ARC Centre of Excellence for Plant Energy Biology

Pre-release edition

Citations for experimentally-shown DNA transcription factor binding motifs in plants have been collated by hand from published literature and computationally matched to all occurrences in MSU’s 1kb upstream DNA sequences for rice. Motifs of six or more bases are recognised, but smaller motifs that occur in 75% or more of loci have been excluded. The presence of the motif doesn’t indicate experimental confirmation in rice unless cited.

Usage When Searching Rice DB Usage Viewing Rice DB Results
  • Published motif names can be searched in Rice DB.
  • Nucleotide sequences (six or more bases, or consensus motifs with up to two wildcards) can be found in Rice DB.
  • Experimentally-known motifs are shown in summary results, and details can be requested as "experimental DNA motifs".
Example: ATCGAC
Example: show experimental DNA motifs for LOC_Os03g03770.1
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System Information

Transcript of last update

Took 10 minutes, 13 seconds, 545 millis starting Sun, 24 Jun 2012 08:54:19 GMT:
Using /var/folders/75/983jwhw537q11ck7b_b0zwf80000gn/T/RiceDB/ExperimentalMotifs_
Using db.local/downloaded/ExperimentalMotifs_
Using Exp.shown.motifs.to.match.csv Thu Jun 14 12:12:31 WST 2012
Loading motifs with wildcard chars
Fanning out wildcards
Generating matched motifs (hexamers and above)
Skipped GGGCC: Motif too short (try 6 or more nucleotides)
Skipped TTGAC: Motif too short (try 6 or more nucleotides)
Skipped CAACA: Motif too short (try 6 or more nucleotides)
Calculating stats
Full text indexed