Regulatory conservation of protein coding and microRNA genes in vertebrates: lessons from the opossum genome

Table 2 Promoter and site conservation between human and eight vertebrate species

Human versus	Promoters			Sites			BRPR
	Number of orthologous genes	Block coverage	Block nucleotide identity	Number of detectable sites	% detected	Site nucleotide identity
Chimp	512	94.06%	98.27%	1,157	94.81%	98.74%	1.009
Mouse	506	24.20%	73.39%	1,146	72.34%	82.91%	2.887
Rat	496	23.09%	73.21%	1,129	67.14%	83.00%	2.757
Dog	507	46.05%	75.37%	1,151	73.59%	84.77%	1.535
Opossum	389	6.72%	74.63%	912	41.23%	83.93%	5.647
Chicken	189	3.21%	74.43%	451	21.73%	85.06%	6.184
Fugu	127	3.25%	72.87%	286	11.89%	83.98%	3.331
Tetraodon	166	2.50%	73.09%	363	12.12%	80.95%	4.227

Analysis of 1,162 known human transcription factor binding sites (TFBSs) associated with the promoters of 513 human genes between human and eight vertebrate species. The number of genes orthologous to human genes in each species, their conservation block coverage, and their average block identity are presented; also, the number of TFBSs associated with these orthologous genes in each species, the percentage of sites located in conserved regions between species, and the average nucleotide identity within TFBSs are reported. The base regulatory potential rate (BRPR) statistic is calculated from these data for each pair of genomes (see text). Block coverage is the percentage of the upstream region that is covered by conserved blocks (>50 base pairs with >65% identity); the block nucleotide identity is the percentage of nucleotides in all conserved blocks that are identical to the human sequence; and site nucleotide identity the percentage nucleotides in all detected TFBSs that are identical to the human sequence.

ISSN: 1474-760X