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Evidence for selection on synonymous mutations affecting stability of mRNA secondary structure in mammals

JV Chamary and Laurence D Hurst

Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK

author email corresponding author email

Genome Biology 2005, 6:R75doi:10.1186/gb-2005-6-9-r75


Published:	16 August 2005

Subject areas: Evolution, Genetics, Genome studies, Bioinformatics

Additional files

Additional 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

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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(ΔG^Sh.4-fold), GC12 skew versus GC3 skew (separately for base-paired and unpaired sites) and Z(ΔG^Re-sub.N3) versus K_sat base-paired sites.

Format: DOC Size: 26KB Download file

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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

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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