last update: 02/27/2007


Search | background | matrices & thresholds | input & output | caveats


NOT ALL HIGH-SCORES are ESEs !

  • The presence of a high-score motif in a sequence does NOT necessarily identify that sequence as an exonic splicing enhancer in its native context. For example, a nearby silencer element may prevent the SR protein from binding.
  • The default threshold values are based on statistical analysis and empirical data, but they are still somewhat arbitrary. Any refinements or updates will be incorporated as they become available
  • There is at best only a rough correlation between numerical scores and ESE activity of high-score motifs. For example, the maximum score is not necessarily the most effective ESE.
  • The score values of ESEs corresponding to different SR proteins cannot be compared to each other.
  • The program currently searches the ESE motifs corresponding to four SR proteins. There are several other SR proteins for which the ESE motifs have not yet been identified, at least by the strategy used here.
  • The ESE motifs were identified using human SR proteins. Their relevance to other species depends on the extent of conservation of each SR protein.


Krainer Lab and Zhang Lab, Cold Spring Harbor Laboratory, all rights reserved
Questions/suggestions email: Woody Lin.