Editing Inverted repeat (section)

{{Short description|Nucleic acid sequence}}
An '''inverted repeat''' (or '''IR''') is a single stranded sequence of [[nucleotide]]s followed downstream by its [[complementarity (molecular biology)|reverse complement]].<ref name="Ussery2008">{{cite book |title=Computing for Comparative Microbial Genomics: Bioinformatics for Microbiologists |chapter=Word Frequencies, Repeats, and Repeat-related Structures in Bacterial Genomes |series=Computational Biology |volume=8 |pages=133–144 |first1=David W. |last1=Ussery |first2=Trudy |last2=Wassenaar |first3=Stefano |last3=Borini |publisher=Springer |edition=1 |date=2008-12-22 |isbn=978-1-84800-254-8}}</ref> The intervening sequence of nucleotides between the initial sequence and the reverse complement can be any length including zero. For example, {{color|blue|5'---TTACGnnnnnn}}{{color|green|CGTAA---3'}} is an inverted repeat sequence. When the intervening length is zero, the composite sequence is a [[palindromic sequence]].<ref>{{cite journal | pmid=25409465 |  doi= 10.1371/journal.pone.0113349 |title= detectIR: A Novel Program for Detecting Perfect and Imperfect Inverted Repeats Using Complex Numbers and Vector Calculation |first1= Congting |last1= Ye |first2= Guoli |last2= Ji |first3= Chun |last3= Liang |year= 2014 |journal= PLOS ONE |volume= 9 |issue= 11 |page= e113349| pmc= 4237412 | bibcode= 2014PLoSO...9k3349Y | doi-access= free }}</ref>

Both inverted repeats and [[direct repeat]]s constitute types of [[Nucleic acid sequence|nucleotide sequences]] that occur repetitively. <!--The [[human genome]] has many nucleotide sequences that occur repeatedly and as such, can be grouped in two simple classes: repetitive and unique sequences.<ref name=Eichler />-->  These [[repeated sequence (DNA)|repeated DNA sequences]] often range from a pair of nucleotides to a whole [[gene]], while the proximity of the repeat sequences varies between widely dispersed and simple [[tandemly arrayed genes|tandem arrays]].<ref name=Sutherland>{{cite journal|last=Richards|first=GR|author2=Richards, RI|title=Simple tandem DNA repeats and human genetic disease|journal=Proceedings of the National Academy of Sciences of the United States of America|date=Apr 25, 1995|volume=92|issue=9|pages=3636–41|pmid=7731957|bibcode=1995PNAS...92.3636S|doi=10.1073/pnas.92.9.3636|pmc=42017|doi-access=free}}</ref> The short [[tandem repeat]] sequences may exist as just a few copies in a small region to thousands of copies dispersed all over the genome of most [[eukaryotes]].<ref name=VAN>{{cite journal|last=van Belkum|first=A |author2=Scherer, S |author3=van Alphen, L |author4=Verbrugh, H|title=Short-sequence DNA repeats in prokaryotic genomes|journal=Microbiology and Molecular Biology Reviews|date=June 1998|volume=62|issue=2|pages=275–93|doi=10.1128/MMBR.62.2.275-293.1998 |pmid=9618442|pmc=98915}}</ref> Repeat sequences with about 10–100 [[base pair]]s are known as [[minisatellite]]s, while shorter repeat sequences having mostly 2–4 base pairs are known as [[microsatellite]]s.<ref name=Ramel>{{cite journal|last=Ramel|first=C|title=Mini- and microsatellites|journal=Environmental Health Perspectives|date=June 1997|volume=105|pages=781–9|pmid=9255562|pmc=1470042|issue=Suppl 4|doi=10.2307/3433284|jstor=3433284}}</ref>  The most common repeats include the dinucleotide repeats, which have the [[nitrogenous base|bases]] AC on one DNA strand, and GT on the complementary strand.<ref name=Sutherland /> Some elements of the [[genome]] with unique sequences function as [[exons]], [[introns]] and regulatory DNA.<ref name=Eichler>{{cite journal|last=Eichler|first=EE|title=Masquerading repeats: paralogous pitfalls of the human genome|journal=Genome Research|date=August 1998|volume=8|issue=8|pages=758–62|pmid=9724321|doi=10.1101/gr.8.8.758 |doi-access=free}}</ref> Though the most familiar loci of the repetitive sequences are the [[centromere]] and the [[telomere]],<ref name=Eichler /> a large portion of the repeated sequences in the genome are found among the [[noncoding DNA]].<ref name=Ramel />

Inverted repeats have a number of important biological functions.  They define the boundaries in [[transposon]]s and indicate regions capable of self-complementary [[base pairing]] (regions within a single sequence which can base pair with each other). These properties play an important role in genome instability<ref name=Voineagu /> and contribute not only to [[cellular evolution]] and [[genetic diversity]]<ref>{{cite journal|last=Lin|first=CT|author2=Lin, WH |author3=Lyu, YL |author4= Whang-Peng, J |title=Inverted repeats as genetic elements for promoting DNA inverted duplication: implications in gene amplification|journal=Nucleic Acids Research|date=Sep 1, 2001|volume=29|issue=17|pages=3529–38|pmid=11522822|doi=10.1093/nar/29.17.3529|pmc=55881}}</ref> but also to [[mutation]] and [[disease]].<ref name=bissler />  In order to study these effects in detail, a number of programs and databases have been developed to assist in discovery and annotation of inverted repeats in various genomes.