First exons and introns - A survey of GC content and gene structure in the human genome

Krishna R. Kalari, Melanie Casavant, Thomas B. Bair, Henry L. Keen, Josep M. Comeron, Thomas L. Casavant, Todd E. Scheetz

Research output: Contribution to journalArticlepeer-review

35 Scopus citations


Most transcriptional regulatory elements are located in non-coding DNA. In particular, some first introns play a vital role in transcriptional control and splicing. The length and GC-content of first exons and introns in complex organisms suggests that these structural units are likely to be important functional elements in large genomes. Hence, in this paper we perform a systematic comparison of exon-intron structure and GC content on all known genes in the human genome. Our in-silico analysis found that the GC content of introns and exons varies significantly depending on their length. On average, the first intron of a gene is significantly longer than other introns in the same gene. Our results also show that first introns and exons are more GC rich than last and internal. This study provides insight into the structure of eukaryotic genes. These results confirm and expand the previously identified regulatory potential of first exons and introns.

Original languageEnglish (US)
Pages (from-to)237-242
Number of pages6
JournalIn Silico Biology
Issue number3
StatePublished - 2006


  • GC-content
  • Gene structure
  • Intron length

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics
  • Computational Mathematics
  • Computational Theory and Mathematics


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