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]

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。


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]

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/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]

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/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]