Table 2. Sequence contexts for cytidine deamination.
| Hot spots |
|
Cold spots |
|
|---|---|---|---|
| Site | No. C → U | Site | No. C → U |
| TTTCCCCGC |
173 |
TAACACA |
1 |
| ATTCCCCAA |
120 |
GCACCTT |
1 |
| ATTTCCCCG |
117 |
TAGCATT |
2 |
| TTCTCCATC |
111 |
TTACCTC |
2 |
| TTCCCCGCT |
106 |
GCACTTT |
4 |
| CATTCCCCA |
86 |
CTACTAT |
4 |
| TTCCCCAAA |
75 |
AAACTAA |
5 |
| CTCTCCTTT |
63 |
CTACTAC |
5 |
| TTTCTCCAT |
60 |
CTACTAT |
6 |
| TCTTTCTGC |
59 |
GTGCTGA |
7 |
| |
|
ATGCTTG |
7 |
| |
|
|
|
| HHYYYCNNN |
|
NHRCHNN |
|
| WRC | SYC |
The 10 hottest and 11 coldest spots are given along with their substitution frequencies among 431 sequences. The consensus sequence motifs are given where R = G or A; Y = T or C; H = T, C or A; W = T or A; S = C or G; N = any base. Given separately at the bottom are the corresponding sequence motifs for the phylogenetically related AID cytidine deaminase derived from an in vitro assay. From Pham et al. (15).