TY  - JOUR
A1  - Zhang, Zhaolei
A1  - Harrison, Paul M.
A1  - Liu, Yin
A1  - Gerstein, Mark
T1  - Millions of Years of Evolution Preserved: A Comprehensive Catalog of the Processed Pseudogenes in the Human Genome
Y1  - 2003/12/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 2541 
EP  - 2558 
DO  - 10.1101/gr.1429003 
VL  - 13 
IS  - 12 
UR  - http://genome.cshlp.org/content/13/12/2541.abstract 
N2  - Processed pseudogenes were created by reverse-transcription of mRNAs; they provide snapshots of ancient genes existing millions of years ago in the genome. To find them in the present-day human, we developed a pipeline using features such as intron-absence, frame-disruption, polyadenylation, and truncation. This has enabled us to identify in recent genome drafts ∼8000 processed pseudogenes (distributed from http://pseudogene.org). Overall, processed pseudogenes are very similar to their closest corresponding human gene, being 94% complete in coding regions, with sequence similarity of 75% for amino acids and 86% for nucleotides. Their chromosomal distribution appears random and dispersed, with the numbers on chromosomes proportional to length, suggesting sustained “bombardment” over evolution. However, it does vary with GC-content: Processed pseudogenes occur mostly in intermediate GC-content regions. This is similar to Alus but contrasts with functional genes and L1-repeats. Pseudogenes, moreover, have age profiles similar to Alus. The number of pseudogenes associated with a given gene follows a power-law relationship, with a few genes giving rise to many pseudogenes and most giving rise to few. The prevalence of processed pseudogenes agrees well with germ-line gene expression. Highly expressed ribosomal proteins account for ∼20% of the total. Other notables include cyclophilin-A, keratin, GAPDH, and cytochrome c. 
ER  -