Variome Data Standards(V1.0 beta)
- 3. Data analysis standards
- 4. Nomenclature standards
4.6 Nucleotides and Amino Acid nomenclature [7]
The nucleotide and amino acid symbols using in this database follow the Nomenclature for Incompletely Specified Bases in Nucleic Acid Sequences (see IUBMB (NC-IUB)) as the DNA and amino acid nomenclature of the HGVS (Human Genome Variation Society) recommends [7].DNA [8-12]:
| Symbol | Meaning | Description |
|---|---|---|
| A | A | Adenine |
| C | C | Cytosine |
| G | G | Guanine |
| T | T | Thymine |
| B | C, G or T | not-A (B follows A in alphabet) |
| D | A, G or T | not-C (D follows C in alphabet) |
| H | A, C or T | not-G (H follows G in alphabet) |
| K | G or T | Keto |
| M | A or C | aMino |
| N | A, C, G or T | aNy |
| R | A or G | puRine |
| S | G or C | Strong interaction (3 H-bonds) |
| V | A, C or G | not-T / not-U ( V follows U ) |
| W | A or T | Weak interaction (2 H-bonds) |
| Y | C or T | pYrimidine |
| Amino acid | Single-letter code | Triplet (5'-3') | Possible Genotic Codons |
|---|---|---|---|
| Terminator | . | TRR (TAR and TGA) | TAA, TAG, TGA (translation termination) |
| Alanine | A | GCN | GCA, GCC, GCG, GCT |
| Aspartic acid or asparagine | B | RAY | AAC, AAT, GAC, GAT |
| Cysteine | C | TGY | TGC, TGT |
| Aspartic acid | D | GAY | GAC, GAT |
| Glutamic acid | E | GAR | GAA, GAG |
| Phenylalanine | F | TTY | TTC, TTT |
| Glycine | G | GGN | GGA, GGC, GGG, GGT |
| Histidine | H | CAY | CAC, CAT |
| Isoleucine | I | ATH | ATA, ATC, ATT |
| Lysine | K | AAR | AAA, AAG |
| Leucine | L | YTN (CTN and TTR) | CTA, CTC, CTG, CTT, TTA, TTG |
| Methionine | M | ATG | ATG (translation initiation) |
| Asparagine | N | AAY | AAC, AAT |
| Proline | P | CCN | CCA, CCC, CCG, CCT |
| Glutamine | Q | CAR | CAA, CAG |
| Arginine | R | MGN (CGN and AGR) | AGA, AGG, CGA, CGC, CGG, CGT |
| Serine | S | WSN (TCN and AGY) | AGC, AGT, TCA, TCC, TCG, TCT |
| Threonine | T | ACN | ACA, ACC, ACG, ACT |
| Selenocysteine | U | Sec | TGA |
| Valine | V | GTN | GTA, GTC, GTG, GTT |
| Tryptophan | W | TGG | TGG |
| Unknown | X | NNN | NNN |
| Tyrosine | Y | TAY | TAC, TAT |
| Glutamic acid or glutamine | Z | SAR |