Characterization of the splice sites in GT-AG and GC-AG introns in higher eukaryotes using full-length cDNAs

Sumie Kitamura-Abe, Hitomi Itoh, Takanori Washio, Akihiro Tsutsumi, Masaru Tomita

Research output: Contribution to journalArticle

17 Citations (Scopus)

Abstract

For the purpose of analyzing the relation between the splice sites and the order of introns, we conducted the following analysis for the GT-AG and GC-AG splice site groups. First, the pre-mRNAs of H. sapiens, M. musculus, D. melanogaster, A. thaliana and O. sativa were sampled by mapping the full-length cDNA to the genomes. Next, the consensus sequences at different regions of pre-mRNAs were analyzed in the five species. We also investigated the mononucleotide and dinucleotide frequencies in the extensive regions around the 5′ splice sites (5′ss) and 3′ splice sites (3′ss). As a result, differential frequencies of nucleotides at the first 5′ss in both the GT-AG and GC-AG splice site groups were observed in A. thaliana and O. sativa pre-mRNAs. The trend, which indicates that GC 5′ss possess strong consensus sequences, was observed not only in mammalian pre-mRNAs but also in the pre-mRNAs of D. melanogaster, A. thaliana and O. sativa. Furthermore, we examined the consensus sequences of the constitutive and alternative splice sites. It was suggested that in the case of the alternative GC-AG introns, the tendency to have a weak consensus sequence at 5′ss is different between H. sapiens and M. musculus pre-mRNAs.

Original languageEnglish
Pages (from-to)309-331
Number of pages23
JournalJournal of Bioinformatics and Computational Biology
Volume2
Issue number2
DOIs
Publication statusPublished - 2004 Jun

Fingerprint

RNA Splice Sites
RNA Precursors
Eukaryota
Introns
Complementary DNA
Consensus Sequence
Nucleotides
Messenger RNA
Genes
Genome

Keywords

  • Alternative splicing
  • Full-length cDNA
  • GC-AG intron

ASJC Scopus subject areas

  • Medicine(all)
  • Cell Biology

Cite this

Characterization of the splice sites in GT-AG and GC-AG introns in higher eukaryotes using full-length cDNAs. / Kitamura-Abe, Sumie; Itoh, Hitomi; Washio, Takanori; Tsutsumi, Akihiro; Tomita, Masaru.

In: Journal of Bioinformatics and Computational Biology, Vol. 2, No. 2, 06.2004, p. 309-331.

Research output: Contribution to journalArticle

Kitamura-Abe, Sumie ; Itoh, Hitomi ; Washio, Takanori ; Tsutsumi, Akihiro ; Tomita, Masaru. / Characterization of the splice sites in GT-AG and GC-AG introns in higher eukaryotes using full-length cDNAs. In: Journal of Bioinformatics and Computational Biology. 2004 ; Vol. 2, No. 2. pp. 309-331.
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