Oligo Designer Accepted Inputs and Definition

Oligo Designer » Oligo Designer Accepted Inputs and Definition

Sequence Representation

Oligo Designer uses the standard definitions (IUB codes):

Nucleic Acid Code	Definition
A	Adenosine
C	Cytosine
G	Guanine
T	Thymidine
U	Uracil
R	G A (puRine)
Y	T C (pYrimidine)
K	G T (Ketone)
M	A C (aMino group)
S	G C (Strong interaction)
W	A T (Weak interaction)
B	G T C (not A) (B comes after A)
D	G A T (not C) (D comes after C)
H	A C T (not G) (H comes after G)
V	G C A (not T, not U) (V comes after U)
N	A G C T (aNy)

RNA Codon Table

The DNA codon table is identical to that of the RNA except U is replaced by T.

nonpolar

polar

basic

acidic

(stop codon)

		Second Base
		U		C		A		G
First Base	U	UUU	(Phe/F) Phenylalanine	UCU	(Ser/S) Serine	UAU	(Tyr/Y) Tyrosine	UGU	(Cys/C) Cysteine	U
		UUC		UCC		UAC		UGC		C
		UUA	(Leu/L) Leucine	UCA		UAA	Stop (Ochre)	UGA	Stop (Opal)	A
		UUG		UCG		UAG	Stop (Amber)	UGG	(Trp/W) Tryptophan	G
	C	CUU		CCU	(Pro/P) Proline	CAU	(His/H) Histidine	CGU	(Arg/R) Arginine	U
		CUC		CCC		CAC		CGC		C
		CUA		CCA		CAA	(Gln/Q) Glutamine	CGA		A
		CUG		CCG		CAG		CGG		G
	A	AUU	(Ile/I) Isoleucine	ACU	(Thr/T) Threonine	AAU	(Asn/N) Asparagine	AGU	(Ser/S) Serine	U
		AUC		ACC		AAC		AGC		C
		AUA		ACA		AAA	(Lys/K) Lysine	AGA	(Arg/R) Arginine	A
		AUG A	(Met/M) Methionine	ACG		AAG		AGG		G
	G	GUU	(Val/V) Valine	GCU	(Ala/A) Alanine	GAU	(Asp/D) Aspartic acid	GGU	(Gly/G) Glycine	U
		GUC		GCC		GAC		GGC		C
		GUA		GCA		GAA	(Glu/E) Glutamic acid	GGA		A
		GUG		GCG		GAG		GGG		G

^A The codon AUG codes for methionine and can serve as the initiation site where protein translation begins.