Sequence Symbols

GCG uses the letter codes for amino acid codes and nucleotide ambiguity proposed by IUB (Nomenclature Committee, 1985, Eur. J. Biochem. 150; 1-5). These codes are compatible with the codes used by the EMBL, GenBank, and PIR data libraries.

Nucleotides

The meaning of each symbol, its complement, and the Cambridge (Staden) equivalents are shown below. 


               IUB/GCG      Meaning     Complement   Staden/Sanger
                   A             A             T             A
                   C             C             G             C
                   G             G             C             G
                  T/U            T             A             T
                   M           A or C          K             5
                   R           A or G          Y             R
                   W           A or T          W             7
                   S           C or G          S             8
                   Y           C or T          R             Y
                   K           G or T          M             6
                   V        A or C or G        B       not supported
                   H        A or C or T        D       not supported
                   D        A or G or T        H       not supported
                   B        C or G or T        V       not supported
                  X/N     G or A or T or C     X            -/X
(Gap Character)    .    not G or A or T or C   .       not supported

Amino Acids

Here is a list of the standard one-letter amino acid codes and their three-letter equivalents. The synonymous codons and their depiction in the IUB codes are shown. You should recognize that the codons following semicolons (;) are not sufficiently specific to define a single amino acid even though they represent the best possible backtranslation into the IUB codes!


    IUB Symbol   3-letter   Meaning      Codons                Depiction
        A         Ala       Alanine      GCT,GCC,GCA,GCG         !GCX
        B         Asp,Asn   Aspartic,
                            Asparagine   GAT,GAC,AAT,AAC         !RAY
        C         Cys       Cysteine     TGT,TGC                 !TGY
        D         Asp       Aspartic     GAT,GAC                 !GAY
        E         Glu       Glutamic     GAA,GAG                 !GAR
        F         Phe     Phenylalanine  TTT,TTC                 !TTY
        G         Gly       Glycine      GGT,GGC,GGA,GGG         !GGX
        H         His       Histidine    CAT,CAC                 !CAY
        I         Ile       Isoleucine   ATT,ATC,ATA             !ATH
        K         Lys       Lysine       AAA,AAG                 !AAR
        L         Leu       Leucine      TTG,TTA,CTT,CTC,CTA,CTG !TTR,CTX,YTR;YTX
        M         Met       Methionine   ATG                     !ATG
        N         Asn       Asparagine   AAT,AAC                 !AAY
        P         Pro       Proline      CCT,CCC,CCA,CCG         !CCX
        Q         Gln       Glutamine    CAA,CAG                 !CAR
        R         Arg       Arginine     CGT,CGC,CGA,CGG,AGA,AGG !CGX,AGR,MGR;MGX
        S         Ser       Serine       TCT,TCC,TCA,TCG,AGT,AGC !TCX,AGY;WSX
        T         Thr       Threonine    ACT,ACC,ACA,ACG         !ACX
        V         Val       Valine       GTT,GTC,GTA,GTG         !GTX
        W         Trp       Tryptophan   TGG                     !TGG
        X         Xxx       Unknown                              !XXX
        Y         Tyr       Tyrosine     TAT, TAC                !TAY
        Z         Glu,Gln   Glutamic,
                            Glutamine    GAA,GAG,CAA,CAG       !SAR
        *         End       Terminator   TAA, TAG, TGA           !TAR,TRA;TRR