PlantProm: Plant Promoter Database

Database of Plant Promoter Sequences
(Release 2016.03)


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Promoters from direct experiments
Putative TSS map for protein-coding genes
Classification of promoters
Canonical NFMs
Nucleotide composition
Regulatory motifs
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Used in more than 220 publications.
Current release of PlantProm DB contains 576 plant promoters with experimentally verified position of TSS. In contrast to other promoter sets where TSSs, identified by applying full-length cDNA mapping, 5’-end mapping, CAGE and SAGE approaches, remain to be confirmed by direct experimental evidence, our DB compiles published promoter sequences with TSS(s) confirmed by direct experimental approaches. While collecting experimentally verified plant gene promoters the following set of criteria was used.

Current release of PlantProm DB contains the following information:
  1. 1.   DNA sequences of 576 plant promoter regions, 251 bp each, with experimentally verified TSS positions (201).
  2. 2.   Taxonomic and promoter type classification of 576 experimentally verified promoters.
  3. 3.   Nucleotide frequency matrices (NFMs) for canonical promoter elements, such as TATA-box and TSS-motif (Initiator element, Inr) computed for 576 experimentally verified promoters.
  4. 4.   Nucleotide composition of promoter regions before [-200:-1] and after [+1:+51] TSS in various promoter collections.
  5. 5.   Statistically significant motifs of 3,032 known plant transcription factor binding sites (TFBSs) found in 576 experimentally verified promoter sequences.
  6. 6.   Putative TSS maps for 22,257, 23,334, 18,226, 38,702 and 11,037 protein-coding genes of Oryza sativa, Zea mays, Medicago truncatula, Glycine max and Vitis vinifera, respectively.
  7. 7.   Statistically significant motifs of 3,032 known plant TFBSs found in the [-1000:-101] regions of 22,257, 23,334, 18,226, 38,702 and 11,037 protein-coding genes of O. sativa, Z. mays, M. truncatula, G. max and V. vinifera, respectively.

The current release of PlantProm DB allows users to:
  1. ✔   Retrieve and download 576 experimentally verified promoter sequences (all at once, or only for user-chosen species or promoter classes);
  2. ✔   Get a PubMed link for every entry of 576 experimentally verified promoters;
  3. ✔   Retrieve and download TATA-box and INR NFMs.
  4. ✔   Retrieve and download putative TFBS content of 576 experimentally verified promoter sequences.
  5. ✔   Retrieve and download promoter sequences (in FASTA format) and putative TSS map (in both Text and GFF formats) for 113,556 protein-coding genes of O. sativa, Z. mays, M. truncatula, G. max and V. vinifera.
  6. ✔   Retrieve and download putative TFBS content of the [-1000:-101] regions of 22,257, 23,334, 18,226, 38,702 and 11,037 protein-coding genes of O. sativa, Z. mays, M. truncatula, G. max and V. vinifera, respectively.
  7. ✔   Search for promoter sequences by promoter or gene ID.

References:

Shahmuradov IA, Gammerman AJ, Hancock JM, Bramley PM, Solovyev VV (2003) PlantProm: a database of plant promoter sequences. Nucleic Acids Res., 31: 114-117 (PMID: 12519961).

Acknowledgements: PlantProm Database is partially funded by (1) Grant EİF-2010-1(1)-40/27-3 from the Science Development Foundation under of the President of the Republic of Azerbaijan; (2) the King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR) under Awards No URF/1/1976-02 and FCS/1/2448-01; (3) Softberry Inc. (USA); (4) Pakistan HEC Startup Grant Setting up of Bioinformatics Research at the Department of Biosciences, COMSATS Institute of Information Technology.
Please send questions/comments to: Ilham Shahmuradov ilham.shahmuradov@kaust.edu.sa and/or Victor Solovyev victor@softberry.com