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Background  Alternative splicing (AS) of maturing mRNA can generate structurally and functionally distinct transcripts from the same gene. Recent bioinformatic analyses of available genome databases inferred a positive correlation between intron length and AS. To study the interplay between intron length and AS empirically and in more detail, we analyzed the diversity of alternatively spliced transcripts (ASTs) in the  Drosophila  RNA-binding  Bruno-3  ( Bru-3 ) gene. This gene was known to encode thirteen exons separated by introns of diverse sizes, ranging from 71 to 41,973 nucleotides in  D. melanogaster . Although  Bru-3' s structure is expected to be conducive to AS, only two ASTs of this gene were previously described.    Results  Cloning of RT-PCR products of the entire ORF from four species representing three diverged  Drosophila  lineages provided an evolutionary perspective, high sensitivity, and long-range contiguity of splice choices currently unattainable by high-throughput methods. Consequently, we identified three new exons, a new exon fragment and thirty-three previously unknown ASTs of  Bru-3 . All exon-skipping events in the gene were mapped to the exons surrounded by introns of at least 800 nucleotides, whereas exons split by introns of less than 250 nucleotides were always spliced contiguously in mRNA. Cases of exon loss and creation during  Bru-3  evolution in  Drosophila  were also localized within large introns. Notably, we identified a true  de novo  exon gain: exon 8 was created along the lineage of the  obscura  group from intronic sequence between cryptic splice sites conserved among all  Drosophila  species surveyed. Exon 8 was included in mature mRNA by the species representing all the major branches of the  obscura  group. To our knowledge, the origin of exon 8 is the first documented case of exonization of intronic sequence outside vertebrates.    Conclusion  We found that large introns can promote AS via exon-skipping and exon turnover during evolution likely due to frequent errors in their removal from maturing mRNA. Large introns could be a reservoir of genetic diversity, because they have a greater number of mutable sites than short introns. Taken together, gene structure can constrain and/or promote gene evolution.

Large introns in relation to alternative splicing and gene evolution: a case study of Drosophila bruno-3