  Background: Transposed elements (TEs) are known to affect transcriptomes,
because either new exons are generated from intronic transposed elements (this
is called exonization), or the element inserts into the exon, leading to a new
transcript. Several examples in the literature show that isoforms generated by
an exonization are specific to a certain tissue (for example the heart muscle)
or inflict a disease. Thus, exonizations can have negative effects for the
transcriptome of an organism. Results: As we aimed at detecting other tissue-
or tumor-specific isoforms in human and mouse genomes which were generated
through exonization of a transposed element, we designed the automated analysis
pipeline SERpredict (SER = Specific Exonized Retroelement) making use of
Bayesian Statistics. With this pipeline, we found several genes in which a
transposed element formed a tissue- or tumor-specific isoform. Conclusion: Our
results show that SERpredict produces relevant results, demonstrating the
importance of transposed elements in shaping both the human and the mouse
transcriptomes. The effect of transposed elements on the human transcriptome is
several times higher than the effect on the mouse transcriptome, due to the
contribution of the primate-specific Alu elements
