Table IV.

A comparison of the production mechanisms of public D^bNP₃₆₆-specific CDR3β amino acid sequences with and without N-addition.

CDR3βregion									Minimum no. of required n- additions	No. of recombination mechanisms
										Without N- additions	With N- additions
S	G	G	A	N	T	G	Q	L		40	130
agt	ggg	ggg	gca	aac	acc	ggg	cag	ctc	0	14
agt	ggg	ggc	gca	aac	acc	ggg	cag	ctc	0	12
agt	ggg	ggt	gca	aac	acc	ggg	cag	ctc	0	11
agt	ggg	ggg	gcg	aac	acc	ggg	cag	ctc	0	3
S	G	G	G	N	T	G	Q	L		2	80
agt	ggg	ggg	gga	aac	acc	ggg	cag	ctc	0	1
agt	ggg	ggg	ggc	aac	acc	ggg	cag	ctc	0	1
S	G	G	S	N	T	G	Q	L		0	60
agt	ggg	ggg	tca	aac	acc	ggg	cag	ctc	1
agt	ggg	ggc	tca	aac	acc	ggg	cag	ctc	1
Germline genes:
Vβ 8.3: agt gat g, Jβ2S2: t gca aac acc ggg cag ctc
Dβ 1: gggacagggggcg, D β2: gggactgggggggcg

^aShown are the nucleotide sequences that encode commonly public D^bNP₃₆₆-specific CDR3β amino acid sequences and require a minimal number of N-additions to be produced. One possible V(D)J recombination mechanism is shown for each nucleotide sequence, with the nucleotides attributed by the germline Vβ, Dβ and Jβ genes shown in blue, red, and green, respectively. N-additions are shown in black and p-additions are shown in bold text. The number of possible recombination mechanisms that can produce these TCR sequences with no N-additions are shown. These different recombination mechanisms involve different splicings of the germline TCR genes and different p-additions (see Ref. 9 for more detail on different recombination mechanisms). Also shown is the number of different recombination mechanisms allowing for N-additions, determined from a simulation of a random V(D)J recombination process in which one million in-frame TCR sequences were generated (9).