Herzig et al. BMC Genomics 2010, 11:100 http://www.biomedcentral.com/1471-2164/11/100 Table 1: Annotated TRD genes (Continued) GLEAN_06133 GLEAN_06131 GLEAN_26185 GLEAN_26186 GLEAN_21863 GLEAN_20556 GLEAN_05967 GLEAN_04691 GLEAN_04693 GLEAN_10738 GLEAN_12353 GLEAN_22424 GLEAN_20555 GLEAN_08205 GLEAN_19099 GLEAN_05881 GLEAN_10313 GLEAN_25296 GLEAN_19095 GLEAN_19724 GLEAN_19705 ChrUn.1227 ChrUn.1227 ChrUn.2188 ChrUn.2188 ChrUn.5529 ChrUn.4913 ChrUn.41 ChrUn.3566 ChrUn.3566 ChrUn.3620 ChrUn.3793 ChrUn.3970 ChrUn.10149 ChrUn.3458 ChrUn.2982 ChrUn.4123 ChrUn.158 ChrUn.1907 ChrUn.1948 ChrUn.7503 ChrUn.1002 Chr10.30 Chr10.30 Chr10.30 Chr10.30 Chr10.30 Chr10.30 Chr10.30 Chr10.30 Chr10.30 Chr10.30 TRDV1ba TRDV1bb TRDV1bc◇◇◇ TRDV1bd TRDV1be§§§§ TRDV1bf§§§§§ TRDV1bg TRDV1bh TRDV1bi◇ TRDV1bj◇◇ TRDV1bk◇◇ TRDV1bl◇◇◇ TRDV1bm TRDV1bn◇◇◇◇ TRDV1bo◇◇◇◇ TRDV1bp◇◇◇◇◇ TRDV2-1 TRDV2-2¤ TRDV2-2b¤ TRDV3-1¤¤ TRDV3-1b¤¤ TRDV4 TRDD1 TRDD2 TRDD3 TRDD4 TRDD5 TRDJ1 TRDJ2 TRDJ3 TRDC Group Human Mouse Bovine Ovine Swine 39695 62992 10476 33687 9610 10675 250250 5067 19054 538 3915 9390 1843 16972 15173 14961 345140 43992 11302 3142 77577 396663 504600 488743 449660 441241 417750 416717 406656 410369 402706 40263 63563 11031 34255 10170 11244 250849 5528 19618 1129 4506 9945 2409 17538 15739 15497 345657 44509 11819 3667 78102 397245 504612 488757 449672 441249 417760 416770 406598 410417 403988 Page 5 of 19 - - + + - - + + + + + + - - + + - + + - + + - - - - - - - - - 1Gene designations with the same symbols denote gene models that are thought to be representative of the same gene based on analysis of genomic sequence. 2NA denotes identified genes lacking glean models. Table 2 Number of TRD genes among species Locus TRDV1 1 1 52 > 40 > 31 TRDV TRDV2 to TRDV5 2 5 4 3 6 TRDD 3 2 5 ? ? TRD TRDJ 4 2 3 4 4 TRDC 1 1 1 1 1 Reference IMGT http://www.imgt.org and [14] IMGT http://www.imgt.org and [10] Described here [15,23] [21] were found to represent the same gene (see Table 1, as indicated above, and Figure 2) and therefore subsequent analyses were performed after removing redundant sequences. It is likely that the occurrence of redundant sequences is a result of assembly anomalies; however, it is also possible that these duplicated TRDV genes are in fact present within the bovine genome. TRDV gene analysis Deduced amino acid sequences of the 56 TRDV genes identified here were initially aligned using ClustalW2 [28]. Alignments were refined in BioEdit according to the IMGT unique numbering for the V-DOMAIN [29], visualized with Jalview [30] and are shown (Figure 3A) with IMGT numbering and framework regions (FR) and