Plant cis-acting regulatory DNA elements (PLACE) database: 1999

Abstract

PLACE (http://www.dna.affrc.go.jp/htdocs/PLACE/) is a database of nucleotide sequence motifs found in plant cis-acting regulatory DNA elements. Motifs were extracted from previously published reports on genes in vascular plants. In addition to the motifs originally reported, their variations in other genes or in other plant species in later reports are also compiled. Documents for each motif in the PLACE database contains, in addition to a motif sequence, a brief definition and description of each motif, and relevant literature with PubMed ID numbers and GenBank accession numbers where available. Users can search their query sequences for cis-elements using the Signal Scan program at our web site. The results will be reported in one of the three forms. Clicking the PLACE accession numbers in the result report will open the pertinent motif document. Clicking the PubMed or GenBank accession number in the document will allow users to access to these databases, and to read the of the literature or the annotation in the DNA database. This report summarizes the present status of this database and available tools.

A genome-wide cis-regulatory element discovery method based on promoter sequences and gene co-expression networks

“…Nevertheless, the cis -regulatory modules identified by our method still shows significant functional coherence. For example, several motifs in Figure 6b match to the core subsequence (CACGTG) of the well-known abscisic acid responsive element (ABRE) [47]. The CATGCA motif in Figure 6c is part of the RY-repeat element that is specifically required during seed development [47].…”

“…For example, several motifs in Figure 6b match to the core subsequence (CACGTG) of the well-known abscisic acid responsive element (ABRE) [47]. The CATGCA motif in Figure 6c is part of the RY-repeat element that is specifically required during seed development [47]. The motif GGCCCA in Figure 6d matches the UP1ATMSD motif that is over-represented in a list of up-regulated genes after main stem decapitation in Arabidopsis, many of which are predicted to function in protein synthesis [48].…”

“…The motif GGCCCA in Figure 6d matches the UP1ATMSD motif that is over-represented in a list of up-regulated genes after main stem decapitation in Arabidopsis, many of which are predicted to function in protein synthesis [48]. Finally, genes in Figure 6e are involved in cell cycle and are regulated by the CAACGG motif, which contains the myb core motif found in the promoter of Arabidopsis cell cycle regulating cyclin B1:1 gene [47]. …”

An anionic class III peroxidase from zucchini may regulate hypocotyl elongation through its auxin oxidase activity

“…The intronic sequence has been obtained directly from the genomic DNA using 5Ј and 3Ј primers speciWc for APRX. The cis-element contained in the promoter and introns sequences were analyzing with PLACE database (Higo et al 1999). …”

“…This APRX promoter sequence was assessed with the Place database (Higo et al 1999) to detect cis-regulatory elements. Such an analysis could indicate potential regulatory mechanisms for APRX and thus potential insights to its function.…”