Paper Info
Title
Characterization of the splice sites in GT-AG and GC-AG introns in higher eukaryotes using full-length cDNAs.
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.
Year
DOI
Venue
2004
10.1142/S0219720004000570
J. Bioinformatics and Computational Biology
Keywords
Field
DocType
alternative splicing
Genome,Complementary DNA,Biology,splice,Alternative splicing,Intron,RNA splicing,Bioinformatics,Genetics,Splice site mutation,Consensus sequence
Journal
Volume
Issue
ISSN
2
2
0219-7200
Citations 
PageRank 
References 
3
0.50
3
Authors
5
Name
Order
Citations
PageRank
S Kitamura-Abe151.15
Hitomi Itoh230.50
Takanori Washio361.29
Akihiro Tsutsumi430.50
Masaru Tomita51009180.20