BACKGROUND: Gene duplication and exonization of intronic transposed elements are 
two mechanisms that enhance genomic diversity. We examined whether there is less 
selection against exonization of transposed elements in duplicated genes than in 
single-copy genes.
RESULTS: Genome-wide analysis of exonization of transposed elements revealed a 
higher rate of exonization within duplicated genes relative to single-copy 
genes. The gene for TIF-IA, an RNA polymerase I transcription initiation factor, 
underwent a humanoid-specific triplication, all three copies of the gene are 
active transcriptionally, although only one copy retains the ability to generate 
the TIF-IA protein. Prior to TIF-IA triplication, an Alu element was inserted 
into the first intron. In one of the non-protein coding copies, this Alu is 
exonized. We identified a single point mutation leading to exonization in one of 
the gene duplicates. When this mutation was introduced into the TIF-IA coding 
copy, exonization was activated and the level of the protein-coding mRNA was 
reduced substantially. A very low level of exonization was detected in normal 
human cells. However, this exonization was abundant in most leukemia cell lines 
evaluated, although the genomic sequence is unchanged in these cancerous cells 
compared to normal cells.
CONCLUSION: The definition of the Alu element within the TIF-IA gene as an exon 
is restricted to certain types of cancers; the element is not exonized in normal 
human cells. These results further our understanding of the delicate interplay 
between gene duplication and alternative splicing and of the molecular 
evolutionary mechanisms leading to genetic innovations. This implies the 
existence of purifying selection against exonization in single copy genes, with 
duplicate genes free from such constrains.