Sequences of exon 6 and the adjacent intron boundaries of the rat platelet-derived growth factor A-chain gene:

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Updated: Oct 30, 2026

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data
08:35

Identification of Alternative Splicing and Polyadenylation in RNA-seq Data

Published on: June 24, 2021

W Y Hu1, T Nakayama, N Fukuda

  • 1Second Department of Internal Medicine, Nihon University School of Medicine, Tokyo, Japan.

Biochemical Genetics
|April 29, 1998
PubMed

Insights

Two forms of Platelet-Derived Growth Factor A-chain mRNA are produced via alternative splicing. The long form, found in activated cells, terminates translation within exon 6, a finding relevant to vascular smooth muscle cell growth.

Area of Science:

  • Molecular Biology
  • Cell Biology
  • Biochemistry

Background:

  • Platelet-Derived Growth Factor (PDGF) significantly stimulates vascular smooth muscle cell proliferation.
  • Alternative splicing of PDGF A-chain mRNA produces two isoforms: a long form including exon 6 and a short form excluding it.
  • Differential expression of PDGF A-chain isoforms is observed, with the short form in resting cells and the long form in activated cells.

Purpose of the Study:

  • To investigate the presence and characteristics of PDGF A-chain mRNA isoforms in rat vascular smooth muscle cells.
  • To determine the nucleotide sequences of exon 6 and its flanking introns in rat PDGF A-chain.
  • To elucidate the translational termination site of the long-form PDGF A-chain mRNA and identify potential regulatory elements for alternative splicing.

Main Methods:

  • Reverse transcription-polymerase chain reaction (RT-PCR) using primers spanning exon 6.
  • Nucleotide sequencing of exon 6 and intron boundaries from cDNA and genomic DNA.
  • Analysis of PDGF A-chain mRNA splicing and translation.

Main Results:

  • Both long- and short-form PDGF A-chain transcripts were detected in rat vascular smooth muscle cells.
  • The nucleotide sequences of exon 6 and its intron boundaries were determined.
  • Translation of the long-form PDGF A-chain mRNA was found to terminate within the 70-base pair exon 6.
  • Conserved sequences within intron 5 were identified, suggesting a role in regulating alternative RNA splicing.

Conclusions:

  • Rat vascular smooth muscle cells express both long and short forms of PDGF A-chain mRNA.
  • Alternative splicing of PDGF A-chain mRNA, specifically exon 6 inclusion, dictates translational termination.
  • Intron 5 contains conserved sequences potentially involved in the regulation of PDGF A-chain alternative splicing, impacting vascular smooth muscle cell growth.

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