Intron and exon boundaries are constrained by the triplet codons of the reading frame
Intron and exon boundaries are heavily constrained by reading frames, as protein-coding regions maintain a strict three-nucleotide periodicity (triplet codons) that influences splice sites and structural constraints.
The retrieved literature supports the premise that exon architecture and boundaries correlate with and are constrained by the triplet codon reading frame, as evidenced by triplet periodicity observed in coding regions and splice junctions.
Wang L, Stein LD. Localizing triplet periodicity in DNA and cDNA sequences.. 2010. https://doi.org/10.1186/1471-2105-11-550
Paper [3] explains that coding exons exhibit a triplet periodicity due to the underlying series of three-nucleotide codons, which helps locate splice boundaries and reflects reading frame constraints.
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Kaushik K, Sivadas A, Vellarikkal SK, Verma A, Jayarajan R, Pandey S, Sethi T, Maiti S, Scaria V, Sivasubbu S. RNA secondary structure profiling in zebrafish reveals unique regulatory features.. 2018. https://doi.org/10.1186/s12864-018-4497-0
Paper [4] demonstrates that coding regions are characterized by a three-nucleotide periodicity of secondary structure constrained by codons, connecting reading frame structure to exon organization.
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