sequence and were not included in this analysis.
¹ Numbers between parentheses denote: (number of uORFs conserved/total number of uORFs; number of species where uORFs are conserved/total number of species where orthologue could be identified)
² Evidence against translational control by uORFs
³ Evidence for translation using an IRES mechanism
⁴ Pet111 controls translation of another mRNA, but no evidence for uORF control of PET111 expression

ISSN: 1471-2105