. 1999 Apr 13;96(8):4482–4487. doi: 10.1073/pnas.96.8.4482

Table 2.

Codon usage (RSCU values), expression level, and protein length in C. elegans, D. melanogaster, and A. thaliana genes

Codon	Favored	C. elegans				Favored	D. melanogaster				Favored	A. thaliana
		Short proteins		Long proteins			Short proteins		Long proteins			Short proteins		Long proteins
		No EST	High	No EST	High		No EST	High	No EST	High		No EST	High	No EST	High
Arg		25,872	3,833	17,254	40,260		2,404	1,042	12,349	8,030		8,004	1,372	20,572	2,478
AGA		1.87	1.56	2.02	1.86		0.64	0.34	0.57	0.39		2.07	1.92	2.20	2.09
AGG		0.47	0.15	0.51	0.31		0.72	0.47	0.75	0.53	∗	1.17⁺	1.36	1.22	1.24
CGA		1.33	0.62	1.43	1.31		0.77	0.41	0.98	0.86		0.74	0.55	0.70	0.64
CGC	∗	0.58⁺⁺⁺	1.34	0.45⁺	0.57	∗	1.92⁺⁺⁺	2.80	1.83⁺⁺⁺	2.29		0.43	0.41	0.40	0.37
CGG		0.51	0.24	0.51	0.39		0.83	0.47	0.97	0.79		0.53	0.37	0.57	0.54
CGU	∗	1.24⁺⁺⁺	2.09	1.08⁺⁺⁺	1.56	∗	1.11⁺⁺⁺	1.50	0.90⁺⁺	1.15	∗	1.05⁺⁺⁺	1.40	0.91⁺⁺	1.11
Leu		46,057	4,576	32,074	61,200		3,540	1,433	20,782	13,530		12,438	2,191	38,506	4,980
CUA		0.58	0.19	0.63	0.43		0.46	0.23	0.56	0.51		0.62	0.52	0.63	0.59
CUC	∗	0.96⁺⁺⁺	1.92	0.84⁺⁺	1.10	∗	1.08	1.03	0.93	0.92	∗	1.12⁺⁺⁺	1.50	0.92	0.96
CUG		0.76	0.69	0.79	0.73	∗	2.64⁺⁺⁺	3.22	2.59	2.58		0.57	0.56	0.68	0.74
CUU	∗	1.45⁺⁺⁺	1.76	1.41⁺⁺⁺	1.78		0.60	0.41	0.56	0.62		1.54⁺	1.63	1.52	1.57
UUA		0.82	0.19	0.89	0.55		0.27	0.15	0.29	0.30		0.83	0.56	0.89	0.75
UUG		1.43	1.25	1.42	1.42		0.94	0.97	1.06	1.06		1.33	1.24	1.36	1.40
Ser		40,824	4,049	28,694	58,229		3,295	1,121	21,409	11,905		12,722	2,316	35,838	4,297
AGC		0.62⁺	0.78	0.54	0.54		1.53	1.24	1.52	1.44	∗	0.78	0.81	0.75	0.78
AGU		0.92	0.55	1.01	0.90		0.72	0.37	0.88	0.74		0.92	0.75	1.04	0.97
UCA		1.61	0.99	1.65	1.54		0.47	0.36	0.56	0.59		1.17	1.08	1.30	1.24
UCC	∗	0.76⁺⁺⁺	1.39	0.73	0.73	∗	1.76⁺	1.92	1.37	1.43	∗	0.78⁺	0.89	0.67⁺	0.76
UCG		0.79⁺	0.98	0.76⁺	0.87	∗	1.03⁺⁺⁺	1.64	1.23	1.21		0.68	0.59	0.55	0.59
UCU		1.30	1.31	1.32⁺	1.42		0.49	0.47	0.45⁺	0.59		1.67⁺⁺	1.89	1.69	1.66
Thr		30,391	3,260	20,939	41,866		2,498	918	13,725	8,234		7,401	1,452	19,911	2,690
ACA		1.40	0.79	1.51	1.36		0.72	0.60	0.82	0.75		1.12	1.01	1.31	1.21
ACC	∗	0.69⁺⁺⁺	1.50	0.59⁺	0.67	∗	1.74⁺⁺⁺	2.22	1.48⁺	1.58	∗	0.85⁺	0.99	0.72⁺	0.80
ACG		0.57	0.42	0.57	0.53		0.79	0.67	1.08	0.97		0.73	0.57	0.54	0.57
ACU		1.34	1.29	1.33⁺	1.43		0.75	0.51	0.63	0.70		1.30⁺	1.43	1.43	1.42
Pro		23,312	2,961	15,553	34,714		2,442	809	13,932	7,782		6,716	1,373	18,010	2,424
CCA	∗	2.10⁺⁺⁺	2.82	2.03⁺⁺	2.31		0.93	0.78	1.01	0.97		1.27	1.25	1.35	1.38
CCC		0.38	0.19	0.39	0.29	∗	1.52⁺⁺⁺	1.88	1.26	1.31	∗	0.41⁺	0.52	0.43	0.46
CCG		0.72	0.61	0.73	0.65		1.02	0.92	1.28	1.16		0.82	0.76	0.63	0.67
CCU		0.79	0.38	0.86	0.76		0.53	0.42	0.45⁺	0.56		1.50	1.48	1.58	1.48
Ala		29,935	5,149	19,697	49,193		3,432	1,494	18,160	11,932		8,775	2,171	23,348	3,535
GCA		1.35	0.66	1.48	1.21		0.57	0.43	0.74	0.72		1.00	0.82	1.19	1.11
GCC	∗	0.74⁺⁺⁺	1.40	0.66⁺	0.74	∗	2.01⁺⁺⁺	2.32	1.74	1.77	∗	0.68⁺	0.78	0.58	0.60
GCG		0.48	0.31	0.51	0.42		0.59	0.49	0.81	0.66		0.64	0.58	0.50	0.52
GCU	∗	1.42⁺⁺	1.63	1.35⁺⁺	1.62		0.83	0.77	0.71⁺	0.86		1.68⁺	1.82	1.73	1.77
Gly		25,766	4,491	16,959	39,020		3,281	1,284	15,131	10,315		9,656	2,068	23,343	3,579
GGA	∗	2.26⁺⁺⁺	2.77	2.28⁺⁺⁺	2.59		1.23	0.94	1.13	1.12		1.53	1.48	1.43	1.49
GGC		0.50	0.40	0.48	0.36	∗	1.66⁺⁺	1.94	1.70	1.69	∗	0.60	0.59	0.52	0.53
GGG		0.36	0.15	0.37	0.22		0.25	0.16	0.32	0.23		0.54	0.47	0.69	0.61
GGU		0.87	0.69	0.87	0.83		0.86⁺	0.96	0.84⁺	0.96	∗	1.34⁺	1.46	1.36	1.37
Val		31,831	3,934	21,386	45,812		2,662	1,123	13,116	8,981		9,361	1,784	25,453	3,497
GUA		0.67	0.25	0.77	0.59		0.30	0.28	0.43	0.44		0.56	0.47	0.67	0.60
GUC	∗	0.83⁺⁺⁺	1.56	0.74⁺	0.88	∗	1.13⁺	1.29	0.93	0.94	∗	0.81	0.87	0.69	0.69
GUG		0.90	0.71	0.88	0.79	∗	1.79	1.84	1.92	1.81		1.07	1.11	1.02	1.06
GUU		1.60	1.47	1.61⁺	1.74		0.78	0.58	0.72⁺	0.80		1.56	1.56	1.63	1.64
Lys		34,361	4,512	22,049	47,882		2,529	1,441	11,653	9,450		9,257	1,930	24,600	3,135
AAA		1.27	0.59	1.31	1.11		0.59	0.35	0.60	0.54		0.96	0.80	1.00	0.94
AAG	∗	0.73⁺⁺⁺	1.41	0.69⁺⁺	0.89	∗	1.41⁺⁺	1.65	1.40	1.46	∗	1.04⁺	1.20	1.00	1.06
Asn		25,983	2,605	18,131	34,502		1,936	718	11,562	7,439		6,174	998	17,808	2,166
AAC	∗	0.75⁺⁺⁺	1.22	0.70	0.76	∗	1.23⁺⁺	1.47	1.09⁺	1.17	∗	1.03⁺	1.15	0.90⁺	0.99
AAU		1.25	0.78	1.30	1.24		0.77	0.53	0.91	0.83		0.97	0.85	1.10	1.01
Gln		19,766	2,424	13,462	32,392		2,071	665	14,445	8,767		4,845	875	14,059	1,783
CAA		1.37	1.19	1.39	1.37		0.55	0.41	0.60	0.58		1.18	1.07	1.12	1.07
CAG	∗	0.63⁺	0.81	0.61	0.63	∗	1.45⁺	1.59	1.40	1.42	∗	0.82⁺	0.93	0.88	0.93
His		11,626	1,270	7,872	17,198		1,136	342	7,300	3,789		3,222	606	8,933	1,100
CAC	∗	0.75⁺⁺⁺	1.23	0.72	0.73	∗	1.25⁺⁺	1.46	1.21	1.22	∗	0.81⁺	0.90	0.69⁺	0.82
CAU		1.25	0.77	1.28	1.27		0.75	0.54	0.79	0.78		1.19	1.10	1.31	1.18
Glu		30,622	3,979	21,650	55,173		2,508	1,231	13,586	11,132		9,708	1,623	26,319	3,529
GAA		1.30	0.92	1.36	1.30		0.58	0.35	0.62	0.61		1.02	1.00	1.08	1.00
GAG	∗	0.70⁺⁺⁺	1.08	0.64	0.70	∗	1.42⁺⁺	1.65	1.38	1.39	∗	0.98	1.00	0.92⁺	1.00
Asp		25,098	3,551	17,514	43,357		2,166	1,052	11,557	8,516		7,676	1,366	20,700	2,743
GAC	∗	0.66⁺⁺	0.92	0.60	0.58	∗	0.98⁺	1.08	0.95	0.96	∗	0.64⁺	0.72	0.60	0.63
GAU		1.34	1.08	1.40	1.42		1.02	0.92	1.05	1.04		1.36	1.28	1.40	1.37
Tyr		18,124	1,765	11,538	20,250		1,407	500	6,456	3,871		4,061	774	11,149	1,403
UAC	∗	0.84⁺⁺⁺	1.35	0.80⁺	0.89	∗	1.35⁺⁺	1.57	1.24	1.29	∗	0.97⁺⁺	1.19	0.86	0.93
UAU		1.16	0.65	1.20	1.11		0.65	0.43	0.76	0.71		1.03	0.81	1.14	1.07
Cys		12,135	1,016	7,540	12,899		1,174	244	4,433	2,242		2,768	439	7,481	755
UGC	∗	0.87⁺⁺⁺	1.28	0.82	0.84	∗	1.44⁺⁺	1.68	1.44	1.42	∗	0.80⁺	0.89	0.77⁺	0.86
UGU		1.13	0.72	1.18	1.16		0.56	0.32	0.56	0.58		1.20	1.11	1.23	1.14
Phe		29,190	2,470	17,908	28,498		1,536	599	7,614	4,898		6,274	1,039	16,537	2,103
UUC	∗	0.90⁺⁺⁺	1.50	0.88⁺⁺	1.17	∗	1.34⁺⁺	1.59	1.27	1.31	∗	0.98⁺⁺	1.18	0.87	0.93
UUU		1.10	0.50	1.12	0.83		0.66	0.41	0.73	0.69		1.02	0.82	1.13	1.07
Ile		34,721	3,057	23,018	40,126		2,136	937	10,904	7,260		7,243	1,288	20,984	2,753
AUA		0.54	0.10	0.57	0.32		0.51	0.22	0.60	0.49		0.72	0.50	0.79	0.62
AUC	∗	0.84⁺⁺⁺	1.75	0.80⁺⁺	1.01	∗	1.59⁺⁺⁺	1.95	1.41	1.48	∗	1.09⁺⁺	1.33	0.94⁺	1.08
AUU		1.62	1.16	1.63	1.66		0.90	0.83	0.99	1.03		1.20	1.17	1.28	1.29
Codon	Favored	C. elegans				Favored	D. melanogaster				Favored	A. thaliana

Short proteins		Long proteins		Short proteins		Long proteins		Short proteins		Long proteins

No EST	High	No EST	High	No EST	High	No EST	High	No EST	High	No EST	High
Ter		2,543	298	429	663		255	80	232	140		680	122	458	59
UAA		1.43⁺⁺⁺	2.00	1.37⁺⁺⁺	1.75		1.53⁺⁺⁺	1.95	1.14⁺⁺⁺	1.59		1.29⁺	1.40	1.19	0.86
UAG		0.51	0.53	0.58	0.52		0.73	0.79	1.00	0.69		0.64	0.39	0.50⁺	0.66
UGA		1.06	0.46	1.05	0.73		0.74	0.26	0.87	0.73		1.08⁺	1.20	1.31⁺	1.47

No EST and high denote genes with very low (no detected EST) or high expression level. Short and Long proteins denote genes with, respectively, <333 and >570 codons. Favored codons (defined by multivariate analysis) are indicated ∗ (data from Refs. 13, 14, and 21). Optimal codons, defined by a higher RSCU value in highly expressed genes, are indicated +++ (ΔRSCU ≥ 0.30), ++ (ΔRSCU ≥ 0.20), and + (ΔRSCU ≥ 0.08). Numbers in boldface represent the number of codons analyzed.