. 2018 Apr 17;7:e28477. doi: 10.7554/eLife.28477

Table 1. Summary of sequence data used in this paper.

Putative subfamilies within each TcR alpha V family share at least 85% nucleotide identity using nearest-neighbor consensus trees of V segments. Number of TcR alpha nucleotide (NUC), amino acid (AA) sequences or sequence groups within each category. Highlighted columns specifically refer to data used in this study. (See results for detailed descriptions of sequences included within each column.)

Table 1–source data 1. Tab-delimited text file containing sequences used in this paper for analysis of somatic hypermutation of TcR alpha chain.

elife-28477-table1-data1.xlsx^{(32.2KB, xlsx)}

DOI: 10.7554/eLife.28477.008

Alpha V segment	Putative # Sub-families	All cloned sequences	Complete CDR3-J junction^*	Unique V Region ^†		Unique V segment^‡		Unique CDR3-J^§		Groups with identical CDR3-J^#	CDR3-J groups in Study^**	Sequences in each dataset^††
Alpha V segment	Putative # Sub-families	All cloned sequences	Complete CDR3-J junction^*	NUC	AA	NUC	AA	NUC	AA	Groups with identical CDR3-J^#	CDR3-J groups in Study^**	Sequences in each dataset^††
TRA V1	1	40	40	35	34	24	16	34	32	7	4	2, 3, 3, 5
TRA V2	3	18	18	13	13	13	10	12	12	3	1	5
TRA V3	3	217	194	55	52	35	34	51	50	5	1	4
TRA V4	3	60	28	22	22	21	21	21	21	6	2	2, 2
TRA V5	4	35	34	15	13	9	8	13	13	3	1	2
TRA V6	2	9	9	7	7	5	6	7	7	1	0	0
TRA V7	5	96	60	49	48	39	38	48	48	9	2	2, 2
TRA V9	3	19	19	14	14	12	11	13	13	4	0	0
TRA V10	2	45	45	29	26	21	19	27	26	10	2	4, 9
		539	447	239	229	179	163	226	224	48	13	45

^*A full list of these sequences can be found in Table 1—source data 1.

^†V Region includes all bases between the 1 st predicted nucleotide of the V segment to the last predicted nucleotide of the J segment (V and J).

‡V Segment includes all bases between the 1 st predicted nucleotide of the V segment to the last predicted nucleotide of the V segment (V only).

^§CDR3-J includes all bases after the last predicted nucleotide of the V segment to the last predicted nucleotide of the J segment.

#Number of groups with identical CDR3-J sequences, which we used to determine sequence relatedness (see text for details).

**Number of groups with identical CDR3-J sequences used in this study. (Those not used contained no mutation with V segments.).

††Total number of sequences for each alpha V used to assess somatic hypermutation within this study (e.g., for aV1, 4 different clonal groups contained 2, 3, 3, and 5 identical CDR3-J regions, respectively).