Figure 4

HAC1 stem-loop motif used for the genome wide computational consensus search. (a) Predicted secondary structure and sequence flanking both 5' and 3' Ire1p cleavage sites in HAC1 mRNA. Cleavage occurs after a G residue located at the third position of the seven-nucleotide loop. (b) Parameters used for the computer search. A four base-pair stem with a seven-nucleotide loop with C at the first position, and G both at third and sixth positions, are determined experimentally as described previously [14]. Possible base-pairs (N = N') in the stem include AU, UA, GC, CG, UG, GU. The complete output of the computational screen is listed in Additional data file 2.