Marine Iguana Class I Figure 3. Amino acid alignment of Amcr-UA with other vertebrate class I sequences. Coding domains are separated according to Koller and Orr [52] and exon/intron information from the Amcr-UA genomic sequence. Numerical labels in the alignment refer to amino acid positions in the Amcr-UA sequence, not in the alignment itself. Shaded columns indicate amino acid positions that are conserved or have expected functions. These amino acid positions also contain the following additional labels: ‘‘asterisks’’ = conserved peptide-binding residues of antigen N- and C- termini; ‘‘diamonds’’ = salt bridge-forming residues; ‘‘circles’’ = disulfide bridge-forming cysteines; ‘‘squares’’ = N-glycosylation site; ‘‘CD8’’ = expected CD8 binding site. The boxed sequence from Amcr-UA represents the 11 amino acid extension that is encoded in exon 4, which corresponds to the a-3 domain. Information and accession numbers of other vertebrate class I sequences can be found in the methods section. doi:10.1371/journal.pone.0002859.g003 analysis, suggesting that these genes derive from a common ancestral locus whose descendant lineages have not been identified in any other vertebrate group including Sphenodon, which is also a member of the Lepidosauria superorder. However, within squamates, there is moderate support for the basal position of Amcr-UA relative to all other published class I sequences. PLoS ONE | www.plosone.org 6 August 2008 | Volume 3 | Issue 8 | e2859