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PLACE - a Database of Plant Cis-acting Regulatory DNA Elements
http://www.dna.affrc.go.jp/htdocs/PLACE/

Prodoric - prokaryotic database of gene-regulation and molecular networks.
http://www.prodoric.de

TRANSFAC: Database on eukaryotic transcription factors, their DNA-binding sites and DNA-binding profiles
http://www.biobase.de/pages/products/transfac.html