Alignment of human and bovine PrP and physical maps of bovine Prnp. Panel A: Alignment of PrP sequences at human codon E200K and bovine codon E211K. Bovine codon 211 refers to the most common Prnp haplotype containing six octapeptide repeats. For those bovine haplotypes with five or seven octapeptide repeats, the equivalent codons would be numbered 203 and 219, respectively. Panel B: Physical map of bovine Prnp (1691 bp) showing the positions of known polymorphisms and the four possible haplotype sequences of codons 210 and 211 (abbreviations: cE211, acC-Gaa; tE211, acT-Gaa; cK211, acC-Aaa; tK211, acT-Aaa). The map features include: thick shaded arrow, coding sequence; black arrow, 5' and 3' untranslated regions of exon 3; and hatched arrow, bovine repetitive elements. The numbers above the vertical tick marks indicate the polymorphism position relative to the first base of the Prnp start codon (GenBank Accession number AY335912). The letters below the vertical tick marks are International Union of Biochemistry (IUB) ambiguity codes for SNPs in the sense direction (B = c/g/t, K = g/t, M = a/c, R = a/g, W = a/t, and Y = c/t). R1 through R7 refer to octapeptide repeats. R1 through R5 are octapeptide repeats orthologous to those in sheep. The previously reported non-synonymous polymorphisms at codons 46 (S46I) and 145 (S145N) are indicated at nt positions 137 and 461, respectively. The asterisks at nt positions -403, -399, and -276 denote polymorphisms in intron 2 that were not previously reported. Panel C: Amplicons for DNA sequencing or MALDI-TOF MS genotyping. Arrows denote positions of oligonucleotide primers used for amplification, sequencing, or primer extension and MALDI-TOF MS genotyping. The relative position of the 42-bp double stranded synthetic alleles is shown below positions 630 and 631 (i.e., below bovine codons 210 and 211).