We use a shorthand notation to label the cow (C), dog (D), mouse copy 1 (mousemouse copy 2 (M2), rat copy 1 (rat, rat copy 2 (R2), human copy 1 (humanhuman copy 2 (H2), orangutan copy 1 (O1), and orangutan copy 2 (O2) where M1 R1 (H1–O1) and M2 R2 (H2–O2) are one-to-one orthologs.
In the X chromosome we found, close to PPP1R2P9, more PPP1R2-like copies that seem to have arisen by PPP1R2 gene duplication: marmoset (one copy), rat (two copies), mouse (two copies) and pig (one copy).
The alignments were generated from the mouse MSHORT1 copies and rat MSHORT1 RSHORT1 copies (Additional File 1 Figures S3, S4).
All human gene expression was normalized to glyceraldehyde-3-phosphate dehydrogenase (GAPDH) mRNA copies, and rat gene expression was normalized to β-actin mRNA copies in all samples.
This inference was confirmed by the seed sequence comparison showing the same seed region in miR-513b with its orthologous copy in rats and an ancestral copy in the mouse lemur while both miR-513a and miR-513c have a single-base difference from miR-513b in the seed region (Additional file 1: Figure S4).
For the generation of transgenic reporter mice 4 copies of the rat somatostatin gene promoter CRE and the truncated thymidine kinase promoter were fused with the firefly luciferase-encoding gene (Fig. 1A).
The 3.1 kb BamHI-ApaI fragment of 4xSomCRET81Luc[19] including four copies of the rat somatostatin gene promoter CRE (5'-GATCCTCCTTGGCTGACGTCAGAGAGAGAGTA-3'), truncated thymidine kinase promoter (−81 to−57) and the firefly luciferase-encoding gene (Photinus pyralis, Acc.No. M15077) (Fig. 1A) was gel-purified and microinjected into male pronuclei of fertilized eggs from NMRI mice.
We investigated whether PPAR function was sensitive to RARRES3 catalytic activity, by using a PPAR-specific luciferase reporter assay based on three copies of the rat acyl-CoA oxidase peroxisome proliferator response element, Aox-3x-PPRE-Luc.
Two copies of each rat GeneFilters cDNA microarray filter set (set A and set B; each comprised of gene filter releases gf300, gf301 and gf302) were screened in duplicate with labelled cDNA derived from independent preparations of RNA from adenovirus E1-transformed and untransformed BRK cells.
Using the DNA sequence, starting at the ATG start codon and extending through the stop codon of each Sry copy, phylogenetic analysis was performed comparing rat Sry copies to Muennink's Spiny rat (Tokudaia muenninki) copies, mSry, and hSRY.
Looking at my shelves last night, I found that ancient copies of The Rats, Domain and Lair still lurk there.
