Fig. 4

CDR3-IMGT nucleotide sequences retrieved from the cDNA clones with productive (a) and unproductive (b) rearrangements. Nucleotide sequences are shown from codon 104 (2nd-CYS) to codon 118 (J-PHE) (a and b). N-nucleotides added by the deoxynucleotidyltransferase terminal (DNTT, TdT) are indicated in lower cases. Numbers in the left and right columns indicate the number of nucleotides that are trimmed from the 3′V-REGION and 5′J-REGION, respectively; the germline region of the TRGV and TRGJ genes coincides with 0 in the nt V and nt J columns, respectively. In A, clonotypes with the same CDR3-IMGT nucleotide sequence deriving from two or more animals (letters M, L, K and C) are underlined. A shared clonotype (AA) between individuals has per definition a given V and J gene and allele and a given AA sequence for the junction. Three individuals (M, K and C) share the same CDR3 (AA) sequence with the V1-J2 rearrangement (RTV1M1/C1/K2/K3) however the junction in K3 differs from the junction in the other shared clonotypes by a nucleotide difference in the 5′J-REGION which may represent an allele of the TRGJ2 gene. Similarly, for the K and M shared clonotypes with a V1-J3 rearrangement (RTV1K7/5RV1M1), the junction in M1 differs from the junction in K7 by a nucleotide in the 3′V-REGION, which may represent an allele of the TRGV1 gene. This has been described as “convergent recombination” in which a given “public” TR amino acid sequence may be encoded by different nucleotide sequences both within the same and in different individuals [28]. In B, unproductive rearrangements (non-redundant out-of-frame clonotypes column of Table 2) for the presence of a stop codon (*) and for frameshifts in the CDR3, are indicated