Analysis of vkorc1 polymorphisms in Norway rats using the roof rat as outgroup
1 Department of Ecology and Evolutionary Biology, Rice University, 6100 Main Street, MS 170, Houston, Texas 77005, USA
2 Centers for Disease Control and Prevention Division of Vector-Borne Infectious Diseases, Bacterial Diseases Branch, 3150 Rampart Road, Fort Collins, CO 80522, USA
BMC Genetics 2010, 11:43 doi:10.1186/1471-2156-11-43Published: 24 May 2010
Additional file 1:
DNA nucleotide variation in the vkorc1 protein coding region. Shown are variable (polymorphic/divergent) amino acid positions (aa position) and variable nucleotide positions (nt position provided relative to the start codon) for the coding region (E1-E3) of vkorc1. Non-synonymous mutations are labeled as nucleotide change followed by resulting amino acid change. We provide the consensus amino acid and DNA sequences for the roof rat, as deduced from five genotypes (H1-H5) obtained by sequencing the specimens assigned, based on coat color, as two nominal subspecies R. rattus alexandrinus or R. r. frugivorus. The sequences of R. flavipectus and R. losea are provided. Note three polymorphisms in R. losea (Ser35Cys, Ser58Gly, Cys96Cys) are not depicted. Sequences reconstructed from SNP data for the published vkorc1 coding sequence  are shown as part of a group we call R. rattus/other Rattus and R. rattus-like and as R. norvegicus. The published sequence from R. norvegicus, as retrieved from GenBank and Ensembl, was used to aid identification of 'genuine' R. norvegicus sequences/SNPs. These groupings were defined based on phylogenetic analysis (Figure 3). The mouse sequence (M. musculus domesticus) is provided for reference. The bottom panel (ss#) lists the SNP accession numbers . Note the Ser56Pro SNP was not published (Table 1 in ) but was reported as a SNP in R. norvegicus without referring to the source population analyzed. A SNP underlying the Leu120Gln variant has been published , but for a population not included in the previous study . Sample origins are denoted as follows : USA/Santa Cruz (USASan, n = 3), USA/Chicago (USAChi, n = 18) Argentina/Buenos Aires (ArgBA, n = 15), Azores/Terceira (AzoTer n = 5), Indonesia (Indo, n = 16), Thailand (Thailand, n = 2) England Cambridege/Essex (EngCam, n = 17), England/Norfolk (EngNor, n = 2), England/Gloucestershire (EngGlou, n = 1), England/Lincolnshire (EngLin, n = 2), England/Shropshire (EngShr, n = 2), England/Nottinghamshire (EngNot, n = 2), Hungary/Bekes (HunBek, n = 3), Hungary/Maglod (HunMag, n = 9), Korea/Seoul (KorSeo, n = 8), and Japan (Japan, n = 6).
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