Identification and validation of evolutionarily conserved unusually short pre-mRNA introns in the human genome

Makoto K. Shimada, Noriko Sasaki-Haraguchi, Akila Mayeda

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6 Citations (Scopus)


According to the length distribution of human introns, there is a large population of short introns with a threshold of 65 nucleotides (nt) and a peak at 85 nt. Using human genome and transcriptome databases, we investigated the introns shorter than 66 nt, termed ultra-short introns, the identities of which are scarcely known. Here, we provide for the first time a list of bona fide human ultra-short introns, which have never been characterized elsewhere. By conducting BLAST searches of the databases, we screened 22 introns (37–65 nt) with conserved lengths and sequences among closely related species. We then provide experimental and bioinformatic evidence for the splicing of 15 introns, of which 12 introns were remarkably G-rich and 9 introns contained completely inefficient splice sites and/or branch sites. These unorthodox characteristics of ultra-short introns suggest that there are unknown splicing mechanisms that differ from the well-established mechanism.

Original languageEnglish
Pages (from-to)10376-10388
Number of pages13
JournalInternational journal of molecular sciences
Issue number5
Publication statusPublished - 07-05-2015


All Science Journal Classification (ASJC) codes

  • Catalysis
  • Molecular Biology
  • Computer Science Applications
  • Spectroscopy
  • Physical and Theoretical Chemistry
  • Organic Chemistry
  • Inorganic Chemistry

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