DDBJ Annotated/Assembled Sequences
Codes Used in Sequence Description
Nucleotide
Nucleotide Base Codes
The nucleotide base codes that are used with the International
Nucleotide Sequence Database is as follows.
Sequence data is expressed with small letters only. Capital letter will
be automatically converted to small letter.
| Symbol | Meaning | Explanation |
|---|---|---|
| a | a | adenine |
| c | c | cytosine |
| g | g | guanine |
| t | t | thymine in DNA; uracil in RNA |
| m | a or c | amino |
| r | a or g | purine |
| w | a or t | |
| s | c or g | |
| y | c or t | pyrimidine |
| k | g or t | keto |
| v | a or c or g | not t |
| h | a or c or t | not g |
| d | a or g or t | not c |
| b | c or g or t | not a |
| n | a or c or g or t | any |
[References]
- Cornish-Bowden, A. Nucl Acid Res 13, 3021-3030 (1985)
- Feature Table Definition: 7.4.1 Nucleotide base codes (IUPAC)
Modified Base Abbreviations
An example for description of the modified base in FEATURES line.
Example
FEATURES Location/Qualifiers
modified_base 15
/mod_base="m2g"
| Abbreviation | Modified base description |
|---|---|
| ac4c | 4-acetylcytidine |
| chm5u | 5-(carboxyhydroxylmethyl)uridine |
| cm | 2’-O-methylcytidine |
| cmnm5s2u | 5-carboxymethylaminomethyl-2-thiouridine |
| cmnm5u | 5-carboxymethylaminomethyluridine |
| dhu | dihydrouridine |
| fm | 2’-O-methylpseudouridine |
| gal q | beta,D-galactosylqueuosine |
| gm | 2’-O-methylguanosine |
| i | inosine |
| i6a | N6-isopentenyladenosine |
| m1a | 1-methyladenosine |
| m1f | 1-methylpseudouridine |
| m1g | 1-methylguanosine |
| m1i | 1-methylinosine |
| m22g | 2,2-dimethylguanosine |
| m2a | 2-methyladenosine |
| m2g | 2-methylguanosine |
| m3c | 3-methylcytidine |
| m4c | N4-methylcytosine |
| m5c | 5-methylcytidine |
| m6a | N6-methyladenosine |
| m7g | 7-methylguanosine |
| mam5u | 5-methylaminomethyluridine |
| mam5s2u | 5-methoxyaminomethyl-2-thiouridine |
| man q | beta,D-mannosylqueuosine |
| mcm5s2u | 5-methoxycarbonylmethyl-2-thiouridine |
| mcm5u | 5-methoxycarbonylmethyluridine |
| mo5u | 5-methoxyuridine |
| ms2i6a | 2-methylthio-N6-isopentenyladenosine |
| ms2t6a | N-((9-beta-D-ribofuranosyl-2-methyltiopurin-6-yl)carbamoyl)threonine |
| mt6a | N-((9-beta-D-ribofuranosylpurine-6-yl)N-methyl-carbamoyl)threonine |
| mv | uridine-5-oxyacetic acid methylester |
| o5u | uridine-5-oxyacetic acid (v) |
| osyw | wybutoxosine |
| p | pseudouridine |
| q | queuosine |
| s2c | 2-thiocytidine |
| s2t | 5-methyl-2-thiouridine |
| s2u | 2-thiouridine |
| s4u | 4-thiouridine |
| m5u | 5-methyluridine |
| t6a | N-((9-beta-D-ribofuranosylpurine-6-yl)carbamoyl)threonine |
| tm | 2’-O-methyl-5-methyluridine |
| um | 2’-O-methyluridine |
| yw | wybutosine |
| x | 3-(3-amino-3-carboxypropyl)uridine, (acp3)u |
| OTHER | Other (/note qualifier に修飾塩基を記載します) |
[References]
- Sprinzl, M. and Gauss, D.H. Nucl Acid Res 10, r1 (1982).(note that in Cornish_Bowden, A. Nucl Acid Res 13, 3021-3030 (1985)the IUPAC-IUB declined to recommend a set of abbreviations for modified nucleotides)
- Feature Table Definition: 7.4.2 Modified base abbreviations
Amino Acid
Amino Acid Codes
The amino acid code that is used with the International Nucleotide
Sequence Database is as follows.
These amino acids are described with one letter abbreviation in
/translation qualifier of CDS
feature.
The listed amino acid abbreviations are legal values for qualifiers
/transl_except and
/anticodon.
Those that are not included in “Amino acid codes”, please refer to
Modified and unusual Amino Acids.
| Abbreviation | 1 letter abbreviation | Amino acid name |
|---|---|---|
| Ala | A | Alanine |
| Arg | R | Arginine |
| Asn | N | Asparagine |
| Asp | D | Aspartic acid |
| Cys | C | Cysteine |
| Gln | Q | Glutamine |
| Glu | E | Glutamic acid |
| Gly | G | Glycine |
| His | H | Histidine |
| Ile | I | Isoleucine |
| Leu | L | Leucine |
| Lys | K | Lysine |
| Met | M | Methionine |
| Phe | F | Phenylalanine |
| Pro | P | Proline |
| Pyl | O | Pyrrolysine |
| Ser | S | Serine |
| Sec | U | Selenocysteine |
| Thr | T | Threonine |
| Trp | W | Tryptophan |
| Tyr | Y | Tyrosine |
| Val | V | Valine |
| Asx | B | Aspartic acid or Asparagine |
| Glx | Z | Glutamic acid or Glutamine |
| Xaa | X | Any amino acid |
| Xle | J | Leucine or Isoleucine |
| TERM | termination codon |
[References]
- IUPAC-IUB Joint Commission on Biochemical Nomenclature.Nomenclature and Symbolism for Amino Acids and Peptides. Eur. J. Biochem. 138: 9-37 (1984).
- Feature Table Definition: 7.4.3 Amino acid abbreviations
Modified and Unusual Amino Acids
For other amino acids, those that are not included in Amino Acid Codes, abbreviation listed below is used. All of these amino acids are described with one letter abbreviation “X” in /translation qualifier of CDS feature.
| Abbreviation | Amino acid name |
|---|---|
| Aad | 2-Aminoadipic acid |
| bAad | 3-Aminoadipic acid |
| bAla | beta-Alanine, beta-Aminoproprionic acid |
| Abu | 2-Aminobutyric acid |
| 4Abu | 4-Aminobutyric acid, piperidinic acid |
| Acp | 6-Aminocaproic acid |
| Ahe | 2-Aminoheptanoic acid |
| Aib | 2-Aminoisobutyric acid |
| bAib | 3-Aminoisobutyric acid |
| Apm | 2-Aminopimelic acid |
| Dbu | 2,4-Diaminobutyric acid |
| Des | Desmosine |
| Dpm | 2,2’-Diaminopimelic acid |
| Dpr | 2,3-Diaminoproprionic acid |
| EtGly | N-Ethylglycine |
| EtAsn | N-Ethylasparagine |
| Hyl | Hydroxylysine |
| aHyl | allo-Hydroxylysine |
| 3Hyp | 3-Hydroxyproline |
| 4Hyp | 4-Hydroxyproline |
| Ide | Isodesmosine |
| aIle | allo-Isoleucine |
| MeGly | N-Methylglycine, sarcosine |
| MeIle | N-Methylisoleucine |
| MeLys | 6-N-Methyllysine |
| MeVal | N-Methylvaline |
| Nva | Norvaline |
| Nle | Norleucine |
| Orn | Ornithine |
| OTHER | Other ( (Amino acid not found in this list should be described in /note qualifier) |
[References]