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Related Concept Videos

Multi-species Conserved Sequences02:51

Multi-species Conserved Sequences

Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
Although the genome of each species varies greatly from each other, a few sequences are highly conserved. Such conserved DNA...
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,...
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.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
Genome-wide Association Studies-GWAS01:11

Genome-wide Association Studies-GWAS

Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...

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Related Experiment Video

Updated: Jun 1, 2026

Rare Event Detection Using Error-corrected DNA and RNA Sequencing
10:36

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Published on: August 3, 2018

SNPs occur in regions with less genomic sequence conservation.

John C Castle1

  • 1Rosetta Inpharmatics LLC, Seattle, Washington, United States of America. john.castle@tron-mainz.de

Plos One
|June 16, 2011
PubMed
Summary

Single nucleotide polymorphism (SNP) rates correlate with genomic sequence conservation. Functional and regulatory regions exhibit fewer SNPs and higher conservation, indicating evolutionary constraints.

Area of Science:

  • Genomics
  • Molecular Biology
  • Evolutionary Biology

Background:

  • Single nucleotide polymorphisms (SNPs) represent intra-species genetic variation.
  • Cross-species genomic sequence conservation reflects inter-species variation.
  • Understanding the relationship between SNP rates and conservation is key to identifying functional genomic regions.

Purpose of the Study:

  • To investigate SNP rates and genomic sequence conservation adjacent to mRNA processing regions.
  • To determine if functional regions exhibit fewer SNPs and higher conservation.
  • To confirm findings using both mouse and human genomic data.

Main Methods:

  • Analysis of SNP rates and cross-species genomic sequence conservation.
  • Examination of regions including protein start/stop codons, splice sites, miRNA binding sites, and polyadenylation sites.

More Related Videos

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
14:06

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

Related Experiment Videos

Last Updated: Jun 1, 2026

Rare Event Detection Using Error-corrected DNA and RNA Sequencing
10:36

Rare Event Detection Using Error-corrected DNA and RNA Sequencing

Published on: August 3, 2018

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER
14:06

Detection of Rare Genomic Variants from Pooled Sequencing Using SPLINTER

Published on: June 23, 2012

  • Comparison of SNP rates and conservation across different genomic elements.

    • Main Results:

    • More SNPs were observed in less conserved regions, and functional regions had fewer SNPs.
    • Regulatory sites showed lower SNP rates and higher conservation.
    • Within coding regions, codon position three had the highest SNP rates and lowest conservation, while codon position two had the fewest SNPs.

    Conclusions:

    • SNPs, indicative of recent genetic variation, are more frequent in less evolutionarily conserved regions.
    • High conservation and low SNP rates at regulatory and splice sites underscore their functional importance.
    • Codon degeneracy influences SNP rates within coding sequences, with relaxed constraint at the third position.