Figure 1

URR alignment of the λ-PVs. Nucleotide sequence alignment of the upstream regulatory region (URR) or noncoding region (NCR1), from the stop codon of L1 to the start codon of E6, including the feline papillomaviruses (PVs) Felis domesticus PV type 1 (FdPV1), Lynx rufus PV type 1 (LrPV1), Puma concolor PV type 1 (PcPV1), Panthera leo persica PV type 1 (PlpPV1), and Uncia uncia PV type 1 (UuPV1), and the nonfeline carnivore PVs canine oral PV (COPV) and Procyon lotor PV type 1 (PlPV1), all of which belong to the genus λ-PV. Nucleotides are shaded according to the degree of conservation (black = 100% conserved; dark gray = 80% to 99% conserved; light gray = 60% to 79% conserved; no shade = <60% conserved). The conserved and putative E2 binding sites (E2BSs) and the E1 binding site (E1BS) are indicated. In LrPV-1, an E1BS is located at nucleotides 8,151-8,167, flanked by two conserved E2BSs at nucleotides 8,068-8,079 and 8,215-8,226. Two additional modified putative E2BSs were identified at nucleotides 8,117-8,128 (ACC-N6-GTT) and 8,195-8,206 (GCC-N6-GGT). The E1BS in PcPV-1 is located at nucleotides 8,226-8,242, surrounded by conserved E2BSs at nucleotides 8,143-8,154 and 8,289-8,300, and putative modified E2BSs at nucleotides 8,193-8,204 (ACC-N6-GTT) and 8,269-8,280 (CAC-N6-GGT). In PlpPV-1 we identified an E1BS at nucleotide 8,091-4, two conserved E2BSs at nucleotides 8,057-8,068 and 52-63, and modified putative E2BS motifs at nucleotides 8,007-8,018 (ACC-N6-GTT; a position where all other sequences in the alignment exhibited a conserved E2BS) and at nucleotides 32-43 (GCC-N6-GGT). The E1BS in UuPV-1 is located at nucleotides 7,983-7,999, with three conserved E2BSs at nucleotides 7,899-7,910, 7,949-7,960 and 8,047-8,058, and a putative modified E2BS (GCC-N6-GGT) at nucleotides 8,027-8,038. The TATA box of the E6 promotor in LrPV-1, PcPV-1, PlpPV-1, FdPV-1, COPV, and PlPV-1, and a possible degenerate TATA box (TTTAA) in UuPV-1 is indicated.