Based on public database searches, the ROL6 sequence shows some embedded MYBbinding motifs yet very little homology to any known plant cis-acting elements and may contain one or more novel root-preferred cis-ac
DATABASE ORGANISATION The central ‘node’ of our database is the name of a site within a plant species. The site behind the name can then be represented by a matrix, a consensus, individual site sequences on particular promoters, or by all of these together. Thanks to the organization ...
URS1 core hexamer sequence (50-GGCGGC-30 or its reverse complement24)) within the À1;000 to +500 nucleotide region relative to the ATG start codon as +1, and also were classified as ''verified ORFs'' in the Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/) (Fig. ...
Using the PLACE database, we ensured that each of these 4 bp sequences are not conserved cis element themselves [34]. By performing a similar analysis on each control sequence, we compared the frequency of the ACGT (N) ACGT motif with the corresponding frequencies of control sequences for ...
2.2.2.1 New cardiac TF prediction by database mining The restricted expression of a TF in a tissue or organ-specific manner could indicate that this TF has a role in defining the identity of that particular tissue or organ. Following this rationale, traditionally TFs were selected to be studie...
2009) against specific SRA database entries of interest, using BlastN. Read sequences that matched more than one query CDS were not considered further to guarantee match specificity. The specific matches were quantified, and their match statistics paired with the results of the run for each cork...
2g). Most differential recording was directionally concordant with the summed expression of transcription factors assigned by the JASPAR database to the transcription factor motif of a given synthetic CRE recorder (13 out of 17, P = 0.02, binomial test; Extended Data Fig. 5d,e). However,...
The Plant Genome Database: [http://www.plantgdb.org/], ClustalW2 Sequence Alignment: [http://www.ebi.ac.uk/Tools/clustalw2/index.html], Page RD: Visualizing phylogenetic trees using TreeView. Curr Protoc Bioinformatics. 2002, 6: 6-2. Google Scholar Wu Z, Irizarry AR, Gentleman R,...
The UCSC genome browser database: 2021 update. Nucleic Acids Res. 2021;49(D1):D1046–57. 45. Fornes O, Castro-Mondragon JA, Khan A, van der Lee R, Zhang X, Rich- mond PA, Modi BP, Correard S, Gheorghe M, Baranasic D, et al. JASPAR 2020: update of the open-access data...
In order to test the significance of these frequencies, we used four palindromic – TAGC, CGTA, GCTA, ATGC, and four non-palindromic – AGCT, TGCA, CTAG, GATC se- quences as controls. Using the PLACE database, we en- sured that each of these 4 bp sequences are not...