Editing Pseudogene (section)

==Properties==

Pseudogenes are usually characterized by a combination of similarity or [[Sequence homology|homology]] to a known gene, together with a loss of some functionality. That is, although every pseudogene has a [[DNA]] sequence that is similar to some functional gene, they are usually unable to produce functional final protein products.<ref name="Mighell_2000">{{cite journal | vauthors = Mighell AJ, Smith NR, Robinson PA, Markham AF | title = Vertebrate pseudogenes | journal = FEBS Letters | volume = 468 | issue = 2–3 | pages = 109–114 | date = February 2000 | pmid = 10692568 | doi = 10.1016/S0014-5793(00)01199-6 | s2cid = 42204036 | doi-access = free }}</ref> 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.
#Homology is implied by sequence similarity between the DNA sequences of the pseudogene and a known gene. After [[sequence alignment|aligning]] the two sequences, the percentage of identical [[base pair]]s 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 [[Convergent evolution]]).
#Nonfunctionality can manifest itself in many ways. Normally, a gene must go through several steps to a fully functional protein: [[Transcription (genetics)|Transcription]], [[pre-mRNA processing]], [[translation (biology)|translation]], and [[protein folding]] 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 [[stop codon]]s and [[frameshift mutation|frameshifts]], which almost universally prevent the translation of a functional protein product.

Pseudogenes for [[RNA]] 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.<ref>{{cite journal | vauthors = Robicheau BM, Susko E, Harrigan AM, Snyder M | title = Ribosomal RNA Genes Contribute to the Formation of Pseudogenes and Junk DNA in the Human Genome | journal = Genome Biology and Evolution | volume = 9 | issue = 2 | pages = 380–397 | date = February 2017 | pmid = 28204512 | pmc = 5381670 | doi = 10.1093/gbe/evw307 }}</ref>

Pseudogenes can complicate molecular genetic studies. For example, amplification of a gene by [[polymerase chain reaction|PCR]] may simultaneously amplify a pseudogene that shares similar sequences. This is known as PCR bias or amplification bias. Similarly, pseudogenes are sometimes [[DNA annotation|annotated]] as genes in [[genome]] sequences.

Processed pseudogenes often pose a problem for [[gene prediction]] 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.<ref name="Van_Baren_Brent_2006">{{cite journal | vauthors = van Baren MJ, Brent MR | title = Iterative gene prediction and pseudogene removal improves genome annotation | journal = Genome Research | volume = 16 | issue = 5 | pages = 678–685 | date = May 2006 | pmid = 16651666 | pmc = 1457044 | doi = 10.1101/gr.4766206 }}</ref>

In 2014, 140 human pseudogenes have been shown to be translated.<ref>{{cite journal | vauthors = Kim MS, Pinto SM, Getnet D, Nirujogi RS, Manda SS, Chaerkady R, Madugundu AK, Kelkar DS, Isserlin R, Jain S, Thomas JK, Muthusamy B, Leal-Rojas P, Kumar P, Sahasrabuddhe NA, Balakrishnan L, Advani J, George B, Renuse S, Selvan LD, Patil AH, Nanjappa V, Radhakrishnan A, Prasad S, Subbannayya T, Raju R, Kumar M, Sreenivasamurthy SK, Marimuthu A, Sathe GJ, Chavan S, Datta KK, Subbannayya Y, Sahu A, Yelamanchi SD, Jayaram S, Rajagopalan P, Sharma J, Murthy KR, Syed N, Goel R, Khan AA, Ahmad S, Dey G, Mudgal K, Chatterjee A, Huang TC, Zhong J, Wu X, Shaw PG, Freed D, Zahari MS, Mukherjee KK, Shankar S, Mahadevan A, Lam H, Mitchell CJ, Shankar SK, Satishchandra P, Schroeder JT, Sirdeshmukh R, Maitra A, Leach SD, Drake CG, Halushka MK, Prasad TS, Hruban RH, Kerr CL, Bader GD, Iacobuzio-Donahue CA, Gowda H, Pandey A | display-authors = 6 | title = A draft map of the human proteome | journal = Nature | volume = 509 | issue = 7502 | pages = 575–581 | date = May 2014 | pmid = 24870542 | pmc = 4403737 | doi = 10.1038/nature13302 | bibcode = 2014Natur.509..575K }}</ref> However, the function, if any, of the protein products is unknown.