In mammals a considerable 92% of genes contain introns, with hundreds and 
hundreds of these introns reaching the incredible size of over 50,000 
nucleotides. These "large introns" must be spliced out of the pre-mRNA in a 
timely fashion, which involves bringing together distant 5' and 3' acceptor and 
donor splice sites. In invertebrates, especially Drosophila, it has been shown 
that larger introns can be spliced efficiently through a process known as 
recursive splicing-a consecutive splicing from the 5'-end at a series of 
combined donor-acceptor splice sites called RP-sites. Using a computational 
analysis of the genomic sequences, we show that vertebrates lack the proper 
enrichment of RP-sites in their large introns, and, therefore, require some 
other method to aid splicing. We analyzed over 15,000 non-redundant, large 
introns from six mammals, 1,600 from chicken and zebrafish, and 560 
non-redundant large introns from five invertebrates. Our bioinformatic 
investigation demonstrates that, unlike the studied invertebrates, the studied 
vertebrate genomes contain consistently abundant amounts of direct and 
complementary strand interspersed repetitive elements (mainly SINEs and LINEs) 
that may form stems with each other in large introns. This examination showed 
that predicted stems are indeed abundant and stable in the large introns of 
mammals. We hypothesize that such stems with long loops within large introns 
allow intron splice sites to find each other more quickly by folding the 
intronic RNA upon itself at smaller intervals and, thus, reducing the distance 
between donor and acceptor sites.