For example, the mouse genome contains over 25,000 tRNA genes and pseudogenes [ 16], while the rat genome contains over 175,000 tRNA genes and pseudogenes [ 17].
This has been a recent expansion peculiar to the mouse, since the rat genome contains only three pairs of Abpa/ Abpbg paralogues, and the human and chimpanzee genomes contain only a single pair whose members are both pseudogenes.
Human populations have been studied more extensively for breast cancer genetic risk than have rat populations; therefore, it is not surprising that human studies have yielded a considerable number of genome-wide significantly associated SNPs in alleles where it is not known if the rat genome contains a concordant allele.
The mouse and rat genomes contain the most, approximately five times as many as the primate genomes.
Although this region of the rat genome assembly contains many gaps (including 5 contig gaps) there is no evidence, as there was for previous mouse assemblies, from unplaced genomic and cDNA sequences for additional Abp gene paralogues.
Affymetrix GeneChip Rat Genome U34A arrays containing each 8'799 probes including full-length or annotated rat genes and several thousands of rat EST clusters consisting of redundant probes spanning an identical transcript were hybridized with the target cRNAs at 45°C for 16 h, washed and stained by using the Gene Chip Fluidics Station.
The rat genome 230_2.0 array contains >31,000 probe sets representing >17,734 unique UniGenes, containing probes for 57 of the 86 genes (66.3%) within our region of interest [rat chromosome 1: 204.38–207.48 Mb (Solberg Woods et al. 2010, 2012)].
No signal was obtained using rat genomic DNA (data not shown), proving specificity of the primers for human G72, as the rat genome does not contain a G72 gene (see below, and [ 1]).
The Affymetrix Rat Genome 230 2.0 GeneChip contains 31,000 probesets representing 28, 000 well substantiated rat genes.
Enhancer activity has been reported to be associated with exon 6 of keratin 18 [20], although the key AP-1 binding site is not evolutionarily conserved as the same region in the rat genome does not contain this site and it only leads to a three- to four-fold increase in reporter gene activity above the basal promoter.
