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Indel is a molecular biology term for an insertion or deletion of bases in the genome of an organism. It is classified among small genetic variations, measuring from 1 to 10 000 base pairs in length, including insertion and deletion events that may be separated by many years, and may not be related to each other in any way. A microindel is defined as an indel that results in a net change of 1 to 50 nucleotides. In
coding region The coding region of a gene, also known as the CDS (from ''coding sequence''), is the portion of a gene's DNA or RNA that codes for protein. Studying the length, composition, regulation, splicing, structures, and functions of coding regions compare ...
s of the genome, unless the length of an indel is a multiple of 3, it will produce a
frameshift mutation A frameshift mutation (also called a framing error or a reading frame shift) is a genetic mutation Image:Darwin Hybrid Tulip Mutation 2014-05-01.jpg, A tulip flower exhibiting a partially yellow petal due to a mutation in its genes In biology ...

frameshift mutation
. For example, a common microindel which results in a frameshift causes
Bloom syndrome Bloom syndrome (often abbreviated as BS in literature) is a rare autosome, autosomal recessive genetic disorder characterized by short stature, predisposition to the development of cancer, and genomic instability. BS is caused by mutations in the ' ...
in the Jewish or Japanese population. Indels can be contrasted with a
point mutation A point mutation or substitution is a genetic mutation where a single nucleotide base is changed, inserted or deleted from a DNA or RNA sequence of an organism's genome. Point mutations have a variety of effects on the downstream protein product ...

point mutation
. An indel inserts and deletes nucleotides from a sequence, while a point mutation is a form of substitution that ''replaces'' one of the
nucleotides Nucleotides are organic molecules , CH4; is among the simplest organic compounds. In chemistry, organic compounds are generally any chemical compounds that contain carbon-hydrogen chemical bond, bonds. Due to carbon's ability to Catenation, ...

nucleotides
without changing the overall number in the DNA. Indels can also be contrasted with Tandem Base Mutations (TBM), which may result from fundamentally different mechanisms. A TBM is defined as a substitution at adjacent nucleotides (primarily substitutions at two adjacent nucleotides, but substitutions at three adjacent nucleotides have been observed). Indels, being either insertions, or deletions, can be used as genetic markers in natural populations, especially in
phylogenetic In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, Physiology, physiological mechanism ...

phylogenetic
studies. It has been shown that genomic regions with multiple indels can also be used for species-identification procedures. An indel change of a single base pair in the coding part of an
mRNA In molecular biology, messenger ribonucleic acid (mRNA) is a single-stranded molecule of RNA that corresponds to the genetic sequence of a gene, and is read by a ribosome in the process of Protein biosynthesis, synthesizing a protein. mRNA i ...

mRNA
results in a frameshift during mRNA translation that could lead to an inappropriate (premature)
stop codon Stop may refer to: Places *Stop, Kentucky Stop is an unincorporated area, unincorporated community located in Wayne County, Kentucky, United States. The origin of the name "Stop" is obscure. References Unincorporated communities in Wa ...
in a different frame. Indels that are not multiples of 3 are particularly uncommon in coding regions but relatively common in non-coding regions. There are approximately 192-280 frameshifting indels in each person. Indels are likely to represent between 16% and 25% of all sequence polymorphisms in humans. In fact, in most known genomes, including humans, indel frequency tends to be markedly lower than that of single nucleotide polymorphisms (SNP), except near highly repetitive regions, including homopolymers and
microsatellites A microsatellite is a tract of repetitive DNA in which certain DNA motifs (ranging in length from one to six or more base pairs) are repeated, typically 5–50 times. Microsatellites occur at thousands of locations within an organism's genome ...
. The term "indel" has been co-opted in recent years by genome
scientist A scientist is a person who conducts scientific research The scientific method is an Empirical evidence, empirical method of acquiring knowledge that has characterized the development of science since at least the 17th century. It involves ...

scientist
s for use in the sense described above. This is a change from its original use and meaning, which arose from
systematics Biological Biology is the natural science Natural science is a branch of science Science (from the Latin word ''scientia'', meaning "knowledge") is a systematic enterprise that Scientific method, builds and Taxonomy (general), o ...
. In systematics, researchers could find differences between sequences, such as from two different species. But 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 nucleotides at a locus and species ''B'' has 5 G's at the same locus. If the mode of selection is unknown, one can not tell if species A lost one G (a "deletion" event") or species B gained one G (an "insertion" event). When one cannot infer the
phylogenetic In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, Physiology, physiological mechanism ...

phylogenetic
direction of the sequence change, the sequence change event is referred to as an "indel".


See also

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Insertion (genetics) In genetics Genetics is a branch of biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactio ...
*
Deletion (genetics) In genetics, a deletion (also called gene deletion, deficiency, or deletion mutation) (sign: delta (letter), Δ) is a mutation (a genetic aberration) in which a part of a chromosome or a sequence of DNA is left out during DNA replication. Any numbe ...


References

{{Mutation Mutation Molecular biology