Herzig et al. BMC Genomics 2010, 11:100 http://www.biomedcentral.com/1471-2164/11/100 Table 5: Classification of bovine TRDV1 cDNA sequences (Continued) BVd1.19 Vdelta1.35 SB-C21 BTDV36 U73386 EF175173 FJ907531 D13659 TRDV1S20 NN NN TRDV1S19 TRDV1ad TRDV1ae TRDV1u ND 1 0 5 Page 14 of 19 8 9 10 11 1A dash indicates redundant sequence for which a GenBank accession number was not obtained. 2NN indicates sequence for which no Provisional Nomenclature exists. 3ND indicates cDNA sequences for which no corresponding gene could be identified in this study. 4Number of nucleotides that are different between the Provisional IMGT Nomenclature and the corresponding gene sequences between amino acid positions 1 and 104 (2nd-CYS); indicates sequence that lacks corresponding gene. 5Genes listed as corresponding are the closest matches; however, classification of these genes was unclear. 6cDNA sequence used for comparison was partial. Table 6 TRDD gene usage in CDR3 of bovine rearranged sequences by TRDV genes of different subgroups TRDV subgroup Number of sequences Number of times TRDD gene identified evaluated (Percentage of all TRDD genes used) TRDD1 TRDD2 TRDD3 TRDD4 TRDV1 73 33 (24.3) 33 (24.3) 18 (13.2) 23 (16.9) TRDV2 17 6 (16.2) 9 (24.3) 7 (18.9) 9 (24.3) TRDV3 17 9 (29.0) 3 (9.7) 10 (32.2) 4 (12.9) TRDV4 36 9 (14.8) 16 (26.2) 11 (18.0) 16 (26.2) TRDD5 29 (21.3) 6 (16.2) 5 (16.1) 9 (14.8) Figure 7 TRD rearranged CDR3 sequences and TRDD gene usage. TRD rearranged CDR3 nucleotide sequences, and their corresponding deduced amino acid sequences, derived from cDNA from peripheral blood mononuclear cells, were aligned to demonstrate TRDD usage. Germline TRDD sequences are shown above representative TRDV1, TRDV2, TRDV3 and TRDV4 sequences containing between one and five TRDD genes. TRDD genes are shaded and gene usage was determined by the presence of at least six nucleotides of a particular TRDD gene. Sufficient cDNA sequence was analyzed to determine TRDV gene usage; however, the sequences shown here have been truncated after the 2nd-CYS 104 and at the beginning of the TRDJ gene. TRDV3 and TRDV4. We confirmed the presence of three TRDJ and five TRDD genes [20] and evaluated TRD junctional diversity incorporating these genes. Furthermore, we described the existence of 52 TRDV1 genes (46 of them functional and six of them ORF), evaluated them for their sequence characteristics and further classified them into eleven sets based on phylogenetic analysis. As for other mammals, the bovine TRD locus was found embedded within the TRA locus and thus TRDV1 genes were distributed amongst the TRAV genes. Indeed, there were a num- ber of genes for which assignment to the TRAV or TRDV group was ambiguous. It is important to note that the presence of TRAV/DV genes is certain and