Table 2.
Genes containing NMD signatures in the IR events found in pfd4, pfd2,4,6 and lsm8-1 mutants
| Genes with NMD-features | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Genes with events | Genes analyzed | PTCa | 3′UTR > 350ntb | SC→intron > 55ntc | 5′uORFd | uORF overlape | NMD genes (%)f | Non-NMD genes (%)g | |
| pfd2,4,6 at 20°C | 195 | 183 | 102 | 124 | 141 | 65 | 16 | 173 (94.5) | 10 (5.5) |
| lsm8-1 at 20°C | 898 | 842 | 531 | 583 | 761 | 229 | 80 | 816 (96.9) | 26 (3.1) |
| pfd4 at 4°C | 216 | 201 | 60 | 127 | 92 | 67 | 21 | 172 (85.6) | 29 (14.4) |
| lsm8-1 at 4°C | 1031 | 970 | 628 | 678 | 877 | 250 | 84 | 941 (97.0) | 29 (3.0) |
aPremature termination codon (PTC) and a 3′UTR longer than 350nt.
b3′UTR longer than 350nt.
cMore than 55 nt between stop codon (SC) and a downstream intron.
dUpstream open reading frame (uORF) longer than 35 amino acids.
euORF overlapping with the start codon of the main ORF.
fTotal number of genes containing at least one retained intron causing NMD features.
gTotal number of genes containing retained introns that do not generate NMD features.