TY - JOUR
T1 - Characterization of the splice sites in GT-AG and GC-AG introns in higher eukaryotes using full-length cDNAs
AU - Kitamura-Abe, Sumie
AU - Itoh, Hitomi
AU - Washio, Takanori
AU - Tsutsumi, Akihiro
AU - Tomita, Masaru
N1 - Funding Information:
We would like to thank Prof. Masaru Shimbo, Prof. Yoichi Iida, Prof. Mineichi Kudo, Prof. Nobuyuki Takahashi, Assistant Prof. Rintaro Saito and Mr. Atsushi Sakurai for their helpful discussions. We also thank Rice Full-Length cDNA Consortium (National Institute of Agrobiological Sciences Rice Full-Length cDNA Project Team; Foundation of Advancement of International Science Genome Sequencing & Analysis Group; RIKEN) for providing the full-length cDNA data on rice. This work was supported by the Ministry of Agriculture, Forestry and Fisheries of Japan (Rice Genome Project SY-1104).
Copyright:
Copyright 2008 Elsevier B.V., All rights reserved.
PY - 2004/6
Y1 - 2004/6
N2 - 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.
AB - 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.
KW - Alternative splicing
KW - Full-length cDNA
KW - GC-AG intron
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U2 - 10.1142/S0219720004000570
DO - 10.1142/S0219720004000570
M3 - Article
C2 - 15297984
AN - SCOPUS:4143115768
SN - 0219-7200
VL - 2
SP - 309
EP - 331
JO - Journal of Bioinformatics and Computational Biology
JF - Journal of Bioinformatics and Computational Biology
IS - 2
ER -