Genomic Expression Patterns for Chromosome 11 in Muscle and Chromosome 7 in Prostate Gland

<p>Expression pattern of Chromosome 11 in muscle, bases 66,783,001 to 66,932,000 (above), and Chromosome 7 in prostate gland, bases 17,036,001 to 17,210,000 (below). The upward and downward bars from N indicate the expression levels of the forward and reverse strands at the block, respectively. The genomic positional expression patterns of the two regions showed high similarity.</p

Patterns of Evolution in Promoter Subcategories

<div><p>(A) The percentage of all mouse TSSs assigned to each category. Dark blue shows the percentage assigned to the category annotated to the left, and light blue the reciprocal category (e.g., non-CpG is the reciprocal of CpG). The colour coding is consistent with (B–E). The “map” category refers to whether the TSS could be mapped to the annotated 5′-most end of a known protein-coding gene (dark blue), could not mapped to a gene (light blue), or maps internally to an annotated gene extent (grey). See <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020030#s3" target="_blank">Materials and Methods</a> for details of category assignment.</p> <p>(B–E) Single nucleotide resolution estimates of substitution rates calculated from promoters assigned to the indicated categories. Only rates calculated from mouse–dog comparisons are shown. The 95% confidence intervals have been excluded for clarity. Red horizontal lines show <i>K</i> for ARs, nucleotide position is shown on the <i>x-</i>axis relative to the TSS at +1 (grey vertical line), and <i>K</i> is shown on the <i>y-</i>axis. Although there are three categories indicated for gene mapping in (A), only two are shown for clarity.</p></div

Genomic Expression Pattern and Sequence Similarity for Chromosome 11 in Muscle and Chromosome 7 in Prostate Gland

<p>Sequence similarity is shown for the same regions as in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.0020044#pgen-0020044-g002" target="_blank">Figure 2</a>. Expression patterns for Chromosome 11 in muscle and Chromosome 7 in prostate gland are shown at the right and at the top, respectively. The dot matrix shows the low sequence similarity of the two regions.</p

High-Resolution Pairwise Substitution Rate Estimates <i>(K)</i> across Promoter Region Alignments

<div><p>The <i>x-</i>axis denotes nucleotide position relative to the TSS reference position at +1 (grey vertical line). Error bars (lighter shading) show 95% confidence intervals for each data point.</p> <p>(A) Rates calculated from mouse-based alignments.</p> <p>(B) Rates calculated from human-based alignments.</p></div

Proportion of Putative Donor (GT) and Acceptor (AG) Splice Sites That Are Located In-Frame Relative to the Splice Sites in CDS, UTR, and Noncoding Regions

<p>This figure shows the fraction of AG dinucleotides that occur at distance that is a multiple of three in the first 100 intronic bases upstream of acceptor (3′) splice sites of exons that show splice variation at their acceptor sites, and the fraction of GT dinucleotides that occur at a distance that is a multiple of three in the first 100 intronic bases downstream of donor (5′) splice sites of exons that show splice variations at their donor sites. Occurrences of AG or GT within the first four bases flanking the splice sites were not counted. The estimated fraction is in the middle of the gray bar, with the gray bar indicating two standard errors. The dashed line shows the fraction 1/3 that would be expected by chance.</p