Codon Usage table update

Mike Cherry 726-5955 CHERRY at FRODO.MGH.HARVARD.EDU
Wed Oct 28 12:54:49 EST 1992


Arabidopsis thaliana codon usage.

Of the 410 Arabidopsis sequences in AAtDB 1-2 from GenBank 73 and EMBL
32 including updates through October 15, 1992. A total of 315
sequences had a coding region defined and contained zero or one
termination codon. The total number of codons used to produce this
table was over 100,000.

This table was constructed using the GCG program CodonFrequency.

Questions about this table should be directed to:

Mike Cherry
Department of Molecular Biology
Massachusetts General Hospital
cherry at frodo.mgh.harvard.edu

Meaning of the columns:
AmAcid   -  three letter code for the amino acid designated by the codon
Codon    -  Codon sequence
Number   -  Total number of occurances of this codon in the input set
/1000    -  Number of occurances of this codon per 1000 codons in the
            input set
Fraction -  Fraction of occurance of this codon is used from the set of
            codons representing the same amino acid

AmAcid  Codon     Number    /1000     Fraction   ..
 
Gly     GGG      964.00      9.49      0.12
Gly     GGA     3241.00     31.91      0.39
Gly     GGT     3001.00     29.55      0.36
Gly     GGC     1078.00     10.61      0.13
 
Glu     GAG     3487.00     34.33      0.54
Glu     GAA     3002.00     29.56      0.46
Asp     GAT     3275.00     32.24      0.61
Asp     GAC     2117.00     20.84      0.39
 
Val     GTG     1811.00     17.83      0.26
Val     GTA      736.00      7.25      0.11
Val     GTT     2799.00     27.56      0.40
Val     GTC     1586.00     15.61      0.23
 
Ala     GCG      888.00      8.74      0.11
Ala     GCA     1708.00     16.82      0.22
Ala     GCT     3711.00     36.54      0.47
Ala     GCC     1510.00     14.87      0.19
 
Arg     AGG     1253.00     12.34      0.24
Arg     AGA     1617.00     15.92      0.31
Ser     AGT     1181.00     11.63      0.15
Ser     AGC     1109.00     10.92      0.14
 
Lys     AAG     3933.00     38.72      0.60
Lys     AAA     2592.00     25.52      0.40
Asn     AAT     1691.00     16.65      0.40
Asn     AAC     2501.00     24.62      0.60
 
Met     ATG     2725.00     26.83      1.00
Ile     ATA      902.00      8.88      0.16
Ile     ATT     2224.00     21.90      0.41
Ile     ATC     2362.00     23.25      0.43
 
Thr     ACG      675.00      6.65      0.12
Thr     ACA     1444.00     14.22      0.26
Thr     ACT     2001.00     19.70      0.36
Thr     ACC     1468.00     14.45      0.26
 
Trp     TGG     1119.00     11.02      1.00
End     TGA      106.00      1.04      0.40
Cys     TGT      868.00      8.55      0.54
Cys     TGC      745.00      7.33      0.46
 
End     TAG       51.00      0.50      0.19
End     TAA      108.00      1.06      0.41
Tyr     TAT     1072.00     10.55      0.37
Tyr     TAC     1805.00     17.77      0.63
 
Leu     TTG     2021.00     19.90      0.23
Leu     TTA      889.00      8.75      0.10
Phe     TTT     1737.00     17.10      0.42
Phe     TTC     2448.00     24.10      0.58
 
Ser     TCG      752.00      7.40      0.10
Ser     TCA     1406.00     13.84      0.18
Ser     TCT     2108.00     20.75      0.27
Ser     TCC     1145.00     11.27      0.15
 
Arg     CGG      345.00      3.40      0.07
Arg     CGA      478.00      4.71      0.09
Arg     CGT     1115.00     10.98      0.22
Arg     CGC      362.00      3.56      0.07
 
Gln     CAG     1782.00     17.54      0.50
Gln     CAA     1783.00     17.55      0.50
His     CAT      978.00      9.63      0.50
His     CAC      970.00      9.55      0.50
 
Leu     CTG      851.00      8.38      0.10
Leu     CTA      838.00      8.25      0.10
Leu     CTT     2399.00     23.62      0.27
Leu     CTC     1806.00     17.78      0.21
 
Pro     CCG      788.00      7.76      0.16
Pro     CCA     1688.00     16.62      0.35
Pro     CCT     1759.00     17.32      0.36
Pro     CCC      657.00      6.47      0.13



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