Editing Coding region (section)

== Composition ==
[[File:Transitions-transversions.png|thumb|286x286px|'''Point mutation types:''' transitions (blue) are elevated compared to transversions (red) in GC-rich coding regions.]]
The evidence suggests that there is a general interdependence between base composition patterns and coding region availability.<ref>{{cite journal | vauthors = Lercher MJ, Urrutia AO, Pavlícek A, Hurst LD | title = A unification of mosaic structures in the human genome | journal = Human Molecular Genetics | volume = 12 | issue = 19 | pages = 2411–5 | date = October 2003 | pmid = 12915446 | doi = 10.1093/hmg/ddg251 | doi-access = free }}</ref> The coding region is thought to contain a higher [[GC-content]] than non-coding regions. There is further research that discovered that the longer the coding strand, the higher the GC-content. Short coding strands are comparatively still GC-poor, similar to the low GC-content of the base composition translational [[stop codon]]s like TAG, TAA, and TGA.<ref>{{cite journal | vauthors = Oliver JL, Marín A | title = A relationship between GC content and coding-sequence length | journal = Journal of Molecular Evolution | volume = 43 | issue = 3 | pages = 216–23 | date = September 1996 | pmid = 8703087 | doi = 10.1007/pl00006080 | bibcode = 1996JMolE..43..216O }}</ref>

GC-rich areas are also where the ratio [[point mutation]] type is altered slightly: there are more [[Transition (genetics)|transitions]], which are changes from purine to purine or pyrimidine to pyrimidine, compared to [[transversion]]s, which are changes from purine to pyrimidine or pyrimidine to purine. The transitions are less likely to change the encoded amino acid and remain a [[silent mutation]] (especially if they occur in the third [[nucleotide]] of a codon) which is usually beneficial to the organism during translation and protein formation.<ref>{{Cite web|url=http://rosalind.info/glossary/gene-coding-region/|title=ROSALIND {{!}} Glossary {{!}} Gene coding region|website=rosalind.info|access-date=2019-10-31}}</ref>

This indicates that essential coding regions (gene-rich) are higher in GC-content and more stable and resistant to [[mutation]] compared to accessory and non-essential regions (gene-poor).<ref>{{cite journal | vauthors = Vinogradov AE | title = DNA helix: the importance of being GC-rich | journal = Nucleic Acids Research | volume = 31 | issue = 7 | pages = 1838–44 | date = April 2003 | pmid = 12654999 | pmc = 152811 | doi = 10.1093/nar/gkg296 }}</ref> However, it is still unclear whether this came about through neutral and random mutation or through a pattern of [[Natural selection|selection]].<ref>{{cite journal | vauthors = Bohlin J, Eldholm V, Pettersson JH, Brynildsrud O, Snipen L | title = The nucleotide composition of microbial genomes indicates differential patterns of selection on core and accessory genomes | journal = BMC Genomics | volume = 18 | issue = 1 | pages = 151 | date = February 2017 | pmid = 28187704 | pmc = 5303225 | doi = 10.1186/s12864-017-3543-7 | doi-access = free }}</ref> There is also debate on whether the methods used, such as gene windows, to ascertain the relationship between GC-content and coding region are accurate and unbiased.<ref>{{cite journal | vauthors = Sémon M, Mouchiroud D, Duret L | title = Relationship between gene expression and GC-content in mammals: statistical significance and biological relevance | journal = Human Molecular Genetics | volume = 14 | issue = 3 | pages = 421–7 | date = February 2005 | pmid = 15590696 | doi = 10.1093/hmg/ddi038 | doi-access = free }}</ref>