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Published online before print October 15, 2001, 10.1101/gr.188001
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Vol. 11, Issue 11, 1848-1853, November 2001

LETTER
The Contribution of Exon-Skipping Events on Chromosome 22 to Protein Coding Diversity

Winston A. Hide,1,3 Vladimir N. Babenko,1,2 Peter A. van Heusden, Cathal Seoighe, and Janet F. Kelso

South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa

Completion of the human genome sequence provides evidence for a gene count with lower bound 30,000-40,000. Significant protein complexity may derive in part from multiple transcript isoforms. Recent EST based studies have revealed that alternate transcription, including alternative splicing, polyadenylation and transcription start sites, occurs within at least 30-40% of human genes. Transcript form surveys have yet to integrate the genomic context, expression, frequency, and contribution to protein diversity of isoform variation. We determine here the degree to which protein coding diversity may be influenced by alternate expression of transcripts by exhaustive manual confirmation of genome sequence annotation, and comparison to available transcript data to accurately associate skipped exon isoforms with genomic sequence. Relative expression levels of transcripts are estimated from EST database representation. The rigorous in silico method accurately identifies exon skipping using verified genome sequence. 545 genes have been studied in this first hand-curated assessment of exon skipping on chromosome 22. Combining manual assessment with software screening of exon boundaries provides a highly accurate and internally consistent indication of skipping frequency. 57 of 62 exon skipping events occur in the protein coding regions of 52 genes. A single gene, (FBXO7) expresses an exon repetition. 59% of highly represented multi-exon genes are likely to express exon-skipped isoforms in ratios that vary from 1:1 to 1:>100. The proportion of all transcripts corresponding to multi-exon genes that exhibit an exon skip is estimated to be 5%.

1 These authors contributed equally to this work.

2 Present address: Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA, USA.

3 Corresponding author.

11:1848-1853 ©2001 by Cold Spring Harbor Laboratory Press  ISSN 1088-9051/01 $5.00
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