Pseudogene

<h2 id="properties">Properties</h2>
Pseudogenes are usually characterized by a combination of similarity or <a href="/facts/Sequence_homology/mCIVStrA">homology</a> to a known gene, together with a loss of some functionality. That is, although every pseudogene has a <a href="/facts/DNA/nB89Iauz">DNA</a> sequence that is similar to some functional gene, they are usually unable to produce functional final protein products.<a class="footnote-ref" id="fnref:1" href="#fn:1">1</a> Pseudogenes are sometimes difficult to identify and characterize in genomes, because the two requirements of similarity and loss of functionality are usually implied through sequence alignments rather than biologically proven.

<ol><li>Homology is implied by sequence similarity between the DNA sequences of the pseudogene and a known gene. After <a href="/facts/Sequence_alignment/p8GQfF7b">aligning</a> the two sequences, the percentage of identical <a href="/facts/Base_pair/xmPpPQ9W">base pairs</a> is computed. A high sequence identity means that it is highly likely that these two sequences diverged from a common ancestral sequence (are homologous), and highly unlikely that these two sequences have evolved independently (see <a href="/facts/Convergent_evolution/dd0L8z4R">Convergent evolution</a>).</li>
<li>Nonfunctionality can manifest itself in many ways. Normally, a gene must go through several steps to a fully functional protein: <a href="/facts/Transcription_(genetics)/bDgp9HDN">Transcription</a>, <a href="/facts/Pre-mRNA_processing/Hp9Ww9Nk">pre-mRNA processing</a>, <a href="/facts/Translation_(biology)/JcPC1rth">translation</a>, and <a href="/facts/Protein_folding/rf3nR2Y1">protein folding</a> are all required parts of this process. If any of these steps fails, then the sequence may be considered nonfunctional. In high-throughput pseudogene identification, the most commonly identified disablements are premature <a href="/facts/Stop_codon/1yuAkq9X">stop codons</a> and <a href="/facts/Frameshift_mutation/ncWrMHqm">frameshifts</a>, which almost universally prevent the translation of a functional protein product.</li></ol>
Pseudogenes for <a href="/facts/RNA/HxPeNfNj">RNA</a> genes are usually more difficult to discover as they do not need to be translated and thus do not have "reading frames". A number of rRNA pseudogenes have been identified on the basis of changes in rDNA array ends.<a class="footnote-ref" id="fnref:2" href="#fn:2">2</a>
Pseudogenes can complicate molecular genetic studies. For example, amplification of a gene by <a href="/facts/Polymerase_chain_reaction/G0jWzJy1">PCR</a> may simultaneously amplify a pseudogene that shares similar sequences. This is known as PCR bias or amplification bias. Similarly, pseudogenes are sometimes <a href="/facts/DNA_annotation/HY6IuzMT">annotated</a> as genes in <a href="/facts/Genome/31Sm08JT">genome</a> sequences.
Processed pseudogenes often pose a problem for <a href="/facts/Gene_prediction/QFdMeIN2">gene prediction</a> programs, often being misidentified as real genes or exons. It has been proposed that the identification of processed pseudogenes can help improve the accuracy of gene prediction methods.<a class="footnote-ref" id="fnref:3" href="#fn:3">3</a>
In 2014, 140 human pseudogenes have been shown to be translated.<a class="footnote-ref" id="fnref:4" href="#fn:4">4</a> However, the function, if any, of the protein products is unknown.

<h2 id="types-and-origin">Types and origin</h2>

There are four main types of pseudogenes, all with distinct mechanisms of origin and characteristic features. The classifications of pseudogenes are as follows:

<h3>Processed</h3>

In higher <a href="/facts/Eukaryote/SkwyPLMA">eukaryotes</a>, particularly <a href="/facts/Mammal/phSwTzBo">mammals</a>, <a href="/facts/Retrotransposition/WbVMhuWR">retrotransposition</a> is a fairly common event that has had a huge impact on the composition of the genome. For example, somewhere between 30 and 44% of the <a href="/facts/Human_genome/VTV85pbn">human genome</a> consists of repetitive elements such as <a href="/facts/Retrotransposon/E0SgHUjT">SINEs</a> and <a href="/facts/Retrotransposon/E0SgHUjT">LINEs</a> (see <a href="/facts/Retrotransposons/E0SgHUjT">retrotransposons</a>).<a class="footnote-ref" id="fnref:5" href="#fn:5">5</a><a class="footnote-ref" id="fnref:6" href="#fn:6">6</a> In the process of retrotransposition, a portion of the <a href="/facts/Messenger_RNA/oUL6qxQn">mRNA</a> or <a href="/facts/HnRNA/4UXtKPHw">hnRNA</a> transcript of a gene is spontaneously <a href="/facts/Reverse_transcription/Vc1lGk8P">reverse transcribed</a> back into DNA and inserted into chromosomal DNA. Although retrotransposons usually create copies of themselves, it has been shown in an in vitro system that they can create retrotransposed copies of random genes, too.<a class="footnote-ref" id="fnref:7" href="#fn:7">7</a> Once these pseudogenes are inserted back into the genome, they usually contain a <a href="/facts/Polyadenylation/ILnXUBKP">poly-A tail</a>, and usually have had their introns <a href="/facts/Splicing_(genetics)/a2QEvCRI">spliced out</a>; these are both hallmark features of <a href="/facts/CDNA/P2nWeY4T">cDNAs</a>. However, because they are derived from an RNA product, processed pseudogenes also lack the upstream promoters of normal genes; thus, they are considered "dead on arrival", becoming non-functional pseudogenes immediately upon the retrotransposition event.<a class="footnote-ref" id="fnref:8" href="#fn:8">8</a> However, these insertions occasionally contribute exons to existing genes, usually via <a href="/facts/Alternative_splicing/nNRwPVNK">alternatively spliced</a> transcripts.<a class="footnote-ref" id="fnref:9" href="#fn:9">9</a> A further characteristic of processed pseudogenes is common truncation of the 5' end relative to the parent sequence, which is a result of the relatively non-processive retrotransposition mechanism that creates processed pseudogenes.<a class="footnote-ref" id="fnref:10" href="#fn:10">10</a> Processed pseudogenes are continually being created in primates.<a class="footnote-ref" id="fnref:11" href="#fn:11">11</a> Human populations, for example, have distinct sets of processed pseudogenes across its individuals.<a class="footnote-ref" id="fnref:12" href="#fn:12">12</a>
It has been shown that processed pseudogenes accumulate mutations faster than non-processed pseudogenes.<a class="footnote-ref" id="fnref:13" href="#fn:13">13</a>

<h3>Non-processed (duplicated)</h3>

<a href="/facts/Gene_duplication/CcfJYsDF">Gene duplication</a> is another common and important process in the evolution of genomes. A copy of a functional gene may arise as a result of a gene duplication event caused by <a href="/facts/Homologous_recombination/WU0IIVVv">homologous recombination</a> at, for example, repetitive <a href="/facts/Short_interspersed_element/E0SgHUjT">SINE</a> sequences on misaligned chromosomes and subsequently acquire <a href="/facts/Mutation/Ee4NnWbY">mutations</a> that cause the copy to lose the original gene's function. Duplicated pseudogenes usually have all the same characteristics as genes, including an intact <a href="/facts/Exon/8KWJtLuN">exon</a>-<a href="/facts/Intron/LS6YdBEK">intron</a> structure and regulatory sequences. The loss of a duplicated gene's functionality usually has little effect on an organism's <a href="/facts/Fitness_(biology)/MYpAGGey">fitness</a>, since an intact functional copy still exists. According to some evolutionary models, shared duplicated pseudogenes indicate the evolutionary relatedness of humans and the other primates.<a class="footnote-ref" id="fnref:14" href="#fn:14">14</a> If pseudogenization is due to gene duplication, it usually occurs in the first few million years after the gene duplication, provided the gene has not been subjected to any <a href="/facts/Selection_pressure/8zrwXR50">selection pressure</a>.<a class="footnote-ref" id="fnref:15" href="#fn:15">15</a> Gene duplication generates functional <a href="/facts/Gene_redundancy/lD9rEwTQ">redundancy</a> and it is not normally advantageous to carry two identical genes. Mutations that disrupt either the structure or the function of either of the two genes are not deleterious and will not be removed through the selection process. As a result, the gene that has been mutated gradually becomes a pseudogene and will be either unexpressed or functionless. This kind of evolutionary fate is shown by population <a href="/facts/Genetic_model/zUJdKJd3">genetic modeling</a><a class="footnote-ref" id="fnref:16" href="#fn:16">16</a><a class="footnote-ref" id="fnref:17" href="#fn:17">17</a> and also by <a href="/facts/Genome_analysis/ms8hrgVa">genome analysis</a>.<a class="footnote-ref" id="fnref:18" href="#fn:18">18</a><a class="footnote-ref" id="fnref:19" href="#fn:19">19</a> According to evolutionary context, these pseudogenes will either be deleted or become so distinct from the parental genes so that they will no longer be identifiable. Relatively young pseudogenes can be recognized due to their sequence similarity.<a class="footnote-ref" id="fnref:20" href="#fn:20">20</a>

<h3>Unitary pseudogenes</h3>

Various mutations (such as <a href="/facts/Indel/4GbSXrGm">indels</a> and <a href="/facts/Nonsense_mutation/Sqxnqwvv">nonsense mutations</a>) can prevent a gene from being normally <a href="/facts/Transcription_(biology)/bDgp9HDN">transcribed</a> or <a href="/facts/Translation_(biology)/JcPC1rth">translated</a>, and thus the gene may become less- or non-functional or "deactivated". These are the same mechanisms by which non-processed genes become pseudogenes, but the difference in this case is that the gene was not duplicated before pseudogenization. Normally, such a pseudogene would be unlikely to become fixed in a population, but various population effects, such as <a href="/facts/Genetic_drift/lvoEEctX">genetic drift</a>, a <a href="/facts/Population_bottleneck/VB5DY1jG">population bottleneck</a>, or, in some cases, <a href="/facts/Natural_selection/JXTte6en">natural selection</a>, can lead to fixation. The classic example of a unitary pseudogene is the gene that presumably coded the enzyme <a href="/facts/L-gulonolactone_oxidase/vKjpvsgz">L-gulono-γ-lactone oxidase</a> (GULO) in primates. In all mammals studied besides primates (except guinea pigs), GULO aids in the biosynthesis of <a href="/facts/Ascorbic_acid/IA2f1fTm">ascorbic acid</a> (vitamin C), but it exists as a disabled gene (GULOP) in humans and other primates.<a class="footnote-ref" id="fnref:21" href="#fn:21">21</a><a class="footnote-ref" id="fnref:22" href="#fn:22">22</a> Another more recent example of a disabled gene links the deactivation of the <a href="/facts/Caspase_12/fsja1eEh">caspase 12</a> gene (through a <a href="/facts/Nonsense_mutation/Sqxnqwvv">nonsense mutation</a>) to positive selection in humans.<a class="footnote-ref" id="fnref:23" href="#fn:23">23</a>

<h3>Polymorphic pseudogenes</h3>
Some pseudogenes are still intact in some individuals but inactivated (mutated) in others. Abascal et al. have called these pseudogenes "polymorphic".<a class="footnote-ref" id="fnref:24" href="#fn:24">24</a> They are often <a href="/facts/Zygosity/XzEJ5gPp">homozygous</a> for loss-of-function (LoF) variants, that is, in many people both copies are inactive. Polymorphic pseudogenes often represent non-essential (or dispensable) genes, as opposed to essential genes, and their frequent mutations are actually a criterion to establish them as non-essential.<a class="footnote-ref" id="fnref:25" href="#fn:25">25</a> Lopes-Marques et al. define polymorphic pseudogenes as genes that carry a LoF allele with a frequency higher than 1% (in global or certain sub-populations) and without overt pathogenic consequences when homozygous.<a class="footnote-ref" id="fnref:26" href="#fn:26">26</a>

<h2 id="examples-of-pseudogene-function">Examples of pseudogene function</h2>
While the vast majority of pseudogenes have lost their function, some cases have emerged in which a pseudogene either re-gained its original or a similar function or evolved a new function. In the <a href="/facts/Human_genome/VTV85pbn">human genome</a>, a number of examples have been identified that were originally classified as pseudogenes but later discovered to have a functional, although not necessarily protein-coding, role.<a class="footnote-ref" id="fnref:27" href="#fn:27">27</a><a class="footnote-ref" id="fnref:28" href="#fn:28">28</a>
Examples include the following:

<h3>Protein-coding: "pseudo-pseudogenes"</h3>

The rapid proliferation of <a href="/facts/DNA_sequencing/hsPsNCQW">DNA sequencing</a> technologies has led to the identification of many apparent pseudogenes using <a href="/facts/Gene_prediction/QFdMeIN2">gene prediction</a> techniques. Pseudogenes are often identified by the appearance of a premature <a href="/facts/Stop_codon/1yuAkq9X">stop codon</a> in a predicted mRNA sequence, which would, in theory, prevent synthesis (<a href="/facts/Translation_(biology)/JcPC1rth">translation</a>) of the normal <a href="/facts/Protein/Jxmagu3E">protein</a> product of the original gene. There have been some reports of <a href="/facts/Stop_codon/1yuAkq9X">translational readthrough</a> of such premature stop codons in mammals. As alluded to in the figure above, a small amount of the protein product of such readthrough may still be recognizable and function at some level. If so, the pseudogene can be subject to <a href="/facts/Natural_selection/JXTte6en">natural selection</a>. That appears to have happened during the evolution of <a href="/facts/Drosophila/P4K7RkJl">Drosophila</a> <a href="/facts/Species/oDg6b96r">species</a>.
In 2016 it was reported that four predicted pseudogenes in multiple Drosophila species actually encode proteins with biologically important functions,<a class="footnote-ref" id="fnref:29" href="#fn:29">29</a> "suggesting that such 'pseudo-pseudogenes' could represent a widespread phenomenon". For example, the functional protein (a glutamate <a href="/facts/Olfactory_receptor/cY5n56yy">olfactory receptor</a>) from gene Ir75a is found only in <a href="/facts/Neurons/G7CyTVdH">neurons</a>. This finding of tissue-specific biologically-functional genes that could have been classified as pseudogenes by <a href="/facts/In_silico/g2Cz0ejg">in silico</a> analysis complicates the analysis of sequence data.<a class="footnote-ref" id="fnref:30" href="#fn:30">30</a> Another Drosophilia pseudo-pseudogene is jingwei,<a class="footnote-ref" id="fnref:31" href="#fn:31">31</a><a class="footnote-ref" id="fnref:32" href="#fn:32">32</a> which encodes a functional <a href="/facts/Alcohol_dehydrogenase/XWwHgyad">alcohol dehydrogenase</a> enzyme in vivo.<a class="footnote-ref" id="fnref:33" href="#fn:33">33</a>
As of 2012, it appeared that there are approximately 12,000–14,000 pseudogenes in the human genome.<a class="footnote-ref" id="fnref:34" href="#fn:34">34</a> A 2016 <a href="/facts/Proteogenomics/L8Xat0ne">proteogenomics</a> analysis using <a href="/facts/Mass_spectrometry/RH5WBHJ2">mass spectrometry</a> of peptides identified at least 19,262 human proteins produced from 16,271 genes or clusters of genes, with 8 new protein-coding genes identified that were previously considered pseudogenes.<a class="footnote-ref" id="fnref:35" href="#fn:35">35</a> An earlier analysis found that human PGAM4 (phosphoglycerate mutase),<a class="footnote-ref" id="fnref:36" href="#fn:36">36</a> previously thought to be a pseudogene, is not only functional, but also causes infertility if mutated.<a class="footnote-ref" id="fnref:37" href="#fn:37">37</a><a class="footnote-ref" id="fnref:38" href="#fn:38">38</a>
A number of pseudo-pseudogenes were also found in prokaryotes, where some stop codon substitutions in essential genes appear to be retained, even positively selected for.<a class="footnote-ref" id="fnref:39" href="#fn:39">39</a><a class="footnote-ref" id="fnref:40" href="#fn:40">40</a>

<h3>Non-protein-coding</h3>
siRNAs. Some endogenous <a href="/facts/SiRNA/891ytkD9">siRNAs</a> appear to be derived from pseudogenes, and thus some pseudogenes play a role in regulating protein-coding transcripts, as reviewed.<a class="footnote-ref" id="fnref:41" href="#fn:41">41</a> One of the many examples is psiPPM1K. Processing of RNAs transcribed from psiPPM1K yield siRNAs that can act to suppress the most common type of liver cancer, <a href="/facts/Hepatocellular_carcinoma/lE0P5CqE">hepatocellular carcinoma</a>.<a class="footnote-ref" id="fnref:42" href="#fn:42">42</a> This and much other research has led to considerable excitement about the possibility of targeting pseudogenes with/as therapeutic agents<a class="footnote-ref" id="fnref:43" href="#fn:43">43</a>

piRNAs. Some <a href="/facts/Piwi-interacting_RNA/5JXza7t8">piRNAs</a> are derived from pseudogenes located in piRNA clusters.<a class="footnote-ref" id="fnref:44" href="#fn:44">44</a> Those piRNAs regulate genes via the piRNA pathway in mammalian testes and are crucial for limiting <a href="/facts/Transposable_element/WbVMhuWR">transposable element</a> damage to the genome.<a class="footnote-ref" id="fnref:45" href="#fn:45">45</a>microRNAs. There are many reports of pseudogene transcripts acting as <a href="/facts/MicroRNA/UjqbYYpe">microRNA</a> decoys. Perhaps the earliest definitive example of such a pseudogene involved in cancer is the pseudogene of <a href="/facts/BRAF_(gene)/BYNJuQBg">BRAF</a>. The BRAF gene is a <a href="/facts/Proto-oncogene/WLFu6Ma5">proto-oncogene</a> that, when mutated, is associated with many cancers. Normally, the amount of BRAF protein is kept under control in cells through the action of miRNA. In normal situations, the amount of RNA from BRAF and the pseudogene BRAFP1 compete for miRNA, but the balance of the 2 RNAs is such that cells grow normally. However, when BRAFP1 RNA expression is increased (either experimentally or by natural mutations), less miRNA is available to control the expression of BRAF, and the increased amount of BRAF protein causes cancer.<a class="footnote-ref" id="fnref:46" href="#fn:46">46</a> This sort of competition for regulatory elements by RNAs that are endogenous to the genome has given rise to the term <a href="/facts/CeRNA/jjW4S5to">ceRNA</a>.
PTEN. The <a href="/facts/PTEN_(gene)/Xg6MAcHm">PTEN</a> gene is a known <a href="/facts/Tumor_suppressor_gene/Awte4S51">tumor suppressor gene</a>. The PTEN pseudogene, PTENP1 is a processed pseudogene that is very similar in its genetic sequence to the wild-type gene. However, PTENP1 has a missense mutation which eliminates the <a href="/facts/Codon/zUK0bY1B">codon</a> for the <a href="/facts/Eukaryotic_translation/0A9ezESb">initiating methionine</a> and thus prevents translation of the normal PTEN protein.<a class="footnote-ref" id="fnref:47" href="#fn:47">47</a> In spite of that, PTENP1 appears to play a role in <a href="/facts/Oncogenesis/PC8wc1Mf">oncogenesis</a>. The 3' <a href="/facts/Untranslated_region/Tfk4gD18">UTR</a> of PTENP1 mRNA functions as a decoy of PTEN mRNA by targeting <a href="/facts/Micro_RNA/UjqbYYpe">micro RNAs</a> due to its similarity to the PTEN gene, and overexpression of the 3' UTR resulted in an increase of PTEN protein level.<a class="footnote-ref" id="fnref:48" href="#fn:48">48</a> That is, overexpression of the PTENP1 3' UTR leads to increased regulation and suppression of cancerous tumors. The biology of this system is basically the inverse of the BRAF system described above.
Potogenes. Pseudogenes can, over evolutionary time scales, participate in <a href="/facts/Gene_conversion/QjyuAPB5">gene conversion</a> and other mutational events that may give rise to new or newly functional genes. This has led to the concept that pseudogenes could be viewed as potogenes: potential genes for evolutionary diversification.<a class="footnote-ref" id="fnref:49" href="#fn:49">49</a>

<h2 id="bacterial-pseudogenes">Bacterial pseudogenes</h2>
Pseudogenes are found in <a href="/facts/Bacteria/wC8xSCsU">bacteria</a>.<a class="footnote-ref" id="fnref:50" href="#fn:50">50</a> Most are found in bacteria that are not free-living; that is, they are either <a href="/facts/Symbiont/MrBArRGa">symbionts</a> or <a href="/facts/Obligate_intracellular_parasite/SjsmCTNr">obligate intracellular parasites</a>. Thus, they do not require many genes that are needed by free-living bacteria, such as gene associated with metabolism and DNA repair. However, there is not an order to which functional <a href="/facts/Gene/e1swwPY6">genes</a> are lost first. For example, the oldest pseudogenes in <a href="/facts/Mycobacterium_leprae/UlcawhX9">Mycobacterium leprae</a> are in <a href="/facts/RNA_polymerase/gHd0ET9R">RNA polymerases</a> and the <a href="/facts/Biosynthesis/aFk7Tk7f">biosynthesis</a> of <a href="/facts/Secondary_metabolite/mKnQjBQp">secondary metabolites</a> while the oldest ones in <a href="/facts/Shigella_flexneri/gbUB7Mea">Shigella flexneri</a> and <a href="/facts/Shigella/xKEXoT4w">Shigella typhi</a> are in <a href="/facts/DNA_replication/wrU6RuR3">DNA replication</a>, recombination, and <a href="/facts/DNA_repair/hsURuYYq">repair</a>.<a class="footnote-ref" id="fnref:51" href="#fn:51">51</a>
Since most bacteria that carry pseudogenes are either symbionts or obligate intracellular parasites, genome size eventually reduces. An extreme example is the genome of <a href="/facts/Mycobacterium_leprae/UlcawhX9">Mycobacterium leprae</a>, an obligate parasite and the causative agent of <a href="/facts/Leprosy/FSjTpMEB">leprosy</a>. It has been reported to have 1,133 pseudogenes which give rise to approximately 50% of its <a href="/facts/Transcriptome/h6CC0sR5">transcriptome</a>.<a class="footnote-ref" id="fnref:52" href="#fn:52">52</a> The effect of pseudogenes and genome reduction can be further seen when compared to <a href="/facts/Mycobacterium_marinum/8Xj4fzdw">Mycobacterium marinum</a>, a <a href="/facts/Pathogen/axMXtV1M">pathogen</a> from the same family. Mycobacteirum marinum has a larger genome compared to Mycobacterium leprae because it can survive outside the host; therefore, the genome must contain the genes needed to do so.<a class="footnote-ref" id="fnref:53" href="#fn:53">53</a>
Although genome reduction focuses on what genes are not needed by getting rid of pseudogenes, selective pressures from the host can sway what is kept. In the case of a symbiont from the <a href="/facts/Verrucomicrobiota/mvsaIoJ0">Verrucomicrobiota</a> phylum, there are seven additional copies of the gene coding the mandelalide pathway.<a class="footnote-ref" id="fnref:54" href="#fn:54">54</a> The host, species from Lissoclinum, use mandelalides as part of its defense mechanism.<a class="footnote-ref" id="fnref:55" href="#fn:55">55</a>
The relationship between <a href="/facts/Epistasis/bJAJL90w">epistasis</a> and the domino theory of gene loss was observed in Buchnera aphidicola. The domino theory suggests that if one gene of a cellular process becomes inactivated, then selection in other genes involved relaxes, leading to gene loss.<a class="footnote-ref" id="fnref:56" href="#fn:56">56</a> When comparing <a href="/facts/Buchnera_aphidicola/PKlSLpJ7">Buchnera aphidicola</a> and <a href="/facts/Escherichia_coli/nR4Gvl56">Escherichia coli</a>, it was found that positive epistasis furthers gene loss while negative epistasis hinders it.

<h2 id="see-also">See also</h2>
<ul><li><a href="/facts/List_of_disabled_human_pseudogenes/dLwX5vBJ">List of disabled human pseudogenes</a></li>
<li><a href="/facts/Molecular_evolution/lmMbqfzH">Molecular evolution</a></li>
<li><a href="/facts/Molecular_paleontology/7FrRd8kx">Molecular paleontology</a></li>
<li><a href="/facts/Pseudogene_(database)/3CIJ2QWN">Pseudogene (database)</a></li>
<li><a href="/facts/Retroposon/kBg39cI0">Retroposon</a></li>
<li><a href="/facts/Retrotransposon/E0SgHUjT">Retrotransposon</a></li></ul>

<h2 id="further-reading">Further reading</h2>

<ul><li>Gerstein M, Zheng D (August 2006). "The real life of pseudogenes". Scientific American. 295 (2): 48–55. <a href="/facts/Bibcode_(identifier)/9HtdQSGB">Bibcode</a>:<a href="https://ui.adsabs.harvard.edu/abs/2006SciAm.295b..48G">2006SciAm.295b..48G</a>. <a href="/facts/Doi_(identifier)/muM9Etpq">doi</a>:<a href="https://doi.org/10.1038%2Fscientificamerican0806-48">10.1038/scientificamerican0806-48</a>. <a href="/facts/PMID_(identifier)/JlHAvMHt">PMID</a> <a href="https://pubmed.ncbi.nlm.nih.gov/16866288">16866288</a>.</li>
<li>Torrents D, Suyama M, Zdobnov E, Bork P (December 2003). <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC403797">"A genome-wide survey of human pseudogenes"</a>. Genome Research. 13 (12): 2559–2567. <a href="/facts/Doi_(identifier)/muM9Etpq">doi</a>:<a href="https://doi.org/10.1101%2Fgr.1455503">10.1101/gr.1455503</a>. <a href="/facts/PMC_(identifier)/dX1zMt71">PMC</a> <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC403797">403797</a>. <a href="/facts/PMID_(identifier)/JlHAvMHt">PMID</a> <a href="https://pubmed.ncbi.nlm.nih.gov/14656963">14656963</a>.</li>
<li>Bischof JM, Chiang AP, Scheetz TE, Stone EM, Casavant TL, Sheffield VC, Braun TA (June 2006). <a href="https://doi.org/10.1002%2Fhumu.20335">"Genome-wide identification of pseudogenes capable of disease-causing gene conversion"</a>. Human Mutation. 27 (6): 545–552. <a href="/facts/Doi_(identifier)/muM9Etpq">doi</a>:<a href="https://doi.org/10.1002%2Fhumu.20335">10.1002/humu.20335</a>. <a href="/facts/PMID_(identifier)/JlHAvMHt">PMID</a> <a href="https://pubmed.ncbi.nlm.nih.gov/16671097">16671097</a>. <a href="/facts/S2CID_(identifier)/ldJsHa2Y">S2CID</a> <a href="https://api.semanticscholar.org/CorpusID:20219423">20219423</a>.</li>
<li>Syberg-Olsen MJ, Garber AI, Keeling PJ, McCutcheon JP, Husnik F (July 2022). <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9336565">"Pseudofinder: Detection of Pseudogenes in Prokaryotic Genomes"</a>. Molecular Biology and Evolution. 39 (7). <a href="/facts/Doi_(identifier)/muM9Etpq">doi</a>:<a href="https://doi.org/10.1093%2Fmolbev%2Fmsac153">10.1093/molbev/msac153</a>. <a href="/facts/PMC_(identifier)/dX1zMt71">PMC</a> <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9336565">9336565</a>. <a href="/facts/PMID_(identifier)/JlHAvMHt">PMID</a> <a href="https://pubmed.ncbi.nlm.nih.gov/35801562">35801562</a>.</li></ul>

<h2 id="external-links">External links</h2>
<ul><li><a href="https://web.archive.org/web/20110222111721/http://starbase.sysu.edu.cn/">Pseudogene interaction database, miRNA-pseudogene and protein-pseudogene interaction maps database</a></li>
<li><a href="https://web.archive.org/web/20150211035244/http://www.pseudogene.org/">Yale University pseudogene database</a></li>
<li><a href="https://web.archive.org/web/20140717062856/http://pbil.univ-lyon1.fr/databases/hoppsigen.html">Hoppsigen database</a> (homologous processed pseudogenes)</li>
<li><a href="https://www.bioinfo.mochsl.org.br/rcpedia/">RCPedia - Processed Pseudogene database</a></li></ul>

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</ol>

Pseudogene open-in-new

Pseudogene