Table 2.
Putative bovine TRAV/TRDV gene homology units identified in the UMD3.1 assembly
| Homology unit | TRAV/TRDV gene motif | No. of TRAV/TRDV genes | Size (Kb) | Number of replicons | Variable gene content | |
|---|---|---|---|---|---|---|
| Proportion of homology unit amplified | Post-replication insertion/deletion | |||||
| 1 | 33-29-28-33-34-26-33 | 7 | 39 | 2 | Yes | |
| 2 | 2-3 | 2 | 15 | 7 | ||
| 3 | 38-37 | 2 | 15 | 2 | ||
| 4 | 14-13-9 | 3 | 15 | 5 | ||
| 5 | 22-8-21-20-19-X-X-X-18-12-11-10-9-14-13-Y-9 | 17 (15) | 157 | 6 | Yes | |
| 6 | 25-19-X-X-X-X-18-17-16 | 9 (8) | 80 | 3 | ||
| 7 | DV1-22-26-25-DV1-23-22-8-21-20 | 10 | 71 | 5 | ||
| 8 | DV1-23-22-26-DV1-25-23-22-26-DV1-25 | 11 | 63 | 8 | Yes | Yes |
| 9 | DV1-22-8-DV1-26-25-24-DV1-26-DV1-26 | 12 (8) | 86 | 7 | Yes | Yes |
| 10 | DV1-23-22-24-DV1-23 | 6 | 43 | 2 | ||
For each homology unit the TRAV/TRDV gene motif, the number of genes, the estimated minimal size and the number of replicons identified are shown. Due to the fragmentary nature of the UMD3.1 assembly many of the homology units presented here and many of the copies of the homology units are likely to be incomplete. Therefore the TRAV/TRDV gene motif, number of TRAV/TRDV genes and size of homology units should be considered a minimum. Similarly, we have rationalised the number of replicons for each homology unit to the minimum that could account for all of the partial replications observed in the UMD3.1 assembly and so this should also be considered a minimum. For homology units 5, 6 and 9 no single copy covers the entirety of the homology unit and we have estimated its size by combining data from multiple copies; the number of genes in the most extensive copy of these homology units is indicated in parentheses in the ‘No. of TRAV/TRDV genes’ column. In addition we have summarised where there is evidence in the UMD3.1 assembly of the TRAV/TRDV gene content of copies of a homology unit differing due to either varying proportions of the homology unit being duplicated in different replicative iterations or post-replication insertion/deletion (see Additional file 8).