Database Description

Plant databases

PLACE is a database of motifs found in plant cis-acting regulatory DNA elements based on previously published reports on vascular plants including the variations that have been identified in these motifs in other genes or in other plant species in later publications. The database also contains brief descriptions of individual motifs, literatures with PubMed links, and the corresponding accession numbers in the DDBJ/EMBL/GenBank.

Background and objectives

• A database of nucleotide sequence motifs found in plant cis-acting regulatory DNA elements (cis-elements) with tools for homology searches will be helpful in estimating the mode of gene regulation, regions involved in such regulation, and other pertinent regions in the DNA sequence. In order to provide a compilation of all reported cis-elements of higher plants, we constructed the PLACE database.

1. The cis-elements in this database including motif sequences, descriptions of major features, and references have been compiled by extensive survey of original literatures. Review articles on the regulatory regions of some plant genes were also used to obtain information on specific groups of motifs.


2. The documents of individual motifs can be accessed by keyword search using a browser.


3. The query sequence is searched by the Signal Scan program. The search can be initiated by copy and paste of the query sequence and the results are shown in a few seconds. The Signal Scan output is shown in one of three options:  a list of motifs in alphabetical order, a sequence map, and a list of motifs beginning at the 5' end of the query sequence.


4. The document contains information on the PubMed ID and the GenBank accession number with corresponding links.

• Experimental evidence for each motif is described in the ‘Reference Criteria’ (RC) field. Users of this database must be aware that the motifs compiled here were not strictly examined on this premise. Therefore users are advised to refer to the original reports of individual motifs before using any of the results obtained for publication.