Comprehensive splice-site analysis using comparative genomics.

@article{citeulike:805877, abstract = {We have collected over half a million splice sites from five species-Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans and Arabidopsis thaliana-and classified them into four subtypes: U2-type GT-AG and GC-AG and U12-type GT-AG and AT-AC. We have also found new examples of rare splice-site categories, such as U12-type introns without canonical borders, and U2-dependent AT-AC introns. The splice-site sequences and several tools to explore them are available on a public website (SpliceRack). For the U12-type introns, we find several features conserved across species, as well as a clustering of these introns on genes. Using the information content of the splice-site motifs, and the phylogenetic distance between them, we identify: (i) a higher degree of conservation in the exonic portion of the U2-type splice sites in more complex organisms; (ii) conservation of exonic nucleotides for U12-type splice sites; (iii) divergent evolution of C.elegans 3' splice sites (3'ss) and (iv) distinct evolutionary histories of 5' and 3'ss. Our study proves that the identification of broad patterns in naturally-occurring splice sites, through the analysis of genomic datasets, provides mechanistic and evolutionary insights into pre-mRNA splicing.}, address = {Cold Spring Harbor Laboratory 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.}, author = {Sheth, Nihar and Roca, Xavier and Hastings, Michelle L L. and Roeder, Ted and Krainer, Adrian R R. and Sachidanandam, Ravi }, citeulike-article-id = {805877}, doi = {http://dx.doi.org/10.1093/nar/gkl556}, issn = {1362-4962}, journal = {Nucleic Acids Res}, keywords = {introns\_splicing}, month = {August}, posted-at = {2007-01-22 23:34:28}, priority = {2}, title = {Comprehensive splice-site analysis using comparative genomics.}, url = {http://dx.doi.org/10.1093/nar/gkl556}, year = {2006} }

TY - JOUR ID - citeulike:805877 L3 - citeulike-article-id:805877 TI - Comprehensive splice-site analysis using comparative genomics. JF - Nucleic Acids Res AD - Cold Spring Harbor Laboratory 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA. SN - 1362-4962 N2 - We have collected over half a million splice sites from five species-Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans and Arabidopsis thaliana-and classified them into four subtypes: U2-type GT-AG and GC-AG and U12-type GT-AG and AT-AC. We have also found new examples of rare splice-site categories, such as U12-type introns without canonical borders, and U2-dependent AT-AC introns. The splice-site sequences and several tools to explore them are available on a public website (SpliceRack). For the U12-type introns, we find several features conserved across species, as well as a clustering of these introns on genes. Using the information content of the splice-site motifs, and the phylogenetic distance between them, we identify: (i) a higher degree of conservation in the exonic portion of the U2-type splice sites in more complex organisms; (ii) conservation of exonic nucleotides for U12-type splice sites; (iii) divergent evolution of C.elegans 3' splice sites (3'ss) and (iv) distinct evolutionary histories of 5' and 3'ss. Our study proves that the identification of broad patterns in naturally-occurring splice sites, through the analysis of genomic datasets, provides mechanistic and evolutionary insights into pre-mRNA splicing. KW - introns_splicing AU - Sheth, Nihar AU - Roca, Xavier AU - Hastings, Michelle L AU - Roeder, Ted AU - Krainer, Adrian R AU - Sachidanandam, Ravi PY - 2006/08/12/ UR - http://dx.doi.org/10.1093/nar/gkl556 ER -