Evidence for selection on synonymous mutations affecting stability of mRNA secondary structure in mammalsDepartment of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
Genome Biology 2005, 6:R75doi:10.1186/gb-2005-6-9-r75
Subject areas: Evolution, Genetics, Genome studies, Bioinformatics Additional filesAdditional data file 1: Sequences for all 70 mouse mRNAs in FASTA format. Format: TXT Size: 145KB Download file Additional data file 2: A table of the stability of mRNA secondary structures excluding the Gadd45a gene, where the rat-mouse common ancestor sequence differed slightly using the parsimony and maximum likelihood reconstructions. Format: DOC Size: 30KB Download file This file can be viewed with: Microsoft Word Viewer Additional data file 3: A table of the stability of mRNA secondary structures for short genes (only considers mRNAs shorter than 2,000 nucleotides). Format: DOC Size: 31KB Download file This file can be viewed with: Microsoft Word Viewer Additional data file 4: Stability and relative stability values for individual genes. Format: TXT Size: 17KB Download file Additional data file 5: Sequence identifiers for each mouse gene. Format: TXT Size: 55KB Download file Additional data file 6: Ontology information for each mouse gene. Format: TXT Size: 110KB Download file Additional data file 7: Miscellaneous correlations for short genes, including GC4 skew versus Z(ΔGSh.4-fold), GC12 skew versus GC3 skew (separately for base-paired and unpaired sites) and Z(ΔGRe-sub.N3) versus Ks at base-paired sites. Format: DOC Size: 26KB Download file This file can be viewed with: Microsoft Word Viewer Additional data file 8: A table of correlations between GC skew at first/second sites versus skew at third sites, provided for a series of thresholds where the sites analyzed must have a minimum probability of base-pairing. Format: DOC Size: 33KB Download file This file can be viewed with: Microsoft Word Viewer Additional data file 9: A FASTA file containing three-way alignments of coding sequences from hamster, rat and mouse orthologous genes. Format: TXT Size: 264KB Download file Additional data file 10: A table of correlations for short genes, between the proportion of base-paired sites and non-synonymous or synonymous substitution rates within the coding sequence, base-paired sites and unpaired sites. Format: DOC Size: 26KB Download file This file can be viewed with: Microsoft Word Viewer |


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