By Anat Yarden
Department of Chemical Immunology, The Weizmann Institute of Science, Rehovot 76100, Israel.
The pattern of choices between synonymous codons varies from one gene to another according to the type of genome the gene occurs in (NAR 9, r43, 1981). Thus, codon usage may be biased in a species specific manner. Therefor, the codon usage table of an organism may prove to be useful for designing degenerate oligonucleotide primers for PCR, cloning, etc. In addition, knowledge of codon usage may yield a wide range of information about an open reading frame, such as whether an open reading frame is indeed likely to be a gene (J. Heredity 83:239, 1992). Today codon usage tables are available for many species through anonymous FTP site (132.183.190.10) from Dr. Michael Cherry (CHERRY@FRODO.MGH.HARVARD.EDU)(see also NAR 20 Suppl., 2111-2118, 1992). However, a zebrafish codon usage table has not yet been assembled. I have pulled out of the genebank the available zebrafish sequences (GenBank release 74.0, EMBL release 33.0), and sorted the sequence of exonic fragments from them. Those exonic fragments were used to generate a zebrafish codon usage table by using the "codonfrequency" program available through GCG. Table 1 lists the genes which were included in this analysis (coding sequences from additional gene fragments were also used, but are not listed). The zebrafish codon usage table shown in Table 2 includes the total number of times a specific codon appeared in all the fragments analyzed (appears in brackets) and the preferred ratio by which the various codons were used for a specific amino acid. Additional sequences, when available, can be added periodically to the table in order to increase its statistical value.
Table 1. List of Genes Used for the Zebrafish Codon Usage Analysis
msh-D muscle segment homeobox
zf-cad1 caudal homeobox
epen ependymin
krox-20 zinc finger protein (krox-20)
antp antennapedia class zf'26'
pax(zf-a) drosophila paired homolog
alpha-tropo skeletal muscle alpha-tropomyosin
hox(zf-22) homeobox hox2.2
hox(zf-61) homeobox hox(zf-61)
hox(zf-114) homeobox hox (zf-114)
krox-24 zinc finger protein (krox-24)
hox(zf-21) homeobox hox(zf-21)
zf-54 homeotic zf-54
eng engrailed-like homeobox
zn-cad N-cadherin (Bitzur, Kam & Geiger, unpublished)
Table 2. Zebrafish Codon Usage Table
Gly
GGG 0.18 (41)
GGA 0.31 (70)
GGT 0.21 (49)
GGC 0.30 (68)
Glu
GAG 0.71 (212)
GAA 0.29 (86)
Asp
GAT 0.39 (75)
GAC 0.61 (115)
Val
GTG 0.39 (67)
GTA 0.15 (26)
GTT 0.20 (35)
GTC 0.26 (46)
Ala
GCG 0.16 (41)
GCA 0.22 (56)
GCT 0.31 (78)
GCC 0.31 (79)
Arg
AGG 0.15 (49 )
AGA 0.24 (76)
Ser
AGT 0.15 (57)
AGC 0.20 (76)
Lys
AAG 0.47 (120)
AAA 0.53 (137)
Asn
AAT 0.36 (73)
AAC 0.64 (132)
Met
ATG 1.00 (101)
Ile
ATA 0.23 (41)
ATT 0.28 (50)
ATC 0.49 (86)
Thr
ACG 0.15 (42)
ACA 0.26 (71)
ACT 0.23 (62)
ACC 0.36 (98)
Trp
TGG 1.00 (51)
End
TGA 0.41 (9)
Cys
TGT 0.47 (32)
TGC 0.53 (36)
End
TAG 0.23 (5)
TAA 0.36 (8)
Tyr
TAT 0.38 (54)
TAC 0.63 (90)
Leu
TTG 0.13 (43)
TTA 0.09 (30)
Phe
TTT 0.39 (59)
TTC 0.61 (91)
Ser
TCG 0.08 (30)
TCA 0.20 (76)
TCT 0.18 (70)
TCC 0.20 (78)
Arg
CGG 0.14 (43)
CGA 0.14 (45)
CGT 0.11 (35)
CGC 0.22 (70)
Gln
CAG 0.64 (125)
CAA 0.36 (70)
His
CAT 0.39 (44)
CAC 0.61 (69)
Leu
CTG 0.34 (111)
CTA 0.08 (28)
CTT 0.15 (49)
CTC 0.21 (70)
Pro
CCG 0.16 (39)
CCA 0.27 (66)
CCT 0.24 (59)
CCC 0.32 (77)
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