DDBJ Annotated/Assembled Sequences
配列の記載に用いる略号
塩基
Nucleotide Base Codes
国際塩基配列データベースで使用する核酸コードは以下の通りです。
全て小文字を使用します。大文字で登録された場合には、自動的に小文字に変換されます。
| シンボル | 意味 | 説明 |
|---|---|---|
| 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 |
[参考文献]
- Cornish-Bowden, A. Nucl Acid Res 13, 3021-3030 (1985)
- Feature Table Definition: 7.4.1 Nucleotide base codes (IUPAC)
Modified Base Abbreviations
修飾塩基は、以下の例のように modified base を用いて記載します。
例
FEATURES Location/Qualifiers
modified_base 15
/mod_base="m2g"
| 省略形 | 修飾塩基 |
|---|---|
| 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) |
[参考文献]
- 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
アミノ酸
Amino Acid Codes
国際塩基配列データベースで使用するアミノ酸コードは以下の通りです。
CDS feature の /translation には以下の一文字表記で表されます。
/transl_except, /anticodon に記載するアミノ酸は、以下の省略形を使用します。
これ以外のアミノ酸を記載する場合には、Modified and unusual Amino Acidsを参照して下さい。
| 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 |
[参考文献]
- 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
Amino Acid Codes にないアミノ酸を記載する場合には以下の省略形を使用します。
CDS feature の /translation にはいずれも “X” で表されます。
| 省略形 | アミノ酸 |
|---|---|
| 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 (/note qualifier にアミノ酸を記載します) |
[参考文献]