Genome wide identification and classification of alternative splicing based on EST data

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• Alternative splicing significantly expands proteomic diversity from a limited number of human genes.
• Expressed Sequence Tag (EST) mapping aids in predicting gene structures and splicing events.
• Distinguishing true splicing events from artifacts requires robust quality assessment.

Purpose of the Study:

• To develop a methodology for assigning quality values to predicted exon-intron boundaries.
• To enable high-confidence prediction and large-scale analysis of constitutive and alternative splicing.
• To facilitate a deeper understanding of alternative splicing's role in gene expression.

Main Methods:

• Mapping EST consensus sequences to the genome to predict exon-intron boundaries.
• Developing a quality scoring system for exon-intron boundaries.
• Ranking predicted splicing events (constitutive and alternative) by confidence values.

Main Results:

• Identified 33,270 constitutive splicing events, with 45% exhibiting alternative splicing.
• Validated 15 out of 17 predicted splice events using RT-PCR across 40 tissue samples.
• Found that alternative splicing variants predominantly occur in coding regions but also significantly in non-coding regions.

Conclusions:

• The developed methodology enhances the accuracy of alternative splicing prediction.
• Alternative splicing plays a crucial functional role in both coding and untranslated regions of genes.
• The SpliceNest database provides a resource for visualizing and analyzing predicted alternative splice variants.