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GenScript Codon Usage Frequency Table(chart) Tool

Resources » Bioinformatics Tools

** This online tool shows commonly used genetic codon frequency table in expression host organisms including Escherichia coli and other common host organisms.

Expression Host Organism

Escherichia coli: (Genetic code: Standard)

Triplet	Amino acid	Fraction	Frequency/ Thousand	Number	Triplet	Amino acid	Fraction	Frequency/ Thousand	Number
TTT TTC TTA TTG	F F L L	0.58 0.42 0.14 0.13	22.1 16.0 14.3 13.0	80995 58774 52382 47500	TCT TCC TCA TCG	S S S S	0.17 0.15 0.14 0.14	10.4 9.1 8.9 8.5	38027 33430 32715 31146
TAT TAC TAA TAG	Y Y * *	0.59 0.41 0.61 0.09	17.5 12.2 2.0 0.3	63937 44631 7356 989	TGT TGC TGA TGG	C C * W	0.46 0.54 0.30 1.00	5.2 6.1 1.0 13.9	19138 22188 3623 50991
CTT CTC CTA CTG	L L L L	0.12 0.10 0.04 0.47	11.9 10.2 4.2 48.4	43449 37347 15409 177210	CCT CCC CCA CCG	P P P P	0.18 0.13 0.20 0.49	7.5 5.4 8.6 20.9	27340 19666 31534 76644
CAT CAC CAA CAG	H H Q Q	0.57 0.43 0.34 0.66	12.5 9.3 14.6 28.4	45879 34078 53394 104171	CGT CGC CGA CGG	R R R R	0.36 0.36 0.07 0.11	20.0 19.7 3.8 5.9	73197 72212 13844 21552
ATT ATC ATA ATG	I I I M	0.49 0.39 0.11 1.00	29.8 23.7 6.8 26.4	109072 86796 24984 96695	ACT ACC ACA ACG	T T T T	0.19 0.40 0.17 0.25	10.3 22.0 9.3 13.7	37842 80547 33910 50269
AAT AAC AAA AAG	N N K K	0.49 0.51 0.74 0.26	20.6 21.4 35.3 12.4	75436 78443 129137 45459	AGT AGC AGA AGG	S S R R	0.16 0.25 0.07 0.04	9.9 15.2 3.6 2.1	36097 55551 13152 7607
GTT GTC GTA GTG	V V V V	0.28 0.20 0.17 0.35	19.8 14.3 11.6 24.4	72584 52439 42420 89265	GCT GCC GCA GCG	A A A A	0.18 0.26 0.23 0.33	17.1 24.2 21.2 30.1	62479 88721 77547 110308
GAT GAC GAA GAG	D D E E	0.63 0.37 0.68 0.32	32.7 19.2 39.1 18.7	119939 70394 143353 68609	GGT GGC GGA GGG	G G G G	0.35 0.37 0.13 0.15	25.5 27.1 9.5 11.3	93325 99390 34799 41277

Codon Usage is only one of many DNA sequence features that influence protein expression levels

Can’t improve protein expression even after codon bias adjust?

A lots of parameters affect the protein expression besides codon bias:

GC content
CpG dinucleotides content
Cryptic splicing sites
Codon-context
Negative CpG islands
Premature PolyA sites
Terminal signal
TATA boxes
mRNA secondary structure
SD sequence
RNA instability motif (ARE)
RNA secondary structures
Interaction of codon and anti-codon
Internal chi sites and ribosomal binding sites
Stable free energy of mRNA

GenScript OptimumGene™ algorithm provides a comprehensive solution strategy on optimizing all parameters that are critical to protein expression levels. It can significate increase protein expression level up to 50-fold, provided that the protein expression and purification methods are appropriately applied.

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