Indel: Difference between revisions
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The word '''indel''' is a [[portmanteau]] of [[insertion (genetics)|insertion]] or [[deletion]], referring to the two types of [[Genetics|genetic]] [[mutation]] that are often considered together because of their similar effect and the inability to distinguish between them in a comparison of two sequences. In coding regions of the genome, unless the length of an indel is a multiple of 3, they produce a [[frameshift mutation]]. The most common mutation causing cystic fibrosis in the [[cystic fibrosis]] transmembrane receptor ([[CFTR (gene)|CFTR]]) gene is a deletion of three bases encoding phenylalanine at position 508 of the protein ([[ΔF508]], or p. F508del). |
The word '''indel''' is a [[portmanteau]] of [[insertion (genetics)|insertion]] or [[deletion]], referring to the two types of [[Genetics|genetic]] [[mutation]] that are often considered together because of their similar effect and the inability to distinguish between them in a comparison of two sequences. In coding regions of the genome, unless the length of an indel is a multiple of 3, they produce a [[frameshift mutation]]. The most common mutation causing cystic fibrosis in the [[cystic fibrosis]] transmembrane receptor ([[CFTR (gene)|CFTR]]) gene is a deletion of three bases encoding phenylalanine at position 508 of the protein ([[ΔF508]], or p. F508del). |
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Indels can be contrasted with a '''[[point mutation]]'''; where an Indel inserts or deletes nucleotides from a sequence, a point mutation is a form of substitution that ''replaces'' one of the [[nucleotides]]. |
Indels can be contrasted with a '''[[point mutation]]'''; where an Indel inserts or deletes nucleotides from a sequence, a point mutation is a form of substitution that ''replaces'' one of the [[nucleotides]]. |
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Indels can be used as genetic markers in natural populations, especially in [[phylogenetic]] studies.<ref name="Vali2008">{{cite journal |author=Väli U, Brandström M, Johansson M, Ellegren H |title=Insertion-deletion polymorphisms (indels) as genetic markers in natural populations |journal=BMC Genetic |year=2008 |volume=9 |pages=8 |pmid=18211670}}</ref><ref name="Erixon2008">{{cite journal |author=Erixon P, Oxelman B |title=Whole-gene positive selection, elevated synonymous substitution rates, duplication, and indel evolution of the chloroplast clpP1 gene |journal=PLoS ONE |year=2008 |volume=3 |issue=1 |pages=e1386 |pmid=18167545}}</ref> |
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An "indel" change of a single DNA base encoding part of an mRNA results in a "frameshift" when translating the mRNA and perhaps reading on to an inappropriate (premature) [[stop codon]] in a different frame. Indels are uncommon in coding regions but common in non-coding regions. |
An "indel" change of a single DNA base encoding part of an mRNA results in a "frameshift" when translating the mRNA and perhaps reading on to an inappropriate (premature) [[stop codon]] in a different frame. Indels are uncommon in coding regions but common in non-coding regions. |
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The term "indel" has been co-opted in recent years by genome scientists for use in the sense described above. Note that this is a change from its original use and meaning, which arose from the systematics field, referring to differences between sequences, such as from two different species, in which it was impossible to infer if one species lost the sequence or the other species gained it. For example, species A has a run of 4 G nucleotides at a particular locus, but species B has 5 G's at the same locus. If the mode of selection is unknown, then it is equally plausible that species A could have lost one G (a "deletion" event") or species B could have gained the G (an "insertion" event). In cases where it is impossible to infer phylogenetic direction of the sequence change, the sequence change event will be referred to as an "indel". |
The term "indel" has been co-opted in recent years by genome scientists for use in the sense described above. Note that this is a change from its original use and meaning, which arose from the systematics field, referring to differences between sequences, such as from two different species, in which it was impossible to infer if one species lost the sequence or the other species gained it. For example, species A has a run of 4 [[guanine|G]] nucleotides at a particular locus, but species B has 5 G's at the same locus. If the mode of selection is unknown, then it is equally plausible that species A could have lost one G (a "deletion" event") or species B could have gained the G (an "insertion" event). In cases where it is impossible to infer phylogenetic direction of the sequence change, the sequence change event will be referred to as an "indel". |
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==References== |
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Revision as of 02:50, 21 November 2008
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The word indel is a portmanteau of insertion or deletion, referring to the two types of genetic mutation that are often considered together because of their similar effect and the inability to distinguish between them in a comparison of two sequences. In coding regions of the genome, unless the length of an indel is a multiple of 3, they produce a frameshift mutation. The most common mutation causing cystic fibrosis in the cystic fibrosis transmembrane receptor (CFTR) gene is a deletion of three bases encoding phenylalanine at position 508 of the protein (ΔF508, or p. F508del).
Indels can be contrasted with a point mutation; where an Indel inserts or deletes nucleotides from a sequence, a point mutation is a form of substitution that replaces one of the nucleotides.
Indels can be used as genetic markers in natural populations, especially in phylogenetic studies.[1][2]
An "indel" change of a single DNA base encoding part of an mRNA results in a "frameshift" when translating the mRNA and perhaps reading on to an inappropriate (premature) stop codon in a different frame. Indels are uncommon in coding regions but common in non-coding regions.
The term "indel" has been co-opted in recent years by genome scientists for use in the sense described above. Note that this is a change from its original use and meaning, which arose from the systematics field, referring to differences between sequences, such as from two different species, in which it was impossible to infer if one species lost the sequence or the other species gained it. For example, species A has a run of 4 G nucleotides at a particular locus, but species B has 5 G's at the same locus. If the mode of selection is unknown, then it is equally plausible that species A could have lost one G (a "deletion" event") or species B could have gained the G (an "insertion" event). In cases where it is impossible to infer phylogenetic direction of the sequence change, the sequence change event will be referred to as an "indel".
References
- ^ Väli U, Brandström M, Johansson M, Ellegren H (2008). "Insertion-deletion polymorphisms (indels) as genetic markers in natural populations". BMC Genetic. 9: 8. PMID 18211670.
{{cite journal}}: CS1 maint: multiple names: authors list (link) - ^ Erixon P, Oxelman B (2008). "Whole-gene positive selection, elevated synonymous substitution rates, duplication, and indel evolution of the chloroplast clpP1 gene". PLoS ONE. 3 (1): e1386. PMID 18167545.
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