Abbreviation Codes For Degenerate Bases
The IUPAC has designated the symbols for nucleotides. Apart from the five (A, G, C, T/U) bases, often degenerate bases are used especially for designing PCR primers. These nucleotide codes are listed here. Some primer sequences may also include the character "I", which codes for the non-standard nucleotide Inosine. Inosine occurs in tRNAs, and will pair with Adenine, Cytosine, or Thymine. This character does not appear in the following table however, because it does not represent a degeneracy. While Inosine can serve a similar function as the degeneracy "H", it is an actual nucleotide, rather than a representation of a mix of nucleotides that covers each possible pairing needed.
| Symbol | Description | Bases represented | ||||
|---|---|---|---|---|---|---|
| A | adenosine | A | 1 | |||
| C | cytidine | C | ||||
| G | guanosine | G | ||||
| T | thymidine | T | ||||
| U | uridine | U | ||||
| W | weak | A | T | 2 | ||
| S | strong | C | G | |||
| M | amino | A | C | |||
| K | keto | G | T | |||
| R | purine | A | G | |||
| Y | pyrimidine | C | T | |||
| B | not A (B comes after A) | C | G | T | 3 | |
| D | not C (D comes after C) | A | G | T | ||
| H | not G (H comes after G) | A | C | T | ||
| V | not T (V comes after T and U) | A | C | G | ||
| N or - | any base (not a gap) | A | C | G | T | 4 |
Read more about this topic: Nucleotide
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