RT Journal
A1 Torrents, David
A1 Suyama, Mikita
A1 Zdobnov, Evgeny
A1 Bork, Peer
T1 A Genome-Wide Survey of Human Pseudogenes
JF Genome Research 
JO Genome Research 
YR 2003 
FD December 01 
VO 13 
IS 12 
SP 2559 
OP 2567 
DO 10.1101/gr.1455503 
UL http://genome.cshlp.org/content/13/12/2559.abstract 
AB We screened all intergenic regions in the human genome to identify pseudogenes with a combination of homology searches and a functionality test using the ratio of silent to replacement nucleotide substitutions (KA/KS). We identified 19,724 regions of which 95% ± 3% are estimated to evolve neutrally and thus are likely to encode pseudogenes. Half of these have no detectable truncation in their pseudocoding regions and therefore are not identifiable by methods that require the presence of truncations to prove nonfunctionality. A comparative analysis with the mouse genome showed that 70% of these pseudogenes have a retrotranspositional origin (processed), and the rest arose by segmental duplication (nonprocessed). Although the spread of both types of pseudogenes correlates with chromosome size, nonprocessed pseudogenes appear to be enriched in regions with high gene density. It is likely that the human pseudogenes identified here represent only a small fraction of the total, which probably exceeds the number of genes.