Abstract
Analysis of a set of almost 25,000 donor and acceptor splice sites in Drosophila shows that information content increases near splice sites flanking very long of very short introns and exons.
Highlights
Using cDNA copies of transcripts and corresponding genomic sequences from the Berkeley Drosophila Genome Project, a set of 24,753 donor and acceptor splice sites were computed with a scanning algorithm that tested for single nucleotide insertion, deletion and substitution polymorphisms
Taking advantage of a larger set of 10,284 cDNA sequences posted at the Berkeley Drosophila Genome Project (BDGP), we used BLAST to identify corresponding genomic sequences for 10,057 of these cDNAs
Using an improved scanning algorithm for computing splice sites, we identified 24,753 introns in 7,062 of these cDNAs; 1,172 additional cDNAs had no introns and the scanning algorithm failed for the remaining 1,823 cDNAs, which were not included in our dataset (Table 1)
Summary
Using cDNA copies of transcripts and corresponding genomic sequences from the Berkeley Drosophila Genome Project, a set of 24,753 donor and acceptor splice sites were computed with a scanning algorithm that tested for single nucleotide insertion, deletion and substitution polymorphisms. Using this dataset, we developed a progressive partitioning approach to examining the effects of challenging the spliceosome system. The information at each nucleotide position p for a set of n aligned sequences is defined by the expression: information(p) = 2 - Σ{-fp(α) log2(fp(α)) | α = A, C, G, or U} - γ.
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
