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Variations in the number of STR repeats can cause genetic diseases when they lie within a gene but most of these regions appear to be non-functional junk DNA where the number of repeats can vary considerably from individual to individual. This is why these length differences are used extensively in [[DNA profiling|DNA fingerprinting]].
===Junk DNA===
{{Main|Junk DNA}}
Although many non-coding regions have biological function,<ref name="Costa non-coding32">{{cite book |title=Non-coding RNAs and Epigenetic Regulation of Gene Expression: Drivers of Natural Selection |vauthors=Costa F |date=2012 |publisher=[[Caister Academic Press]] |isbn=978-1-904455-94-3 |veditors=Morris KV |chapter=7 Non-coding RNAs, Epigenomics, and Complexity in Human Cells}}{{page needed|date=June 2022}}</ref><ref name="Nessa32">{{cite book |title=Junk DNA: A Journey Through the Dark Matter of the Genome |vauthors=Carey M |date=2015 |publisher=Columbia University Press |isbn=978-0-231-17084-0 |author-link=Nessa Carey}}{{page needed|date=June 2022}}</ref> some genomes contain sequence that does not have biological function and has been described as "Junk DNA". Though exact definitions differ, this refers broadly to "any DNA sequence that does not play a functional role in development, physiology, or some other organism-level capacity."<ref name="PalazzoGregory20142">{{cite journal | vauthors = Palazzo AF, Gregory TR | title = The case for junk DNA | journal = PLoS Genetics | volume = 10 | issue = 5 | pages = e1004351 | date = May 2014 | pmid = 24809441 | pmc = 4014423 | doi = 10.1371/journal.pgen.1004351 }}</ref> The amount of sequence that falls under this term varies widely between organisms.<ref name=":0" /><ref name=":12" /> The term itself has been contentious as different definitions of what constitutes biological function lead to highly different estimates of what proportion of a genome falls into the category.<ref name=":02">{{cite journal | vauthors = Palazzo AF, Kejiou NS | title = Non-Darwinian Molecular Biology | journal = Frontiers in Genetics | volume = 13 | pages = 831068 | year = 2022 | pmid = 35251134 | pmc = 8888898 | doi = 10.3389/fgene.2022.831068 | doi-access = free }}</ref><ref name=":13">{{cite journal | vauthors = Ponting CP, Hardison RC | title = What fraction of the human genome is functional? | journal = Genome Research | volume = 21 | issue = 11 | pages = 1769–1776 | date = November 2011 | pmid = 21875934 | pmc = 3205562 | doi = 10.1101/gr.116814.110 }}</ref> In particular, the [[ENCODE]] project in the 2000s demonstrated detectable biochemical activity resulting from most parts of the genome ([[Transcription (biology)|transcription to RNA]], [[Transcription factor-binding site|transcription factor binding]], etc).<ref name="eddy2">{{cite journal | vauthors = Eddy SR | title = The C-value paradox, junk DNA and ENCODE | journal = Current Biology | volume = 22 | issue = 21 | pages = R898-R899 | date = November 2012 | pmid = 23137679 | doi = 10.1016/j.cub.2012.10.002 | s2cid = 28289437 | doi-access = free | author-link = Sean Eddy }}</ref><ref>{{cite journal | vauthors = Celniker SE, Dillon LA, Gerstein MB, Gunsalus KC, Henikoff S, Karpen GH, Kellis M, Lai EC, Lieb JD, MacAlpine DM, Micklem G, Piano F, Snyder M, Stein L, White KP, Waterston RH | display-authors = 6 | title = Unlocking the secrets of the genome | journal = Nature | volume = 459 | issue = 7249 | pages = 927–930 | date = June 2009 | pmid = 19536255 | pmc = 2843545 | doi = 10.1038/459927a }}</ref> However, whether this biochemical activity is promiscuous activity in a noisy biological system or evolutionarily relevant biological function has been less clear - and consequently, whether that DNA counts as "junk" or not.<ref name=":12">{{cite journal | vauthors = Ponting CP, Hardison RC | title = What fraction of the human genome is functional? | journal = Genome Research | volume = 21 | issue = 11 | pages = 1769–1776 | date = November 2011 | pmid = 21875934 | pmc = 3205562 | doi = 10.1101/gr.116814.110 }}</ref><ref name=":13" /><ref name="eddy2" />
Junk DNA is DNA that has no biologically relevant function, such as pseudogenes and fragments of once active transposons. Bacteria genomes have very little junk DNA<ref>{{ cite journal | vauthors = Gil R, and Latorre A | date = 2012 | title = Factors behind junk DNA in bacteria | journal = Genes | volume = 3 | pages = 634-650 | doi = 10.3390/genes3040634 }}</ref> but some eukaryotic genomes may have a substantial amount of junk DNA.<ref name="PalazzoGregory2014">{{cite journal | vauthors = Palazzo AF, Gregory TR | title = The case for junk DNA | journal = PLoS Genetics | volume = 10 | issue = 5 | pages = e1004351 | date = May 2014 | pmid = 24809441 | pmc = 4014423 | doi = 10.1371/journal.pgen.1004351 }}</ref> The exact amount of nonfunctional DNA in humans and other species with large genomes has not been determined and there is considerable controversy in the scientific literature.<ref>{{ cite journal | last = Morange | first = Michel | date = 2014 | title = Genome as a Multipurpose Structure Built by Evolution | journal = Perspectives in Biology and Medicine | volume = 57 | pages = 162-171 | doi = 10.1353/pbm.2014.0008 }}</ref><ref>{{cite journal | vauthors = Haerty W, and Ponting CP | title = No Gene in the Genome Makes Sense Except in the Light of Evolution. | year = 2014 | journal = Annual Review of Genomics and Human Genetics | volume =25 | pages = 71-92 | doi = 10.1146/annurev-genom-090413-025621}}</ref> See the article on [[Junk DNA]] for more information.
The nonfunctional DNA in bacterial genomes is mostly located in the intergenic fraction of non-coding DNA but in eukaryotic genomes it may also be found within introns (see [[Introns]]). It's important to note that there are many examples of functional DNA elements in non-coding DNA (see above) and there are no scientists who claim that all non-coding DNA is junk.
==Genome-wide association studies (GWAS) and non-coding DNA==
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