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→Junk DNA: "ENCODE PROJECT" was probably not a useful section title any more. I have attempted to separate out into different broad methodological frameworks, but it could certainly use some refinement. |
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Pseudogenes are mostly former genes that have become non-functional due to mutation but the term also refers to inactive DNA sequences that are derived from RNAs produced by functional genes ([[Pseudogene|processed pseudogenes]]). Pseudogenes are only a small fraction of noncoding DNA in prokaryotic genomes because they are eliminated by negative selection. In some eukaryotes, however, pseudogenes can accumulate because selection isn't powerful enough to eliminate them (see [[Nearly neutral theory of molecular evolution]]).
The human genome contains about 15,000 pseudogenes derived from protein-coding genes and an unknown number derived from noncoding genes.<ref>{{ cite web | url = https://useast.ensembl.org/Homo_sapiens/Info/Annotation | title = Ensemble Human reference genome GRCh38.p13}}</ref> They may cover a substantial fraction of the genome (~5%) since many of them contain former intron sequences
Pseudogenes are junk DNA by definition and they evolve at the neutral rate as expected for junk DNA.<ref>{{ cite journal | vauthors = Xu J, Zhang J | date = 2015 | title = Are human translated pseudogenes functional? | journal = Molecular Biology and Evolution | volume = 33 | issue = 3 | pages = 755–760 | doi = 10.1093/molbev/msv268 | pmid = 26589994 | pmc = 5009996 }}</ref> Some former pseudogenes have secondarily acquired a function and this leads some scientists to speculate that most pseudogenes are not junk because they have a yet-to-be-discovered function.<ref>{{ cite journal | vauthors = Wen YZ, Zheng LL, Qu LH, Ayala FJ, Lun ZR | date = 2012 | title = Pseudogenes are not pseudo any more. | journal = RNA Biology | volume = 9 | issue = 1 | pages = 27–32 | doi = 10.4161/rna.9.1.18277 | pmid = 22258143 | s2cid = 13161678 }}</ref>
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