An Arabidopsis 2010 project to characterize pre-mRNA splicing signals

Original project description (in pdf format, from the grant application)

The SEE-ESE web server (ESE prediction)

The ELPH server (motif finder)

Experimentally determined ESE data

This site is devoted to exonic splicing enhancers. If you are looking for general information about the alternative splicing of plant genes, we recommend the ASIP (Alternative Splicing in Plants) database at Iowa State or the specialized Genome Annotation Database at TIGR, including Splicing Variations and Non-consensus Splice Sites.

Background:

Existing genefinders use information about splice sites and differences between exons and introns, but do not explicitly incorporate information about sequences known as splicing enhancers, which promote incorporation of exons into mRNA (an exception is ExonScan). This is a project to characterize exonic splicing enhancers in Arabidopsis. Although splicing enhancers likely function in splice site selection in many plant genes, and contribute to the regulation of alternative splicing, plant splicing enhancers have not yet been described in detail. Computational analysis of a database of Arabidopsis exons and introns has been used to identify candidate splicing enhancer sequences. The role of these sequences, and sequences from genes that are known to be alternatively spliced, are being tested in transgenic Arabidopsis using a splicing reporter construct. The activity of these enhancers has been examined in transgenes that depend on exon inclusion for expression.

This is NSF Award#0114792 - Arabidopsis 2010: Pre-mRNA Splicing Signals in Arabidopsis

PI,Stephen M. Mount, Ph.D., Associate Professor, Dept. of Cell Biology and Molecular Genetics, University of Maryland. (email: smount@umd.edu)

co-PI,Caren Chang , Ph.D., Associate Professor, Dept. of Cell Biology and Molecular Genetics, University of Maryland.

co-PI,Steven Salzberg, Ph.D., Director, Center for Bioinformatics and Computational Biology , University of Maryland and Professor, Dept. of Computer Science, University of Maryland

ATRIUM The Arabiodopsis thaliana Research Initiative at University of Maryland
TAIR The Arabiodopsis Information Resource
CBCB The Center for Bioinformatics and Computational Biology
TIGR db The TIGR Arabidopsis thaliana Database
ASIP Alternative Splicing in Plants, part of the PlantGDB (Plant Genome Database)
The NSF Arabidopsis 2010 Project 

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