BACKGROUND: Transposed elements (TEs) have a substantial impact on mammalian 
evolution and are involved in numerous genetic diseases. We compared the impact 
of TEs on the human transcriptome and the mouse transcriptome.
RESULTS: We compiled a dataset of all TEs in the human and mouse genomes, 
identifying 3,932,058 and 3,122,416 TEs, respectively. We than extracted TEs 
located within human and mouse genes and, surprisingly, we found that 60% of TEs 
in both human and mouse are located in intronic sequences, even though introns 
comprise only 24% of the human genome. All TE families in both human and mouse 
can exonize. TE families that are shared between human and mouse exhibit the 
same percentage of TE exonization in the two species, but the exonization level 
of Alu, a primate-specific retroelement, is significantly greater than that of 
other TEs within the human genome, leading to a higher level of TE exonization 
in human than in mouse (1,824 exons compared with 506 exons, respectively). We 
detected a primate-specific mechanism for intron gain, in which Alu insertion 
into an exon creates a new intron located in the 3' untranslated region (termed 
'intronization'). Finally, the insertion of TEs into the first and last exons of 
a gene is more frequent in human than in mouse, leading to longer exons in 
human.
CONCLUSION: Our findings reveal many effects of TEs on these two transcriptomes. 
These effects are substantially greater in human than in mouse, which is due to 
the presence of Alu elements in human.