Figure 5. Alignment of Alpha V cDNA clones suggest somatic hypermutation at shark TCRα.

Thymocyte clones for all 11 αV groups with the same CDR3 from six different predicted V genes. Locations of framework regions (FR), complementarity determining regions (CDR), joining regions (J), and constant (C) regions are marked above the scale for each αV. In absence of germline sequence information, we used a Geneious-derived nucleotide consensus sequence for analysis of nucleotide changes in thymocyte clones. Amino acids are shown under the consensus sequence, and dots represent identity to this sequence. Nonsynonymous changes are highlighted in black; synonymous changes are underlined. Gaps are used for alignment purposes and indicate either a shortened sequence (at the beginning or end) or insertions or deletions within the sequence. Sequences are identified by a single clone number or a group of identical clones condensed to a single line (the number of clones are indicated). Clone numbers that contain ‘THY’ are from thymus, ‘PBL’ are from peripheral blood leukocytes, and ‘SPV’ are from spiral valve (intestine). We did not use clones from αV1.3 and αV7.1 because they did not contain mutations in FR or CDR regions. We deposited all 42 sequences into GenBank under accession numbers KY189332 – KY189354 or KY366469 – KY366487.