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 Analyzed | Putative Motif | Genome
|
0-h Peaking | 1-h Peaking | 3-h Peaking | 12-h Peaking | 24-h Peaking | |
|---|---|---|---|---|---|---|---|---|
| Freq. | % | |||||||
| 1-kb upstream regions | aAAAAAAAA* | 20,377 | 30.50 | +44.90% | +40.80% | |||
| bTTTTTTTT* | 20,369 | 30.50 | +37.50% | |||||
| cCACCAC* | 20,002 | 30.00 | +53.30% | +38.80% | +39.80% | +35.10% | ||
| cACCACC | 18,762 | 28.10 | +56.70% | +38.00% | +32.90% | |||
| dGGTGGT | 15,786 | 23.70 | −20.80% | |||||
| eGCCGCC* | 23,601 | 35.40 | +43.80% | −28.00% | −26.30% | |||
| eCGCCGC | 24,318 | 36.50 | +46.10% | −28.00% | −28.50% | |||
| fGCGGCG* | 21,936 | 32.90 | −22.30% | |||||
| fGGCGGC | 21,742 | 32.60 | −25.20% | −21.20% | ||||
| gGGAGGG* | 20,008 | 30.00 | −23.40% | −24.40% | ||||
| gGAGAGA | 23,541 | 35.30 | ||||||
| hTCTCTC* | 26,217 | 39.30 | +47.70% | +47.20% | +45.70% | |||
| hCCCTCC | 23,461 | 35.20 | +44.00% | +43.70% | ||||
| hTCCTCT | 25,331 | 38.00 | +46.60% | +46.50% | +43.30% | |||
| No. of sequences analyzed | 66,710 | 27 | 30 | 384 | 254 | 1,231 | ||
| 3′ UTRs | bTTTTTT1 | 1,058 | 35.00 | +69.20% | ||||
| TTATTG | 435 | 14.40 | +42.30% | |||||
| dGCTGGT | 257 | 8.50 | +30.80% | |||||
| ATTTAT2 | 597 | 19.70 | +38.50% | |||||
| GAATAA1 | 373 | 12.30 | +31.60% | |||||
| No. of sequences analyzed | 3,027 | 2 | 3 | 26 | 19 | 79 | ||