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Related Concept Videos

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Non-LTR Retrotransposons

As the name suggests, non-LTR retrotransposons lack the long terminal repeats characteristic of the LTR retrotransposons. Additionally, both LTR and non-LTR retrotransposons use distinct mechanisms of mobilization. Non-LTR retrotransposons are further divided into two classes - Long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs), both of which occur abundantly in most mammals, including humans. Some of the active non-LTR retrotransposons in humans are L1...
Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
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Single Nucleotide Polymorphisms-SNPs01:05

Single Nucleotide Polymorphisms-SNPs

A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
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Point and Frameshift Mutations

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Related Experiment Video

Updated: Jul 2, 2026

Use of Alu Element Containing Minigenes to Analyze Circular RNAs
13:10

Use of Alu Element Containing Minigenes to Analyze Circular RNAs

Published on: March 10, 2020

Small deletion variants have stable breakpoints commonly associated with alu elements.

Adam J de Smith1, Robin G Walters, Lachlan J M Coin

  • 1Section of Genomic Medicine, Imperial College London, Hammersmith Hospital, London, United Kingdom.

Plos One
|September 5, 2008
PubMed
Summary
This summary is machine-generated.

Common deletions in the human genome originate from a single event, often involving Alu repeats near their breakpoints. These copy number variants (CNVs) suggest distinct mechanisms drive different types of genomic variation.

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Use of Alu Element Containing Minigenes to Analyze Circular RNAs
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Generation of Genomic Deletions in Mammalian Cell Lines via CRISPR/Cas9
09:40

Generation of Genomic Deletions in Mammalian Cell Lines via CRISPR/Cas9

Published on: January 3, 2015

Area of Science:

  • Human Genomics
  • Molecular Biology
  • Population Genetics

Background:

  • Copy number variants (CNVs) are a major source of human genomic variation, impacting over 18% of the euchromatic genome.
  • The origins and stability of CNVs of varying sizes and complexities remain largely unknown.
  • Understanding CNV formation is crucial for interpreting genomic variation and its role in health and disease.

Purpose of the Study:

  • To investigate the precise breakpoints and origins of 20 small, common deletion CNVs.
  • To determine the mechanisms underlying the formation and population-wide prevalence of these deletions.
  • To explore the sequence characteristics at deletion breakpoints and their potential role in CNV generation.

Main Methods:

  • Array comparative genomic hybridization (aCGH) for initial identification of deletions.
  • Polymerase chain reaction (PCR) and DNA sequencing to pinpoint deletion breakpoints.
  • Linkage disequilibrium (LD) analysis and haplotype analysis to assess population genetics.
  • Sequence analysis of flanking regions for repetitive elements and conserved motifs.

Main Results:

  • Identical upstream and downstream breakpoints at the sequence level for all deletions studied, indicating a single origin event.
  • Most deletions showed moderate to strong LD with surrounding SNPs and conserved long-range haplotypes.
  • Enrichment of microhomology and Alu repeat elements (particularly at their poly-A tails) at deletion breakpoints.
  • No enrichment of LINE elements or segmental duplications was observed, contrasting with some previous findings.
  • A conserved motif was identified near breakpoints, though its functional role requires further investigation.

Conclusions:

  • Small, common deletion CNVs likely arise from a single mutational event and subsequently spread through the population.
  • Alu elements and microhomology at breakpoints appear to play a significant role in the formation of these specific deletions.
  • The findings support the existence of distinct subgroups of CNVs, potentially originating through different molecular mechanisms.
  • Further research is needed to elucidate the functional significance of the identified conserved motif in deletion formation.