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Ancient splice junction shadows with relation to blocks in protein structure

V B Strelets1, H A Lim

  • 1Supercomputer Computations Research Institute, Florida State University, Tallahassee 32306-4052, USA.

Bio Systems
|January 1, 1995
PubMed
Summary

Ancient exon-exon junctions, or splice junction shadows, suggest protein building blocks are divisible by three. This study confirms this divisibility, supporting the exon shuffling hypothesis for protein evolution.

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Area of Science:

  • Molecular Evolution
  • Genomics
  • Bioinformatics

Background:

  • Splice junction shadows represent ancient exon-exon junctions.
  • These junctions may indicate primordial amino acid blocks used in protein construction.
  • The divisibility of block lengths by three is crucial for maintaining coding frames during evolution.

Purpose of the Study:

  • To test the hypothesis of intron-mediated recombination in block molecular evolution (exon shuffling).
  • To identify and analyze ancient exon-like blocks within existing coding sequences.
  • To refine methods for detecting splice junction shadows for evolutionary analysis.

Main Methods:

  • Utilized weight matrix prediction to identify ancient splice junction shadows in nucleotide sequences from databases.

Related Experiment Videos

  • Analyzed the distribution of block lengths at the nucleotide and protein levels.
  • Compared findings with previous methods relying solely on recent exons.

    • Main Results:

    • Block length distribution at the nucleotide level shows a strong tendency towards divisibility by three.
    • Observed favorable block lengths of 6, 9, 12, and 15 amino acids at the protein level.
    • The method using splice junction shadows provides a more detailed analysis of block evolution.

    Conclusions:

    • Results support the exon shuffling hypothesis, indicating that protein building blocks are often divisible by three.
    • Identified specific favorable amino acid block lengths that may be significant for protein structure and function.
    • Further refinement of splice junction shadow detection could aid in predicting stable peptide folds and protein structures.