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Most (28/38) of the partial rat sequences are OR genes.
Mouse V1R genome sequences are taken from the March, 2005 assembly and rat sequences are from the June, 2003 assembly.
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Since the wild rat sequences were quiet divergent from the inbred population we did not include these wild rat sequences in the neutrality tests.
The mouse and rat sequences were not included as they additionally each contain two large non-homologous insertions which make alignments problematic.
However, all contigs belonging to the human and rat sequences were assigned correctly, presumably as a consequence of having closely related reference sequences for these organisms.
Upon closer scrutiny, 5 distinct rat sequences were found to have homology within the probe set of mouse Cyp2c54 (see Additional file 3).
Human, mouse and rat sequences were thereafter multiply aligned, and used to further search the human genomic area (chrX:99850000 100250000) using an HMM [ 51].
In this case, the lack of observation of a "c" transcript type in cattle, and likewise in human, is likely due to the fact that the start codon utilized in mouse and rat sequences is not conserved.
The closest human V germlines to the parental rat sequence were found to be IGLV6 57 (66.2% for the light chain) and IGHV3 7 (84.0% for the heavy chain).
This rat sequence was fused into a β-galactosidase expression vector system.
Rat-flotillin-2-EGFP [ 26], which is resistant against the human shRNA sequences due to natural silent substitutions in the rat sequence, was used for flotillin-2 rescue experiments.
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