REBASE defines the following example for RECOGNITION SEQUENCE NOMENCLATURE:
REBASE Recognition sequences representations use the standard abbreviations
(Eur. J. Biochem. 150: 1-5, 1985) to represent ambiguity:
R = G or A
Y = C or T
M = A or C
K = G or T
S = G or C
W = A or T
B = not A (C or G or T)
D = not C (A or G or T)
H = not G (A or C or T)
V = not T (A or C or G)
N = A or C or G or T
These are written from 5' to 3', only one strand being given. If the point of cleavage has been
determined, the precise site is marked with ^. For enzymes such as HgaI, MboII etc.,
which cleave away from their recognition sequence the cleavage sites are indicated in parentheses.
For example HgaI GACGC (5/10) indicates cleavage as follows:
5' GACGCNNNNN^ 3'
3' CTGCGNNNNNNNNNN^ 5'
Typically, the recognition sequences are oriented so that the cleavage sites lie on their 3' side.
ENZYMES WITH UNUSUAL CLEAVAGE PROPERTIES:
Enzymes that cut on both sides of their recognition sequences, such as BcgI, Bsp24I, CjeI and CjePI,
have 4 cleavage sites each instead of 2.
Bsp24I
5' ^NNNNNNNNGACNNNNNNTGGNNNNNNNNNNNN^ 3'
3' ^NNNNNNNNNNNNNCTGNNNNNNACCNNNNNNN^ 5'
This will be described in some REBASE reports as:
Bsp24I (8/13)GACNNNNNNTGG(12/7)
Entries that do not conform to this format are excluded by DNADynamo. Note that recognition sites that contain a "^" to indicate the cleavage site must be palindromes. Enzymes that cut on both sides of their recognition sequences result in two cut site entries on tables of restriction enzyme sites and therefore will never appear on graphic maps showing unique cut sites.