Abstract
We present the second release of the Plant Prom DB (initially lunched in 2003), an annotated, non-redundant collection of proximal promoter sequences for RNA polymerase II (Pol II) with experimentally determined transcription start site(s) (TSS) from 86 plant species. It contains 576 entries including 150, 403 and 23 promoters of monocot, dicot and other plants genes, respectively. The database provides DNA sequences and nucleotide composition characteristics of the promoters upstream and downstream of TSS (-200:+51), taxonomic/promoter type classification of promoters and Nucleotide Frequency Matrices (NFMs) for important promoter elements such as TATA-box, INR-motif, Y-patch and DPE. We demonstrated a difference in general nucleotide composition of promoter sequences between monocots and dicots. The database also contains information on statistically significant motifs of known regulatory elements found in the described promoters. The Plant Prom DB is available at http://cub.comsats.edu.pk.
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