Description

This track identifies predicted Alternative Conserved Exons (human-mouse conservation), as predicted by ACEScan. These are exons that are present in some transcripts, but skipped by alternative splicing in other transcripts in both human and mouse. Alternate use of skipped exons has important consequences during gene expression and in disease.

Methods

Putative alternative conserved exons on mRNAs were identified using a machine-learning algorithm, Regularized Least-Squares Classification. Characteristics of known exons that have been skipped in both human and mouse mRNAs were determined by considering factors such as exon and intron length, splice-site strength, sequence conservation, and region-specific oligonucleotide composition.

A training set was made by comparing known exons that are skipped in some transcripts to exons never skipped. These characteristics were then applied to the whole genome to predict skipped exons in other transcripts. This track displays exons with positive ACEScan scores.

For further details of the method used to generate this annotation, please refer to Yeo et al. (2005).

Credits

Thanks to Gene Yeo at the Crick-Jacobs Center, Salk Institute and Christopher Burge, MIT, for providing this annotation. For additional information on ACEscan predictions please contact geneyeo@salk.edu or cburge@mit.edu.

References

Yeo GW, Van Nostrand E, Holste D, Poggio T, Burge CB (2005), Identification and analysis of alternative splicing events conserved in human and mouse. Proc Natl Acad Sci U S A. 2005 Feb 22;102(8):2850-5.