XB-IMG-123134
Xenbase Image ID: 123134
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Figure 5. Bias of potential stop codons in the splice site sequences.Proportion of the coding exons that truncate the ORF when artificially extended into the intronic region at the splice donor (blue diamonds) or splice acceptor sites (red crosses). The horizontal axis shows the number of artificial codons taken from the intronic sequence (i.e., the 1st, 2nd, 3rd, etc. codon downstream of the splice donor respectively upstream of the splice acceptor). The vertical axis to the left gives the percentage of sites that show an in-frame stop with the theoretical inclusion of the respective codon. For the regions A, B, and C, sequence logos are shown where dotted lines indicate the exon boundary and intrinsic potential stop codons are shaded in grey. When regarding exclusively the extension of one (complete) codon into the intron, one third less ORFs would be truncated when extending at the acceptor site compared to the donor site (A vs. B). The observation can partially be explained by in-frame stop codons intrinsic to the different splice site consensus sequences. A secondary peak of stop codons is observed ∼9 extended codons upstream of the acceptor site at a common position for the branch point (consensus sequence C). Sequence logos have been produced with the tool “seqlogo” [66]. Branch point sequences have been kindly provided by the Ast laboratory (http://ast.bioinfo.tau.ac.il/BranchSite.htm). Image published in: Sammeth M et al. (2008) Sammeth et al. This image is reproduced with permission of the journal and the copyright holder. This is an open-access article distributed under the terms of the Creative Commons Attribution license Larger Image Printer Friendly View |