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Then, we used MultiZ alignment to compare Pldi and its homologues regions in mouse, rat, human, dog, chicken and opossum.
In Table 1 we provide an overview of available literature on HPC markers in mouse, rat, human, dog, and cat.
In order to examine OR promoters in other species, we used UCSC's liftOver utility to obtain orthologous TSS coordinates in the rat, human, dog and cow genomes.
Tests for recurrent positive selection were also taken from Dean et al. [ 49], who analyzed evolutionary rates across five species with the phylogeny of ((mouse, rat), human, (dog, cow)).
SBP2L is consistently larger in size than SBP2 as the average predicted molecular weight of chicken, rat, human, dog, and horse SBP2L is 126 kDa while that of SBP2 from the same species is 98 kDa.
Nevertheless, these three TARs were conserved in rat, human, dog and opossum genomes, matching annotated introns in the orthologous genes in human and rat (Additional file 1, Fig. S5).
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Interestingly we noticed a putative D-Box element (Fig 6A), which is also conserved in the rat, human, bovine, dog and chicken Fbxl21 gene promoters in spite of the very poor sequence conservation between species (data not shown).
Primates (((human, chimpanzee), orangutan), rhesus), rodents: ((mouse, rat), human), laurasiatheria (((dog, horse), cow), human) and ((stickleback, medaka), tetraodon).
Synonymous substitution rates have been found to be correlated among several mammalian species, including mouse, rat, human, and dog.
We obtained protein-coding sequences for the mouse, rat, human, orangutan, dog, and cow from ENSEMBL (Vilella et al. 2009).
To better learn the evolution of this loci, we examined the change in substitution rate during the fixation of 4 species, mouse, rat, human and dog.
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Justyna Jupowicz-Kozak
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