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Pseudogenes
Sean D. Pitman M.D.© January 2005 Latest Update: May 2008 
Table of Contents
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Pseudogenes
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Shared Pseudogenes
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Signs of Function
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One Man's Junk
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Shared Mistakes
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A New Paradigm
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The Human Genome in Numbers
•
Pyknons
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The Key Human-Ape Differences
•
Wade Schauer Essay
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Pseudogenes are DNA sequences that resemble functional genes but are generallythought to have no purpose. In fact many scientists think that pseudogenes are nothingmore than discarded genetic fossils of a bygone era when they did have some sort of important function. Of course, it logically follows that similar pseudogenes that areshared by different species give evidence of common ancestry and even potential timesof divergence.
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For example, the eta-globin pseudogene, which is found in bothhumans and chimps, has been used as an argument for the common ancestry of thetwo species.The first pseudogene was reported in 1977.
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Since that time, a large number of thesegeneshavebeenreported and described in humans and many other species.There are two types of pseudogenes known as "processed" and "unprocessed"pseudogenes.
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Processed genes are found on different chromosomes from their functionalcounterparts. They lack introns and certain regulator genes, often terminate in adenineseries, and are flanked by direct repeats (which are associated with movable geneticelements). They may be complete or incomplete copies of genes or mixtures of several
 
genes. They are believed to have occurred through a 3-step process: Copying DNAinto RNA, editing the introns to make mRNA, and then turning the code in the mRNAback into DNA through a reverse transcription process. This process is thought to havecreated the "L1 family of pseudogenes."
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Other theories include retroviruses as meansof pseudogene transport between different organisms.Unprocessed pseudogenes are usually found in clusters of similar functionalsequences on the same chromosome. They usually have introns and associatedregulatory sequences. Their expression is usually prevented by a "misplaced" stopcodon or codons. There may be other changes from the "original" as the result of deletions, insertions, and point mutations. Some form of mRNA may or may not beproduced depending on the damage to the gene. Many of these are believed to havearisen by gene duplication, which produced an extra copy of the gene. The extra copycould then accumulate mutations without harming the organism since it would still havea completely functional original copy.
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(The evolutionary gene duplication hypothesissuggests that over time, random mutations may produce a new gene with new functionsby using this gene duplicate while maintaining the original gene funtion
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).
 
Shared Pseudogenes
 
It is felt by many, especially evolutionary biologists, that shared pseudogenes, whichhave no function in any form in different species, are examples of common ancestry.Comparison of DNA sequences from humans, chimps, and other mammals shows agreat number of shared pseudogenes. Perhaps the best-known example of a sharedpseudogene is the eta-globin gene.The eta gene is located on chromosome 11 in humans and is fourth in a series of 6beta globin genes (five are functional).
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It has no start codon (AUG) and it has severalstop codons. So obviously, no mRNA is made and therefore no protein. Humans,chimps, and gorillas have the same number of beta-globin genes arranged in the samesequence. The exon sequences within these genes are also similar - as are the exonsof the eta gene.
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It is thought that the eta-globin gene originated by a duplication of the
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