reference for yeast codon preference

Mike Cherry cherry at stout.Stanford.EDU
Thu Jan 26 02:03:06 EST 1995


In article <9501252044.AA01273 at asrr>,  <rproctor at ASRR.ARSUSDA.GOV> wrote:
>A collegue of mine is looking for a reference for yeast codon preferences.
>Can anyone help?  Thanks in advance
>
>Can  you send responses to me?
>Bob Proctor
>rproctor at asrr.arsusda.gov

Here's a codon usage table I just produced.  The "Number" column is
the total number of that codon found in all the exons I processed,
"/1000" is the number of a codon per 1000 codons, and "Fraction" is
the fraction a particular codon is used for its encoded amino acid.

Mike

---------------

Saccharomyces cerevisiae Codon Usage

January 25, 1995
cherry at genome.stanford.edu

This table was built from 1817 exons (822163 codons) contained in the
seven completely sequenced S.c. chromosomes: I, II, III, V, VIII, IX,
and XI. Not all exons from these chromosomes were used.  If a problem
was detected the exon was eliminated from this analysis.  The GCG
CodonFrequency program was used to produce this table.

AmAcid  Codon     Number    /1000     Fraction   ..
 
Gly     GGG     5240.00      6.37      0.13
Gly     GGA     9211.00     11.20      0.22
Gly     GGT     18381.00     22.36      0.45
Gly     GGC     8283.00     10.07      0.20
 
Glu     GAG     16005.00     19.47      0.30
Glu     GAA     36533.00     44.44      0.70
Asp     GAT     30578.00     37.19      0.65
Asp     GAC     16656.00     20.26      0.35
 
Val     GTG     9346.00     11.37      0.20
Val     GTA     9930.00     12.08      0.21
Val     GTT     17411.00     21.18      0.38
Val     GTC     9613.00     11.69      0.21
 
Ala     GCG     5256.00      6.39      0.11
Ala     GCA     13423.00     16.33      0.29
Ala     GCT     16586.00     20.17      0.36
Ala     GCC     10486.00     12.75      0.23
 
Arg     AGG     7808.00      9.50      0.22
Arg     AGA     16827.00     20.47      0.47
Ser     AGT     11883.00     14.45      0.16
Ser     AGC     8461.00     10.29      0.11
 
Lys     AAG     24785.00     30.15      0.42
Lys     AAA     34009.00     41.37      0.58
Asn     AAT     29130.00     35.43      0.59
Asn     AAC     20430.00     24.85      0.41
 
Met     ATG     17171.00     20.89      1.00
Ile     ATA     14812.00     18.02      0.28
Ile     ATT     24715.00     30.06      0.46
Ile     ATC     14156.00     17.22      0.26
 
Thr     ACG     6838.00      8.32      0.14
Thr     ACA     14799.00     18.00      0.30
Thr     ACT     16817.00     20.45      0.34
Thr     ACC     10513.00     12.79      0.21
 
Trp     TGG     8804.00     10.71      1.00
End     TGA      422.00      0.51      0.31
Cys     TGT     6852.00      8.33      0.62
Cys     TGC     4193.00      5.10      0.38
 
End     TAG      298.00      0.36      0.22
End     TAA      638.00      0.78      0.47
Tyr     TAT     15351.00     18.67      0.56
Tyr     TAC     11964.00     14.55      0.44
 
Leu     TTG     22106.00     26.89      0.28
Leu     TTA     21161.00     25.74      0.27
Phe     TTT     21949.00     26.70      0.59
Phe     TTC     15353.00     18.67      0.41
 
Ser     TCG     7380.00      8.98      0.10
Ser     TCA     15628.00     19.01      0.21
Ser     TCT     19552.00     23.78      0.26
Ser     TCC     12003.00     14.60      0.16
 
Arg     CGG     1538.00      1.87      0.04
Arg     CGA     2525.00      3.07      0.07
Arg     CGT     5166.00      6.28      0.14
Arg     CGC     2269.00      2.76      0.06
 
Gln     CAG     10417.00     12.67      0.32
Gln     CAA     22054.00     26.82      0.68
His     CAT     10992.00     13.37      0.63
His     CAC     6538.00      7.95      0.37
 
Leu     CTG     9104.00     11.07      0.12
Leu     CTA     10885.00     13.24      0.14
Leu     CTT     10249.00     12.47      0.13
Leu     CTC     4681.00      5.69      0.06
 
Pro     CCG     4475.00      5.44      0.12
Pro     CCA     14551.00     17.70      0.40
Pro     CCT     11011.00     13.39      0.31
Pro     CCC     5962.00      7.25      0.17



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