Characterization of the splice sites in GT-AG and GC-AG introns in higher eukaryotes using full-length cDNAs.
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.
Laboratory for Bioinformatics, Institute for Advanced Biosciences, Keio University, Fujisawa, Kanagawa 252-8520, Japan. sumie@sfc.keio.ac.jp
Sumie
S
Kitamura-Abe
Hitomi
H
Itoh
Takanori
T
Washio
Akihiro
A
Tsutsumi
Masaru
M
Tomita
D000818:Animals; D017360:Arabidopsis / Q000235:genetics; D001482:Base Composition; D016384:Consensus Sequence / Q000235:genetics; D018076:DNA, Complementary / Q000235:genetics*; D004331:Drosophila melanogaster / Q000235:genetics; D005057:Eukaryotic Cells; D020869:Gene Expression Profiling / Q000379:methods*; D005787:Gene Frequency; D006801:Humans; D007438:Introns / Q000235:genetics*; D051379:Mice; D012275:Oryza / Q000235:genetics; D022821:RNA Splice Sites / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012689:Sequence Homology, Nucleic Acid; D013045:Species Specificity
D018076:DNA, Complementary; D022821:RNA Splice Sites