Herzig et al. BMC Genomics 2010, 11:100 http://www.biomedcentral.com/1471-2164/11/100 Page 11 of 19 Figure 5 Comparison of TRDV gene recombination signal sequences. Sequence logos for recombination signal (RS) sequences are shown for (A) bovine and ovine TRDV1 genes (52 and 12 sequences, respectively). (B) bovine TRDV4 and its ovine, human and murine orthologs (TRDV4, TRDV3 and TRDV5, respectively; four sequences) and (C) remaining human, murine and bovine TRDV genes (human TRDV1, TRDV2; murine TRDV1, TRDV2-1, TRDV2-2, TRDV4; bovine TRDV2-1, TRDV2-2, TRDV3-1; nine sequences). Heptamer and nonamer sequences and spacer lengths are indicated. Logos were generated using WebLogo3 [45]. Table 5) no corresponding TRDV1 genes could be iden- tified although cDNA sequences were found to have fea- tures characteristic of particular sets, as indicated. It is possible that no corresponding genes were found because additional TRDV1 genes are present in the bovine genome but were not identified in this study due to gaps in the analyzed regions of the Btau_3.1 assem- bly. Only cDNA sequences that differed from potential corresponding gene sequences by six or fewer nucleo- tides were classified; however, it remains possible that those cDNA sequences are not in fact representative of the genes indicated. Overall, corresponding genes were identified for most cDNA sequences (35 out of 55 sequences), although 36 of the 52 predicted TRDV1 genes reported here lacked cDNA confirmation and those genes were found to be distributed among all sets.