RNAs containing Alu sequences. Because of the high density of Alu elements found in introns, there are many Alu elements located (in both sense and antisense orientations) within the introns of the primary nuclear transcripts (hnRNAs) found in the nucleus. Even after splicing, a high proportion of mature cytoplasmic mRNAs also contain Alu elements in their 3' non-coding regions. Both of the above types of transcript involve capped (blue circle with C), polyadenylated RNAs where one or more Alu elements is included in either orientation within the transcript. The transcripts made from the Alu RNA polymerase III promoter are not capped, include a genomically encoded A-rich region, and terminate at a typical RNA pol III terminator. The transcripts are similar, but not identical, in the Alu region (wavy light blue line), with an A-tail encoded from the genome that is variable in length and often includes non-A bases. The 3' ends of each Alu RNA are unique, and arise from the flanking sequences of the different genomic Alu elements (Figure 1).
Deininger Genome Biology 2011 12:236 doi:10.1186/gb-2011-12-12-236