Characteristic sequence pattern in the 5- to 20-bp upstream region of primate Alu elements

Yoshimi Toda, Rintaro Saito, Masaru Tomita

Research output: Contribution to journalArticle

10 Citations (Scopus)

Abstract

We conducted comprehensive sequence analysis of 5' flanking regions of primate Alu elements. Information contents were computed and frequencies of 1024 pentanucleotides were measured to approximate the location of a characteristic sequence and to specify its pattern(s), which may be involved in the integration of Alu elements into their host genomes. A large number of samples was used, the wide region of the 5' end of Alu elements was analyzed, and comparisons were made among different subfamilies. Through our analyses, 'TTTTAAAAA' or '(T)(ms)(A)(n)' can be stated as a candidate for the characteristic sequence pattern, which resides around the region 5 to 20 base pairs upstream of the 5' end of Alu elements. This characteristic sequence pattern was more prominent in the sequences of younger Alus, which is a strong indication that the sequence pattern has a role at the time of Alu integration.

Original languageEnglish
Pages (from-to)232-237
Number of pages6
JournalJournal of Molecular Evolution
Volume50
Issue number3
Publication statusPublished - 2000

Fingerprint

Alu Elements
primate
Primates
sequence analysis
genome
sampling
5' Flanking Region
Base Pairing
Sequence Analysis
Genes
Genome
analysis
comparison
young

Keywords

  • Alu elements
  • Integration target
  • Retroposons
  • Retrotranscripts
  • SINEs

ASJC Scopus subject areas

  • Genetics
  • Biochemistry
  • Biochemistry, Genetics and Molecular Biology(all)
  • Genetics(clinical)
  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Agricultural and Biological Sciences(all)
  • Agricultural and Biological Sciences (miscellaneous)

Cite this

Characteristic sequence pattern in the 5- to 20-bp upstream region of primate Alu elements. / Toda, Yoshimi; Saito, Rintaro; Tomita, Masaru.

In: Journal of Molecular Evolution, Vol. 50, No. 3, 2000, p. 232-237.

Research output: Contribution to journalArticle

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