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Table 4 Summary of EST and PCR data on bovine TRAV/TRDV subgroup expression in re-arranged TRA and TRD chains

From: Genomic analysis offers insights into the evolution of the bovine TRA/TRD locus

TRAV/TRDV subgroup EST evidence of use in TRA/TRD rearrangement PCR data (iii)
No. of unique TRA/TRD chain sequences (iv) Total number of unique TRAV/TRDV genes (v) Identical genome matches No. of matches >97% (viii) No. of matches <97% (ix)
Number (vi) Matching TRAV/TRDV gene (vii)
TRA (i) TRD (ii)
AV1   5 3 1 A 2  
AV2    4 3 1 G 2  
AV3   13 8 5 a, b, c, e, f 3  
AV4    2 2 -   2  
AV5   1 1 -    1
AV8   9 7 3 I, l, n 3 1
AV9   2 2 1 K 1  
AV10   5 3 1 B 2  
AV12   10 7 1 D 5 1
AV13   8 7 3 f, j, k 3 1
AV14    2 2 1 E 1  
AV16   4 4 2 a, b 2  
AV17   8 4 2 a, c 2  
AV18    2 2 -   2  
AV19    4 2 1 C 1  
AV20    3 1 1 E   
AV21   4 2 1 C 1  
AV22   11 9 2 aa, w 6 1
AV23   3 2 1 X 1  
AV24    1 1 -   1  
AV25   5 4 1 v 2 1
AV26   5 5 3 aj, s, w 2  
AV27   5 3 -   1 2
AV28   3 2 2 b, c   
AV29   8 4 2 a, b 2  
AV33   7*/ 6 -   1 5
AV34    -   -   -  
AV35   3 2 -   2  
AV36    2 1 1 a   
AV38    10 6 -   5 1
AV39    -      
AV41   1 1 -   1  
AVX   35 23 11 aa, ab, b, f, g, l, p, q, u, w, x 12  
AVY    10 7 3 d, e, g 4  
DV1 111*/ 45 13 af, ah, ai, as, au, b, bb, e, g, aj, bg, j, w 25 7
DV2    2† 1 1 a   
DV3 2† 1 1 a   
DVb3   2† 6 1 b 5  
DVY    29† 2 1 a 1  
Total    341 191 67   103 21
  1. BLAST analysis of the NCBI Bos taurus EST archive (March 2013) using the bovine TRAC and TRDC sequences identified 24 subgroups participating in TRA chain rearrangement (column i) and 4 participating in TRD rearrangement (column ii). Using a combination of bovine TRAV/TRDV subgroup-specific and unbiased SMART TRAC+ and TRDC+ PCR (column iii) 341 unique full or partial TRA/TRD chain transcripts were sequenced (column iv), providing a more comprehensive description of the breadth of TRAV/TRDV subgroup usage in TRA and TRD transcripts. Amongst these sequences 191 unique TRAV/TRDV gene sequences were identified (column v), of which only 67 (35.1%) matched any of the genomic sequences identified in the UMD3.1 assembly (column vi and vii). Twenty-one of the TRAV/TRDV gene sequences (11%) were sufficiently dissimilar to genomic TRAV/TRDV genes (<97% nucleotide identity) to be considered as products of TRAV/TRDV genes absent from the UMD3.1 assembly (column ix), whilst the other 103 sequences (53.9%) showed >97% identity with genomic sequences and may either represent products of novel TRAV/TRDV genes or allelic variants of the genes in the UMD3.1 assembly (column viii). Despite several attempts no amplification could be achieved with TRAV39 subgroup-specific primers and there was no EST data supporting use of genes from this subgroup in rearranged TRA or TRD chains; consequently this is the only subgroup which was predicted to contain functional TRAV/TRDV genes for which there is no evidence of expression in the TRA/TRD repertoires.