yeast homologues of human genes

Fatima Cvrckova FATIMA at AT.AC.UNA.AIMP
Sat Oct 16 12:40:00 EST 1993


Dear Margaret (djdlab at sun.com) and others,

I'm sorry that I can't provide any nice algorithm for designing degenerate 
primers, but I am offering you at least a (hopefully not too destructive) 
comment instead.

The point is that yeast is a beautiful organism offering great possibilities of 
various genetic screen. You mentioned that you would like to clone a yeast 
homologue of a human gene. If there is any reason to expect that this gene is 
important for the yeast, you might perhaps try the functional cloning approach 
as published by J. Kranz and C. Holm, PNAS 87:6629-6633, 1990. However, since 
really important genes usually occur in whole families, you should not build 
everything on such a screen; you might, after all, anyway end up doing the PCR 
after everything else failed.

What follows is a yeast (S. cer.) codon frequency table, produced probably by 
Etienne Schwob some time ago.

Good luck!

Fatima

AmAcid  Codon     Number    /1000     Fraction   ..

Gly     GGG     1116.00      5.16      0.09
Gly     GGA     1850.00      8.55      0.15
Gly     GGT     7562.00     34.95      0.61
Gly     GGC     1930.00      8.92      0.15

Glu     GAG     3670.00     16.96      0.26
Glu     GAA    10685.00     49.38      0.74
Asp     GAT     8052.00     37.21      0.62
Asp     GAC     4892.00     22.61      0.38

Val     GTG     2070.00      9.57      0.15
Val     GTA     2095.00      9.68      0.16
Val     GTT     5936.00     27.43      0.44
Val     GTC     3272.00     15.12      0.24

Ala     GCG     1085.00      5.01      0.08
Ala     GCA     3241.00     14.98      0.23
Ala     GCT     6157.00     28.46      0.44
Ala     GCC     3453.00     15.96      0.25

Arg     AGG     1589.00      7.34      0.17
Arg     AGA     5101.00     23.57      0.54
Ser     AGT     2411.00     11.14      0.14
Ser     AGC     1599.00      7.39      0.09

Lys     AAG     7632.00     35.27      0.49
Lys     AAA     7966.00     36.82      0.51
Asn     AAT     6718.00     31.05      0.54
Asn     AAC     5611.00     25.93      0.46

Met     ATG     4610.00     21.31      1.00
Ile     ATA     2609.00     12.06      0.20
Ile     ATT     6652.00     30.74      0.50
Ile     ATC     3982.00     18.40      0.30

Thr     ACG     1476.00      6.82      0.12
Thr     ACA     3326.00     15.37      0.26
Thr     ACT     4866.00     22.49      0.38
Thr     ACC     3138.00     14.50      0.25

Trp     TGG     2214.00     10.23      1.00
End     TGA      151.00      0.70      0.34
Cys     TGT     1719.00      7.94      0.68
Cys     TGC      821.00      3.79      0.32

End     TAG       78.00      0.36      0.17
End     TAA      219.00      1.01      0.49
Tyr     TAT     3521.00     16.27      0.50
Tyr     TAC     3590.00     16.59      0.50

Leu     TTG     7044.00     32.55      0.36
Leu     TTA     5221.00     24.13      0.27
Phe     TTT     4910.00     22.69      0.53
Phe     TTC     4317.00     19.95      0.47

Ser     TCG     1411.00      6.52      0.08
Ser     TCA     3316.00     15.33      0.19
Ser     TCT     5495.00     25.40      0.32
Ser     TCC     3198.00     14.78      0.18

Arg     CGG      224.00      1.04      0.02
Arg     CGA      455.00      2.10      0.05
Arg     CGT     1590.00      7.35      0.17
Arg     CGC      402.00      1.86      0.04

Gln     CAG     2236.00     10.33      0.26
Gln     CAA     6431.00     29.72      0.74
His     CAT     2696.00     12.46      0.60
His     CAC     1802.00      8.33      0.40

Leu     CTG     1847.00      8.54      0.09
Leu     CTA     2561.00     11.84      0.13
Leu     CTT     2087.00      9.65      0.11
Leu     CTC      865.00      4.00      0.04

Pro     CCG      893.00      4.13      0.09
Pro     CCA     4728.00     21.85      0.49
Pro     CCT     2755.00     12.73      0.29
Pro     CCC     1226.00      5.67      0.13



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