In addition to the mobile elements listed in Table 8-1, DNA copies of a wide variety of mRNAs appear to have become integrated into chromosomal DNA. Since these sequences lack introns and do not have flanking sequences similar to those of functional gene copies, they clearly are not simply duplicated genes that have drifted into nonfunctionality and become pseudogenes, as discussed earlier (see Figure 8-4a). Instead, these DNA segments appear to be retrotransposed copies of spliced and polyadenylated mRNA. Compared with normal genes encoding mRNAs, these inserted segments generally contain multiple mutations, which are thought to have accumulated since they were first reverse-transcribed and randomly integrated into the genome of a germ cell in an ancient ancestor. These nonfunctional genomic copies of mRNAs are referred to as processed pseudogenes. Most processed pseudogenes are flanked by short direct repeats, supporting the hypothesis that they were generated by rare retrotransposition events involving cellular mRNAs.

Other interspersed repeats representing partial or mutant copies of genes encoding small nuclear RNAs (snRNAs) and tRNAs are found in mammalian genomes. Like processed pseudogenes derived from mRNAs, these nonfunctional copies of small RNA genes are flanked by short direct repeats and most likely result from rare retrotransposition events that have accumulated through the course of evolution. Enzymes expressed from a LINE are thought to have carried out all these retrotransposition events involving mRNAs, snRNAs, and tRNAs.