Identification of species-specific and CD94L-specific residues. Comparison of the CD94L protein sequences (blue) with those of the class Ia molecules of their respective species (black). The sequences of the murine class Ib molecules M3, which are orthologous between mouse and rat were also included (green). Sequences from rodent are on the top 15 lines, and from primates on the lower 14 the alignment (see Materials and Methods for key to the abbreviations used). The 'pretty' output of the GCG software was used to generate this alignment of the MHC molecules extra-cellular portions (α1 domain: 1–90, α2: 91–180, α3: 181–270). Positions in agreement with the consensus are indicated by -. The positions of CD94L-specific residues, i.e. those that were found in at least 3 of the 4 CD94L rodent or primate sequences and not in the corresponding class Ia sequences are indicated by a blue number above the alignment. Conversely, certain residues were identified that differed from the general consensus, but were common to all the sequences of at least one species. These positions, where intra-species homogenisation has taken place, are indicated by a red number above the alignment.