ACESCAN2 Web Server

An online tool for identifying candidate cis-elements in alternative and constitutive splicing in mammalian exons


Regulated alternative splicing of exons require the presence of splicing cis-elements present in the exon and within the flanking introns. In a recent study, I have extracted candidate cis-elements overrepresented in aligned exons and aligned intronic regions flanking alternative conserved exons (ACEs), compared to included conserved exons (ICEs). The overrepresented elements in exons (ACE-EXs) and in introns (ACE-INs) can give an indication of the potential of regulated alternative splicing that can take place. Some of these elements, such as GCATG (or TGCAT), a 5-mer component of the FOX-1 binding site (TGCATG) rank high in our list of ACE-INs.

Exonic splicing silencers (ESSs) have recently been identified in an experimental screen by Wang et al., and bioinformatics analyses have suggested a function in suppressing the recognition of decoy exons, some function in alternative spliced exons, and also in alternative 5' splice site and 3' splice site usage.

In another recent study, intronic splicing enhancers (ISEs) have also been identified by the RESCUE-ISE method (Yeo, G et al. in press, PNAS). In the same study, the RESCUE-ESE approach was utilized to predict candidate ESEs (ESEs) in Mouse, Fugu rubripes and Zebrafish.

This webpage takes as input a sequence, and allows the sequence to be checked for presence of these candidate ACE-EXs, ACE-INs, ESSs, ISEs and ESEs.

Choice of Elements

Check if YES, default is NO
ACE-EX in Human (Homo sapiens)
ACE-IN in Human (Homo sapiens)
ESS in Human (Homo sapiens)
ISE in Human (Homo sapiens)
ISE in Mouse (Mus musculus)
ISE in Pufferfish (Fugu rubripes)
ESE in Human (Homo sapiens)
ESE in Mouse (Mus musculus)
ESE in Zebrafish (Danio rerio)
ESE in Pufferfish (Fugu rubripes)

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

Please address comments/questions/suggestions to:
Gene Yeo (,
Chris Burge (

Copyright © 2004