More than one million copies of the approximately 300-bp Alu element are 
interspersed throughout the human genome, with up to 75% of all known genes 
having Alu insertions within their introns and/or UTRs. Transcribed Alu 
sequences can alter splicing patterns by generating new exons, but other impacts 
of intragenic Alu elements on their host RNA are largely unexplored. Recently, 
repeat elements present in the introns or 3'-UTRs of 15 human brain RNAs have 
been shown to be targets for multiple adenosine to inosine (A-to-I) editing. 
Using a statistical approach, we find that editing of transcripts with embedded 
Alu sequences is a global phenomenon in the human transcriptome, observed in 
2674 ( approximately 2%) of all publicly available full-length human cDNAs (n = 
128,406), from >250 libraries and >30 tissue sources. In the vast majority of 
edited RNAs, A-to-I substitutions are clustered within transcribed sense or 
antisense Alu sequences. Edited bases are primarily associated with retained 
introns, extended UTRs, or with transcripts that have no corresponding known 
gene. Therefore, Alu-associated RNA editing may be a mechanism for marking 
nonstandard transcripts, not destined for translation.