What are Alu elements?
Of the 3 billion bp of the haploid human genome, only 3-5% encode proteins, but as much as 45% of the genome is composed of repetitive and transposable elements [10]. One of the most abundant and important of these classes is the short interspersed nuclear repetitive DNA elements, SINEs. Almost all of the human SINEs belong to a single family and are known as Alu elements. There are up to 1.4 × 106 copies of these 300 bp elements in the genome, corresponding to more than one Alu element for about every 3,000 bp of genomic DNA. As these elements are not randomly distributed throughout the genome but rather are biased toward gene-rich regions [11], the conclusion can be drawn that the average human pre-mRNA molecule might contain the surprisingly high number of more than 16 Alu elements (see Figure 2a). Alu elements are conserved along their sequence and do not encode any protein. They can act as insertional mutagens, but the vast majority appear to be genetically inert. Although many Al
