Subject: Neurospora codon usage

From: [email-masked] (Walt Lilly)
Date: 11 Jan 1995 11:42:21 -0800

Does anyone know of a published codon usage table for
Neurospora?  Thanks for your help

Walt Lilly
[email-masked]

---

From: [email-masked] (Robert Brambl)
Date: 11 Jan 1995 13:49:40 -0800

The following is a slightly dated table for Neurospora crassa, based  
upon 38 genes found in GenBank 63, as produced by J. Michael Cherry  
([email-masked]) with the GCG program CodonFrequency.

Duplicates, pseudogenes, mutant and synthetic genes were not  
included. Coding regions were specified using the Feature Table of  
each entry, then checked for accuracy. If more than one stop codon  
was found the sequence was not included.

AmAcid  Codon     Number    /1000     Fraction   ..

Gly     GGG       85.00      6.31      0.09
Gly     GGA      133.00      9.88      0.14
Gly     GGT      312.00     23.17      0.34
Gly     GGC      394.00     29.26      0.43

Glu     GAG      494.00     36.69      0.76
Glu     GAA      159.00     11.81      0.24
Asp     GAT      218.00     16.19      0.38
Asp     GAC      358.00     26.59      0.62

Val     GTG      159.00     11.81      0.20
Val     GTA       72.00      5.35      0.09
Val     GTT      179.00     13.29      0.23
Val     GTC      380.00     28.22      0.48

Ala     GCG      177.00     13.15      0.16
Ala     GCA      136.00     10.10      0.12
Ala     GCT      271.00     20.13      0.25
Ala     GCC      513.00     38.10      0.47

Arg     AGG      167.00     12.40      0.15
Arg     AGA      130.00      9.66      0.12
Ser     AGT       85.00      6.31      0.07
Ser     AGC      195.00     14.48      0.17

Lys     AAG      478.00     35.50      0.90
Lys     AAA       52.00      3.86      0.10
Asn     AAT       73.00      5.42      0.18
Asn     AAC      328.00     24.36      0.82

Met     ATG      254.00     18.87      1.00
Ile     ATA       52.00      3.86      0.10
Ile     ATT      162.00     12.03      0.30
Ile     ATC      319.00     23.69      0.60

Thr     ACG      153.00     11.36      0.19
Thr     ACA      133.00      9.88      0.17
Thr     ACT      144.00     10.70      0.18
Thr     ACC      366.00     27.18      0.46

Trp     TGG      219.00     16.27      1.00
End     TGA      132.00      9.80      0.74
Cys     TGT      102.00      7.58      0.33
Cys     TGC      209.00     15.52      0.67

End     TAG       17.00      1.26      0.10
End     TAA       29.00      2.15      0.16
Tyr     TAT      106.00      7.87      0.29
Tyr     TAC      263.00     19.53      0.71

Leu     TTG      168.00     12.48      0.14
Leu     TTA       65.00      4.83      0.05
Phe     TTT      129.00      9.58      0.28
Phe     TTC      330.00     24.51      0.72

Ser     TCG      227.00     16.86      0.20
Ser     TCA      140.00     10.40      0.12
Ser     TCT      211.00     15.67      0.18
Ser     TCC      300.00     22.28      0.26

Arg     CGG      160.00     11.88      0.15
Arg     CGA      127.00      9.43      0.12
Arg     CGT      213.00     15.82      0.19
Arg     CGC      306.00     22.73      0.28

Gln     CAG      278.00     20.65      0.59
Gln     CAA      192.00     14.26      0.41
His     CAT      161.00     11.96      0.39
His     CAC      252.00     18.72      0.61

Leu     CTG      245.00     18.20      0.20
Leu     CTA       89.00      6.61      0.07
Leu     CTT      216.00     16.04      0.18
Leu     CTC      451.00     33.50      0.37

Pro     CCG      197.00     14.63      0.20
Pro     CCA      190.00     14.11      0.19
Pro     CCT      242.00     17.97      0.24
Pro     CCC      367.00     27.26      0.37