dc.contributor.authorSheth, Nihar
dc.contributor.authorRoca, Xavier
dc.contributor.authorHastings, Michelle L.
dc.contributor.authorRoeder, Ted
dc.contributor.authorKrainer, Adrian R.
dc.contributor.authorSachidanandam, Ravi
dc.date.accessioned2012-12-12T06:18:56Z
dc.date.available2012-12-12T06:18:56Z
dc.date.copyright2006en_US
dc.date.issued2006
dc.identifier.citationSheth, N., Roca, X., Hastings, M. L., Roeder, T., Krainer, A. R., & Sachidanandam, R. (2006). Comprehensive splice-site analysis using comparative genomics. Nucleic Acids Research, 34(14), 3955-3967.en_US
dc.identifier.urihttp://hdl.handle.net/10220/8868
dc.description.abstractWe 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.en_US
dc.language.isoenen_US
dc.relation.ispartofseriesNucleic acids researchen_US
dc.rights© 2006 The Author(s). This paper was published in Nucleic Acids Research and is made available as an electronic reprint (preprint) with permission of The Author(s). The paper can be found at the following official URL: [ http://dx.doi.org/10.1093/nar/gkl556]. One print or electronic copy may be made for personal use only. Systematic or multiple reproduction, distribution to multiple locations via electronic or other means, duplication of any material in this paper for a fee or for commercial purposes, or modification of the content of the paper is prohibited and is subject to penalties under law.en_US
dc.subjectDRNTU::Science::Biological sciences
dc.titleComprehensive splice-site analysis using comparative genomicsen_US
dc.typeJournal Article
dc.contributor.schoolSchool of Biological Sciencesen_US
dc.identifier.doihttp://dx.doi.org/10.1093/nar/gkl556
dc.description.versionPublished versionen_US


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