An online tool for identifying candidate ESEs in vertebrate exons


Specific short oligonucleotide sequences that enhance pre-mRNA splicing when present in exons, termed exonic splicing enhancers (ESEs), play important roles in constitutive and alternative splicing (ESE References). A hybrid computational/experimental method, RESCUE-ESE, was recently developed for identifying sequences with ESE activity. In this approach, specific hexanucleotide sequences are identified as candidate ESEs on the basis that they have both significantly higher frequency of occurrence in exons than in introns and also significantly higher frequency in exons with weak (non-consensus) splice sites than in exons with strong (consensus) splice sites. Representative hexamers from ten different classes of candidate ESEs, together with 6 or 7 bases of flanking sequence context on each side, were introduced into a weak (poorly spliced) exon in a splicing reporter construct. These reporter minigenes were then transfected into cultured cells, where they are transcribed and spliced, and the relative level of inclusion of the test exon was assayed by quantitative (radio-labeled) RT-PCR. Point mutants of these sequences were also analyzed to confirm the precise motifs responsible for ESE activity.

The RESCUE-ESE approach identified 238 hexamers as candidate ESEs using a large database of human genes of known exon-intron structure containing over 30,000 nonredudant exons.

In more recent analyses by Yeo et al., the RESCUE-ESE approach was utilized to predict hexamers as candidate ESEs in other vertebrate genes, namely, Fugu rubipes, Zebrafish and Mouse.

This allows the identification of motifs that are conserved in vertebrates.

This web server allows a sequence to be checked for presence of these candidate ESE hexamers.

Choice of Vertebrate ESEs

Check if YES, default is NO
Human (Homo sapiens)
Mouse (Mus musculus)
Zebrafish (Danio rerio)
Pufferfish (Fugu rubripes)

Enter Your Sequence (RNA or DNA) as plain text or multi-FASTA format
(maximum 4k bases of sequence data)


  • Sequences containing letters other than A, C, G, T, or U that represent unknown nucleotides (e.g., N, R, Y) may be submitted to the web server, but ESEs will not be predicted overlapping these positions.

  • The effect of sequence variation on ESE content can be analyzed by entering both versions of the sequence into the input window.

  • If you use this web server or the set of human RESCUE-ESE hexamers in a published paper, please cite the following reference:

    Fairbrother WG, Yeh RF, Sharp PA, Burge CB. Predictive identification of exonic splicing enhancers in human genes. Science. 2002 Aug 9;297(5583):1007-13.
    Follow the link on this page to download the paper.

  • If you use this web server or the set of vertebrate RESCUE-ESE hexamers in a published paper, please cite the following reference as well:

    Yeo, G, Burge CB. Variation in sequence and organization of splicing regulatory elements in vertebrate genes (submitted).
    Follow the link on this page to download the paper.

  • Please address comments/questions/suggestions to:
    Will Fairbrother (,
    Gene Yeo (,
    Ru-Fang Yeh (, or
    Chris Burge (

    Copyright © 2002

    Web interface by Will Fairbrother and Paul Goldstein