Abstract
The TATA box is one of the best characterized transcription factor binding sites. However, it is not a ubiquitous element of core promoters, and other sequence motifs such as Y Patches seem to play a major role in plants. Here, we present a first genome-wide computational analysis of the TATA box and Y Patch distribution in rice (Oryza sativa L. subsp. japonica) promoter sequences. Utilizing a probabilistic sequence model, we ascertain that only ∼19% of rice genes possess the TATA box, but ∼50% contain one or more Y Patches in their core promoters. By computational processing of identified elements, we generated extended TATA box and Y Patch nucleotide frequency matrices capable of predicting these motifs in plants with a high degree of confidence.
| Original language | English |
|---|---|
| Pages (from-to) | 294-297 |
| Number of pages | 3 |
| Journal | Genome |
| Volume | 52 |
| Issue number | 3 |
| DOIs | |
| Publication status | Published - Mar 2009 |
Keywords
- Core promoter
- Nucleotide frequency matrix
- Oryza sativa L.
- TATA box
- Y Patch