Mus musculus Codon Usage Table

See the most used codons, highest-fraction synonymous codons, and full codon usage frequencies for Mus musculus.

Use frequency to find the most common codons in this organism, and use fraction to compare synonymous codon preference within the same amino acid family.

Escherichia coli Saccharomyces cerevisiae Arabidopsis thaliana Caenorhabditis elegans Cricetulus griseus Drosophila melanogaster Homo sapiens Spodoptera frugiperda Mus musculus Nicotiana tabacum Pichia pastoris Sus scrofa Rattus norvegicus Streptomyces Zea mays

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These settings control the summary cards and the full codon usage table below.

Top Codons by Frequency

Codons ranked by frequency per 1,000 codons in the selected organism.

CTG

Amino acid: L

Fraction 0.39

Freq 40.0

GAG

Amino acid: E

Fraction 0.60

Freq 39.4

CAG

Amino acid: Q

Fraction 0.75

Freq 34.0

AAG

Amino acid: K

Fraction 0.61

Freq 33.7

GTG

Amino acid: V

Fraction 0.46

Freq 29.1

GAC

Amino acid: D

Fraction 0.56

Freq 26.6

GAA

Amino acid: E

Fraction 0.40

Freq 26.5

GCC

Amino acid: A

Fraction 0.38

Freq 26.4

Top Codons by Fraction

Synonymous codons ranked by fraction. Stop codons and single-codon amino acids are excluded.

CAG

Amino acid: Q

Fraction 0.75

Freq 34.0

AAG

Amino acid: K

Fraction 0.61

Freq 33.7

GAG

Amino acid: E

Fraction 0.60

Freq 39.4

CAC

Amino acid: H

Fraction 0.60

Freq 15.2

TAC

Amino acid: Y

Fraction 0.58

Freq 16.5

TTC

Amino acid: F

Fraction 0.57

Freq 22.3

AAC

Amino acid: N

Fraction 0.57

Freq 20.7

GAC

Amino acid: D

Fraction 0.56

Freq 26.6

Preferred Codons by Amino Acid

One preferred codon per amino acid, ranked by frequency to surface practical defaults.

CTG

Amino acid: L

Fraction 0.39

Freq 40.0

GAG

Amino acid: E

Fraction 0.60

Freq 39.4

CAG

Amino acid: Q

Fraction 0.75

Freq 34.0

AAG

Amino acid: K

Fraction 0.61

Freq 33.7

GTG

Amino acid: V

Fraction 0.46

Freq 29.1

GAC

Amino acid: D

Fraction 0.56

Freq 26.6

GCC

Amino acid: A

Fraction 0.38

Freq 26.4

ATC

Amino acid: I

Fraction 0.50

Freq 23.2

Mus musculus (Mamalian/NSO): (Genetic code: Standard)

Print-friendly 2-column table in genetic code order. Frequency is shown per 1,000 codons.

Triplet	Amino acid	Fraction	Frequency/Thousand	Number	Triplet	Amino acid	Fraction	Frequency/Thousand	Number
TTT TTC TTA TTG	F F L L	0.43 0.57 0.06 0.13	17.1 22.3 6.5 13.3	244,935 319,002 92,974 189,840	TCT TCC TCA TCG	S S S S	0.19 0.22 0.14 0.05	15.9 18.1 11.6 4.3	228,046 258,787 165,371 61,116
TAT TAC TAA TAG	Y Y * *	0.43 0.58 0.26 0.22	12.2 16.5 0.6 0.5	175,198 236,579 8,861 7,491	TGT TGC TGA TGG	C C * W	0.48 0.52 0.52 1.00	11.1 12.1 1.2 12.4	158,573 173,509 17,004 177,261
CTT CTC CTA CTG	L L L L	0.13 0.20 0.08 0.39	13.2 20.3 8.0 40.0	188,236 290,198 114,707 571,592	CCT CCC CCA CCG	P P P P	0.30 0.31 0.28 0.10	18.3 18.4 17.1 6.3	261,478 262,874 244,064 89,477
CAT CAC CAA CAG	H H Q Q	0.40 0.60 0.25 0.75	10.2 15.2 11.4 34.0	145,279 217,261 163,794 486,041	CGT CGC CGA CGG	R R R R	0.09 0.18 0.12 0.19	4.7 9.5 6.6 10.3	66,962 136,330 94,626 147,905
ATT ATC ATA ATG	I I I M	0.34 0.50 0.16 1.00	15.6 23.2 7.2 23.1	223,528 332,072 103,441 330,431	ACT ACC ACA ACG	T T T T	0.25 0.35 0.29 0.11	13.6 19.2 15.9 5.8	194,120 274,588 227,958 82,653
AAT AAC AAA AAG	N N K K	0.43 0.57 0.39 0.61	15.5 20.7 21.3 33.7	221,760 296,083 305,128 482,643	AGT AGC AGA AGG	S S R R	0.15 0.24 0.21 0.22	12.3 19.5 11.4 11.7	176,056 279,098 163,062 167,166
GTT GTC GTA GTG	V V V V	0.17 0.25 0.12 0.46	10.7 15.7 7.4 29.1	152,706 224,465 105,532 416,428	GCT GCC GCA GCG	A A A A	0.29 0.38 0.23 0.10	20.1 26.4 15.8 6.6	288,132 378,142 226,309 94,463
GAT GAC GAA GAG	D D E E	0.44 0.56 0.40 0.60	21.1 26.6 26.5 39.4	301,359 380,355 379,216 563,999	GGT GGC GGA GGG	G G G G	0.18 0.33 0.26 0.23	11.5 21.9 16.9 15.4	164,971 312,846 241,435 220,474

Showing 64 entries for Mus musculus (Mamalian/NSO).

Frequency is measured per 1,000 codons. Fraction compares codons that encode the same amino acid.

Questions this table can answer

Which codons are most common in Mus musculus?

Which synonymous codons are preferred in Mus musculus?

Which codons should be checked before expression design?

How to use this page

Use the summary cards to find the most used and highest-fraction codons quickly.

Switch sorting in the full table when you want to compare by frequency, fraction, or count.

Use the full organism list and search codons/amino acids on the Codon Usage Frequency Table.

FAQ

What are the most used codons in Mus musculus?

Use the "Most Used Codons" section to see which codons appear most often in Mus musculus. The ranking is based on frequency per 1,000 codons.

Which codons have the highest fraction in Mus musculus?

Use the "Highest Fraction Codons" section to compare synonymous codons for the same amino acid. Single-codon amino acids and stop codons are excluded so the ranking reflects codon preference rather than trivial 1.00 values.

What is the difference between codon frequency and codon fraction in Mus musculus?

Frequency measures how often a codon appears per 1,000 codons in the dataset. Fraction measures how strongly that codon is preferred relative to alternative codons encoding the same amino acid.

How should I use this Mus musculus codon usage table for optimization?

Start with the preferred-codon summaries to identify likely defaults, then review the full table below before making codon optimization or expression design decisions.