Sequence patterns observed in 5' flanking regions of primate Alu elements

Yoshima Toda, Rintaro Saito, Masaru Tomita

Research output: Contribution to journalArticlepeer-review


Retrotransposons have generally been known to integrate randomly into host genomes. Jurka, however, showed some consensus sequence patterns at insertion sites of some mammalian retrotransposons and proposed enzymatic involvement that mediates integration. Jurka used about 400 complete human Alu and rodent ID sequences which retain full length with identical flanking sequences at both ends. In our study, more than 25,000 Alu sequences longer than 250 bp were used for comprehensive analysis to identify any consensus sequence(s) preceding the 5' end of Alu elements. 'Entropy' at each nucleotide position within 500 bases of the 5' Alu end was computed. Significant drop of entropy was observed between position -20 and -10 of the 5' end of Alu, suggesting the existence of certain consensus sequence(s) in the region. Frequencies of all possible triplets (total of 64) were measured in the same region. Observation that frequencies of triplets 'aaa,' 'taa,' and 'tta' in the 5' flanking sequences were high is consistent with Jurka. However, frequencies of triplets 'att' and 'aca' were also significantly high, which are not the primary candidates for nick site in Jurka.

Original languageEnglish
Pages (from-to)369-374
Number of pages6
JournalAnnals of the New York Academy of Sciences
Publication statusPublished - 1999

ASJC Scopus subject areas

  • General Neuroscience
  • General Biochemistry,Genetics and Molecular Biology
  • History and Philosophy of Science


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