Editing Stop codon (section)

== Properties ==
=== Standard codons ===
In the standard genetic code, there are three different termination codons:

{|class="wikitable" style="border: none; text-align: center;"
|-
! colspan="2" | Codon
! rowspan="2" | [[DNA codon table|Standard code]]<br>(Translation table 1)
! rowspan="2" style="border:none; width:1px;" |
! rowspan="2" | Name
|-
! DNA
! RNA
|-
| <code>TAG</code> || <code>UAG</code>
| style="background-color:#B0B0B0;" | <code>STOP = Ter</code> <code>(*)</code>
| style="border: none; width: 1px;" |
| style="background-color: none;" | "amber"
|-
| <code>TAA</code> || <code>UAA</code>
| style="background-color:#B0B0B0;" | <code>STOP = Ter</code> <code>(*)</code>
| style="border: none; width: 1px;" |
| style="background-color: none;" | "ochre"
|-
| <code>TGA</code> || <code>UGA</code>
| style="background-color:#B0B0B0;" | <code>STOP = Ter</code> <code>(*)</code>
| style="border: none; width: 1px;" |
| style="background-color: none;" | "opal" (or "umber")
|}

=== Alternative stop codons ===
There are [[Genetic code#Variations|variations on the standard genetic code]], and alternative stop codons have been found in the [[Mitochondrial DNA|mitochondrial genome]]s of [[vertebrate]]s,<ref>{{Cite journal |last1=Barrell |first1=B. G. |last2=Bankier |first2=A. T. |last3=Drouin |first3=J. |date=1979-11-08 |title=A different genetic code in human mitochondria |url=http://www.nature.com/articles/282189a0 |journal=Nature |language=en |volume=282 |issue=5735 |pages=189–194 |doi=10.1038/282189a0 |pmid=226894 |bibcode=1979Natur.282..189B |s2cid=4335828 |issn=0028-0836|url-access=subscription }}</ref> ''[[Scenedesmus obliquus]]'',<ref name="Nedelcu2000">{{Cite journal |journal=Genome Research |date=June 2000 |volume=10 |issue=6 |pages=819–831 |title=The complete mitochondrial DNA sequence of ''Scenedesmus obliquus'' reflects an intermediate stage in the evolution of the green algal mitochondrial genome |first1=A.M. |last1=Nedelcu |first2=R.W. |last2=Lee |first3=G. |last3=Lemieux |first4=M.W. |last4=Gray |first5=G. |last5=Burger |pmid=10854413 |pmc=310893 |doi=10.1101/gr.10.6.819 }}</ref> and ''[[Thraustochytrid|Thraustochytrium]]''.<ref>{{Cite journal |last1=Wideman |first1=Jeremy G. |last2=Monier |first2=Adam |last3=Rodríguez-Martínez |first3=Raquel |last4=Leonard |first4=Guy |last5=Cook |first5=Emily |last6=Poirier |first6=Camille |last7=Maguire |first7=Finlay |last8=Milner |first8=David S. |last9=Irwin |first9=Nicholas A. T. |last10=Moore |first10=Karen |last11=Santoro |first11=Alyson E. |date=2019-11-25 |title=Unexpected mitochondrial genome diversity revealed by targeted single-cell genomics of heterotrophic flagellated protists |url=https://www.nature.com/articles/s41564-019-0605-4 |journal=Nature Microbiology |volume=5 |issue=1 |pages=154–165 |doi=10.1038/s41564-019-0605-4 |pmid=31768028 |issn=2058-5276|hdl=10871/39819 |s2cid=208279678 |hdl-access=free }}</ref>

{| class="wikitable" style="border:none; text-align:center;"
|+ Table of alternative stop codons and comparison with the standard genetic code
|-
! rowspan="2" style="width: 250px;" | Genetic code
! rowspan="2" style="width: 25px;" | Translation <br/> table
! colspan="2" | Codon
! rowspan="2" colspan="3" style="width: 200px;" | Translation <br/> with this code
! rowspan="2" style="border:none; width:1px;" |
! rowspan="2" style="width: 50px;" | Standard translation
|-
! style="width: 25px;" | DNA
! style="width: 25px;" | RNA
|-
| rowspan="2" | [[Vertebrate mitochondrial code|Vertebrate mitochondrial]] || rowspan="2" | 2 || <code>AGA</code> || <code>AGA</code> || colspan="3" style="background-color:#B0B0B0;" | <code>STOP = Ter</code> <code>(*)</code> || style="border: none; width: 1px;" | || style="background-color:#bbbfe0;" | <code>Arg</code> <code>(R)</code>
|-
| <code>AGG</code> || <code>AGG</code> || colspan="3" style="background-color:#B0B0B0;" | <code>STOP = Ter</code> <code>(*)</code> || style="border: none; width: 1px;" | || style="background-color:#bbbfe0;" | <code>Arg</code> <code>(R)</code>
|-
| rowspan="1" | [[Scenedesmus obliquus mitochondrial code|''Scenedesmus obliquus'' mitochondrial]] || rowspan="1" | 22 || |<code>TCA</code> || |<code>UCA</code> || colspan="3" style="background-color:#B0B0B0;" | <code>STOP = Ter</code> <code>(*)</code> || style="border: none; width: 1px;" | || style="background-color:#b3dec0;" | <code>Ser</code> <code>(S)</code>
|-
| rowspan="1" | [[Thraustochytrium mitochondrial code|''Thraustochytrium'' mitochondrial]] || rowspan="1" | 23 || <code>TTA</code> || <code>UUA</code> || colspan="3" style="background-color:#B0B0B0;" | <code>STOP = Ter</code> <code>(*)</code> || style="border: none; width: 1px;" | || style="background-color:#ffe75f;" | <code>Leu</code> <code>(L)</code>
|}

{| class="wikitable" style="border:none; text-align:center;"
| style="width: 250px;" | [[Amino acids|Amino-acid]] biochemical properties
| style="background-color:#ffe75f; width: 75px;" | Nonpolar
| style="background-color:#b3dec0; width: 75px;" | Polar
| style="background-color:#bbbfe0; width: 75px;" | Basic
| style="background-color:#f8b7d3; width: 75px;" | Acidic
| style="border: none; width: 1px;" |
| style="background-color:#B0B0B0;" | Termination: stop codon
|}

=== Reassigned stop codons ===
The nuclear genetic code is flexible as illustrated by variant genetic codes that reassign standard stop codons to amino acids.<ref name="Swart2016">{{Cite journal |last1=Swart |first1=Estienne Carl |last2=Serra |first2=Valentina |last3=Petroni |first3=Giulio |last4=Nowacki |first4=Mariusz |year=2016 |title=Genetic Codes with No Dedicated Stop Codon: Context-Dependent Translation Termination |journal=Cell |volume=166 |issue=3 |pages=691–702 |doi=10.1016/j.cell.2016.06.020 |pmc=4967479 |pmid=27426948 }}</ref>

{| class="wikitable" style="border:none; text-align:center;"
|+ Table of conditional stop codons and comparison with the standard genetic code
|-
! rowspan="2" style="width: 250px;" | Genetic code
! rowspan="2" style="width: 25px;" | Translation <br/> table
! colspan="2" | Codon
! rowspan="2" colspan="3" style="width: 200px;" | Conditional <br/> translation
! rowspan="2" style="border:none; width:1px;" |
! rowspan="2" style="width: 50px;" | Standard translation
|-
! style="width: 25px;" | DNA
! style="width: 25px;" | RNA
|-
| rowspan="1" | [[Karyorelict nuclear code|Karyorelict nuclear]] || 27 || <code>TGA</code> || <code>UGA</code> || style="width: 50px; background-color:#B0B0B0;" | <code>Ter</code> <code>(*)</code> || style="width: 10px;" | or || style="width: 50px; background-color:#ffe75f;" | <code>Trp</code> <code>(W)</code> || style="border: none; width: 1px;" | || style="background-color:#B0B0B0;" | <code>Ter</code> <code>(*)</code>
|-
| rowspan="3" | [[Condylostoma nuclear code|''Condylostoma'' nuclear]] || rowspan="3" | 28 || <code>TAA</code> || <code>UAA</code> || style="width: 50px; background-color:#B0B0B0;" | <code>Ter</code> <code>(*)</code> || style="width: 10px;" | or || style="width: 50px; background-color:#b3dec0;" | <code>Gln</code> <code>(Q)</code> || style="border: none; width: 1px;" | || style="background-color:#B0B0B0;" | <code>Ter</code> <code>(*)</code>
|-
| <code>TAG</code> || <code>UAG</code> || style="width: 50px; background-color:#B0B0B0;" | <code>Ter</code> <code>(*)</code> || style="width: 10px;" | or || style="width: 50px; background-color:#b3dec0;" | <code>Gln</code> <code>(Q)</code> || style="border: none; width: 1px;" | || style="background-color:#B0B0B0;" | <code>Ter</code> <code>(*)</code>
|-
| <code>TGA</code> || <code>UGA</code> || style="width: 50px; background-color:#B0B0B0;" | <code>Ter</code> <code>(*)</code> || style="width: 10px;" | or || style="width: 50px; background-color:#ffe75f;" | <code>Trp</code> <code>(W)</code> || style="border: none; width: 1px;" | || style="background-color:#B0B0B0;" | <code>Ter</code> <code>(*)</code>
|-
| rowspan="2" | [[Blastocrithidia nuclear code|''Blastocrithidia'' nuclear]] || rowspan="2" | 31 || <code>TAA</code> || <code>UAA</code> || style="width: 50px; background-color:#B0B0B0;" | <code>Ter</code> <code>(*)</code> || style="width: 10px;" | or || style="width: 50px; background-color:#f8b7d3;" | <code>Glu</code> <code>(E)</code> || style="border: none; width: 1px;" | || style="background-color:#B0B0B0;" | <code>Ter</code> <code>(*)</code>
|-
| <code>TAG</code> || <code>UAG</code> || style="width: 50px; background-color:#B0B0B0;" | <code>Ter</code> <code>(*)</code> || style="width: 10px;" | or || style="width: 50px; background-color:#f8b7d3;" |  <code>Glu</code> <code>(E)</code> || style="border: none; width: 1px;" | || style="background-color:#B0B0B0;" | <code>Ter</code> <code>(*)</code>
|}

=== Translation ===
In 1986, convincing evidence was provided that [[selenocysteine]] (Sec) was incorporated co-translationally. Moreover, the codon partially directing its incorporation in the polypeptide chain was identified as UGA also known as the opal termination codon.<ref>{{cite journal |pages=4650–4 |doi=10.1073/pnas.83.13.4650 |title=Nucleotide sequence and expression of the selenocysteine-containing polypeptide of formate dehydrogenase (formate-hydrogen-lyase-linked) from Escherichia coli |year=1986 |last1=Zinoni |first1=F |last2=Birkmann |first2=A |last3=Stadtman |first3=T |last4=Böck |first4=A |journal=Proceedings of the National Academy of Sciences |volume=83 |issue=13 |pmid= 2941757|pmc=323799 |bibcode=1986PNAS...83.4650Z |doi-access=free }}</ref> Different mechanisms for overriding the termination function of this codon have been identified in prokaryotes and in eukaryotes.<ref>{{cite book |last1=Böck |first1=A |title=Encyclopedia of Biological Chemistry |chapter=Selenoprotein Synthesis |year=2013 |pages=210–3 |doi=10.1016/B978-0-12-378630-2.00025-6 |isbn=978-0-12-378631-9 |chapter-url=https://www.sciencedirect.com/science/article/pii/B9780123786302000256 |access-date=23 August 2021}}</ref> A particular difference between these kingdoms is that cis elements seem restricted to the neighborhood of the UAG codon in prokaryotes while in eukaryotes this restriction is not present. Instead such locations seem disfavored albeit not prohibited.<ref>{{cite journal |last1=Mix |first1=H |last2=Lobanov |first2=A |last3=Gladyshev |first3=V |title=SECIS elements in the coding regions of selenoprotein transcripts are functional in higher eukaryotes |journal=Nucleic Acids Research |date=2007 |volume=35 |issue=2 |pages=414–423 |doi=10.1093/nar/gkl1060 |pmid=17169995 |url=https://academic.oup.com/nar/article/35/2/414/2400734|pmc=1802603 }}</ref>

In 2003, a landmark paper described the identification of all known selenoproteins in humans: 25 in total.<ref>{{cite journal |last1=Kryukov |first1=G |last2=Gladyshev |first2=V |title=Characterization of mammalian selenoproteomes |journal=Science |date=2003 |volume=300 |issue=5624 |pages=1439–43 |doi=10.1126/science.1083516 |pmid=12775843 |bibcode=2003Sci...300.1439K |s2cid=10363908 |url=https://www.science.org/doi/full/10.1126/science.1083516|url-access=subscription }}</ref> Similar analyses have been run for other organisms.

The UAG codon can translate into [[pyrrolysine]] (Pyl) in a similar manner.

=== Genomic distribution ===
Distribution of stop codons within the genome of an organism is non-random and can correlate with [[GC-content]].<ref>{{Cite journal|title=Stop codons in bacteria are not selectively equivalent|doi=10.1186/1745-6150-7-30|journal=Biology Direct|pmid=22974057|pmc=3549826|year=2012|volume=7|pages=30|vauthors=Povolotskaya IS, Kondrashov FA, Ledda A, Vlasov PK |doi-access=free }}</ref><ref name="Comprehensive Analysis of Stop Codo">{{cite journal |pages=775–806 |doi=10.1074/jbc.M114.606632 |title=Comprehensive Analysis of Stop Codon Usage in Bacteria and Its Correlation with Release Factor Abundance|year=2014 |last1=Korkmaz|first1=Gürkan |last2=Holm |first2=Mikael |last3=Wiens|first3=Tobias |last4=Sanyal|first4=Suparna |journal=The Journal of Biological Chemistry |volume=289 |issue=44 |pmid=25217634 |pmc=4215218|doi-access=free }}</ref> For example, the ''E. coli'' K-12 genome contains 2705 TAA (63%), 1257 TGA (29%), and 326 TAG (8%) stop codons (GC content 50.8%).<ref>{{cite web |title=''Escherichia coli'' str. K-12 substr. MG1655, complete genome [Genbank Accession Number: U00096] |publisher=NCBI |work=GenBank |url=https://www.ncbi.nlm.nih.gov/nuccore/U00096 |access-date=2013-01-27}}</ref> Also the substrates for the stop codons release factor 1 or release factor 2 are strongly correlated to the abundance of stop codons.<ref name="Comprehensive Analysis of Stop Codo"/> Large scale study of bacteria with a broad range of GC-contents shows that while the frequency of occurrence of TAA is negatively correlated to the GC-content and the frequency of occurrence of TGA is positively correlated to the GC-content, the frequency of occurrence of the TAG stop codon, which is often the minimally used stop codon in a genome, is not influenced by the GC-content.<ref>{{cite journal |pages=6718–25 |doi=10.1128/JB.00682-08 |title= Role of Premature Stop Codons in Bacterial Evolution |year=2008 |last1=Wong|first1=Tit-Yee |last2= Fernandes |first2=Sanjit |last3=Sankhon|first3=Naby |last4=Leong|first4=Patrick P | last5=Kuo|first5=Jimmy |last6=Liu|first6=Jong-Kang |journal=Journal of Bacteriology |volume=190 |issue=20 |pmid=18708500 |pmc=2566208}}</ref>

=== Recognition ===
Recognition of stop codons in bacteria have been associated with the so-called 'tripeptide anticodon',<ref>{{cite journal |doi=10.1038/35001115 |title= A tripeptide 'anticodon' deciphers stop codons in messenger RNA |year=1999 |last1=Ito|first1=Koichi |last2= Uno|first2=Makiko |last3=Nakamura|first3=Yoshikazu |journal=Nature |volume=403 |issue= 6770 |pages= 680–4 |pmid=10688208 |s2cid= 4331695 }}</ref> a highly conserved amino acid motif in RF1 (PxT) and RF2 (SPF). Even though this is supported by structural studies, it was shown that the tripeptide anticodon hypothesis is an oversimplification.<ref>{{cite journal |doi=10.1074/jbc.M117.785238 |title= R213I mutation in release factor 2 (RF2) is one step forward for engineering an omnipotent release factor in bacteria ''Escherichia coli''|year=2017 |last1=Korkmaz|first1=Gürkan |last2= Sanyal|first2=Suparna |journal=Journal of Biological Chemistry|volume=292 |issue= 36|pages= 15134–42|pmid=28743745 |pmc=5592688|doi-access= free}}</ref>