Table I.

Comparison of the presence of the putative motifs within the genome and the subsets that showed maximum expression at a given time point

The sequences analyzed were all 1-kb upstream regions (66,710) and all 3′ UTR sequences (3,027) obtained from the full genome sequence information files from TIGR. For the 1-kb upstream and 3′ UTR genome sets, the number of sequences in which the motif occurred (Freq.) and the corresponding percentage (%) of all sequences that this represents are shown. A z-score analysis was carried out (Supplemental Table S6C), and the putative motifs found to be significantly overrepresented and underrepresented (+ and − at P < 0.01) are shown next to the percentage of sequences in which the motif occurred. For the putative 1-kb upstream motifs, asterisks indicate that these motifs partially/fully match known rice elements found in the Rice Cis-Element Search and/or PlantCare databases. Previous analysis of 3′ UTR sequences (Ohme-Takagi et al., 19932; Narsai et al., 20071) have suggested the involvement of these motifs in mRNA stability. Elements that contain some overlapping bases are indicated by the same superscript letter.

Sequences AnalyzedPutative MotifGenome0-h Peaking1-h Peaking3-h Peaking12-h Peaking24-h Peaking
Freq.%
1-kb upstream regionsaAAAAAAAA*20,37730.50+44.90%+40.80%
bTTTTTTTT*20,36930.50+37.50%
cCACCAC*20,00230.00+53.30%+38.80%+39.80%+35.10%
cACCACC18,76228.10+56.70%+38.00%+32.90%
dGGTGGT15,78623.70−20.80%
eGCCGCC*23,60135.40+43.80%−28.00%−26.30%
eCGCCGC24,31836.50+46.10%−28.00%−28.50%
fGCGGCG*21,93632.90−22.30%
fGGCGGC21,74232.60−25.20%−21.20%
gGGAGGG*20,00830.00−23.40%−24.40%
gGAGAGA23,54135.30
hTCTCTC*26,21739.30+47.70%+47.20%+45.70%
hCCCTCC23,46135.20+44.00%+43.70%
hTCCTCT25,33138.00+46.60%+46.50%+43.30%
No. of sequences analyzed66,71027303842541,231
3′ UTRsbTTTTTT11,05835.00+69.20%
TTATTG43514.40+42.30%
dGCTGGT2578.50+30.80%
ATTTAT259719.70+38.50%
GAATAA137312.30+31.60%
No. of sequences analyzed3,02723261979