Analysis of the Elephant Immunoglobulin Genes Figure 2. Alignment of the amino acid sequences of the nine elephant c genes. The deduced amino acid sequences of three c chain-coding exons and two membrane exons of nine elephant c genes are aligned. The first exons (CH1) of c1 and c2 are both missing due to gaps. A premature stop codon is marked with a star and a frameshift mutation is marked by shadowing in the CH3 exon of c3. In each panel, the amino acid residues that are identical to the top sequences are represented by dots. The dashes were used to adjust the alignment. The hinge exons are not included in the figure. doi:10.1371/journal.pone.0016889.g002 Fig. 7, which shows that each family contains characteristic sequence intervals that are distinct from other families. JH gene segments. There were six germline JH gene segments found in the elephant IgH locus (Fig. 8). All the JH segments had conserved nucleotide sequences at the 39 end. JH1 was pseudogenized by replacement of a Tryptophan (W) residue by a stop codon. Elephant immunoglobulin light chains k chain. Immunoglobulin k chain genes of elephant were identified on three scaffolds: 202, 50, and 86. A schematic diagram is shown in Fig. 9. Of the 153 germline Vk segments from the three scaffolds, 53 were regarded as potentially functional genes and 100 as pseudogenes. Based on sequence similarity analysis, 142 of the Vk segments can be assigned to eight families (Vk1,Vk8) (Table Figure 3. Dot plot comparison of the elephant Sm with human, pig, and mouse Sm regions. The dots represent homologies with a search length of 30 bp and maximum of 9 bp mismatches. The elephant Sm region shows substantial nucleotide sequence homology with those of human, mouse, and pig. doi:10.1371/journal.pone.0016889.g003 PLoS ONE | www.plosone.org 4 February 2011 | Volume 6 | Issue 2 | e16889