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Detection of Processed Pseudogenes Based on cDNA Mapping to the Human Genome

Processed pseudogenes are defined as those obtained by reverse transcription of messenger RNAs followed by reintegration into genomic DNA and subsequent degradation with disablements (premature stop codons and frameshifts). Estimates of the pseudogene population in the human genome range from about 9,000 [2] to 33,000 [1], but their exact number still remains unclear. Processed pseudogenes have been detected basically by the combination of sequence similarity searches against the known gene collection and the ratio of non-synonymous versus synonymous substitutions (KA/KS) [3, 4]. The existence of polyadenylation sites and signals on the genome sequence is also useful information for detecting processed pseudogenes [2]. However, these methods may fail to find some processed pseudogenes such as splice variants and intron-containing pseudogenes. We attempted to detect processed pseudogenes based on cDNA mapping and sequence analysis of their 3’ terminal signals.