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Related Experiment Video

Updated: Sep 3, 2025

In vivo Application of the REMOTE-control System for the Manipulation of Endogenous Gene Expression
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Imaging Intron Evolution.

Maria Antonietta Panaro1, Rosa Calvello1, Daniela Valeria Miniero1

  • 1Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via Orabona, 4, 70126 Bari, Italy.

Methods and Protocols
|July 27, 2022
PubMed
Summary
This summary is machine-generated.

Intron evolution can be visualized using NCBI BLAST and UCSC Genome Browser tools. These methods reveal conserved sequences and transposable element insertions, aiding in understanding intron dynamics across species.

Keywords:
BLAST dot plotsGHRMultiz alignment and conservation toolSLC25A21intron evolution

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Area of Science:

  • Genomics
  • Molecular Evolution
  • Bioinformatics

Background:

  • Intron sequences evolve rapidly, posing challenges for evolutionary analysis.
  • Conserved regions within introns can provide insights into regulatory elements and evolutionary pressures.

Purpose of the Study:

  • To demonstrate effective visualization techniques for intron evolution using bioinformatics tools.
  • To analyze intron conservation patterns in specific genes across vertebrate species.

Main Methods:

  • Utilizing NCBI BLAST's dot plot function for pairwise sequence alignment and gap identification.
  • Employing the UCSC Genome Browser's Multiz alignment tool for visualizing vertebrate-wide conservation.
  • Analyzing intron sequences of mitochondrial solute carrier 21 (SLC25A21) and growth hormone receptor (GHR) genes.

Main Results:

  • Dot plots effectively identify non-conserved regions and transposable element insertions within introns.
  • UCSC Genome Browser visualizes varying levels of intron conservation across vertebrates.
  • Specific conserved nucleotide sequences were identified in SLC25A21 introns, with increasing conservation from chicken/human to mouse/human.
  • GHR introns showed less conservation, with early signals in chicken/human alignments.
  • Conservation sites within SLC25A21 introns were not always congruent between species or with overall vertebrate conservation.

Conclusions:

  • NCBI BLAST and UCSC Genome Browser are powerful tools for studying intron evolution.
  • Intron conservation patterns vary significantly between genes and species.
  • Intron analysis provides a deeper understanding of molecular evolution and gene regulation across vertebrates.