ESEffinder: a web resource to identify exonic splicing enhancers

ESEffinder: a web resource to identify exonic splicing enhancers

Received February 14, 2003; Revised and Accepted April 7, 2003 | Luca Cartegni, Jinhua Wang, Zhengwei Zhu, Michael Q. Zhang and Adrian R. Krainer*
ESEfinder is a web-based resource designed to identify exonic splicing enhancers (ESEs) and predict the effects of mutations on ESE function. ESEs are regulatory elements that influence pre-mRNA splicing, particularly in exons undergoing alternative splicing. The tool uses weight matrices derived from functional SELEX experiments to score potential ESEs in query sequences. These matrices are specific to four human SR proteins: SF2/ASF, SC35, SRp40, and SRp55. ESEfinder provides a user-friendly interface for inputting query sequences and displaying results, including high-score motifs and graphical representations. The tool has been successfully applied to various genes, including *ACF*, *BRCA1*, *BRCA2*, *FBNF*, *IGF1*, *PDHA1*, *SMN1*, *SMN2*, *TNFRSF5*, and *CFTR*. While ESEfinder is a valuable tool for predicting ESE disruption, it is important to note that the presence of a high-score motif does not guarantee functional ESE activity, and experimental validation remains essential. The development of reliable prediction tools for ESEs will enhance our understanding of gene expression and the interpretation of genetic mutations.ESEfinder is a web-based resource designed to identify exonic splicing enhancers (ESEs) and predict the effects of mutations on ESE function. ESEs are regulatory elements that influence pre-mRNA splicing, particularly in exons undergoing alternative splicing. The tool uses weight matrices derived from functional SELEX experiments to score potential ESEs in query sequences. These matrices are specific to four human SR proteins: SF2/ASF, SC35, SRp40, and SRp55. ESEfinder provides a user-friendly interface for inputting query sequences and displaying results, including high-score motifs and graphical representations. The tool has been successfully applied to various genes, including *ACF*, *BRCA1*, *BRCA2*, *FBNF*, *IGF1*, *PDHA1*, *SMN1*, *SMN2*, *TNFRSF5*, and *CFTR*. While ESEfinder is a valuable tool for predicting ESE disruption, it is important to note that the presence of a high-score motif does not guarantee functional ESE activity, and experimental validation remains essential. The development of reliable prediction tools for ESEs will enhance our understanding of gene expression and the interpretation of genetic mutations.
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