Complex Codon Usage Pattern and Compositional Features of Retroviruses

Table 2

Translational optimal codons.

Amino acid	Codon^#	High		Low
		RSCU	Number	RSCU	Number
Phe	UUU*	1.64	184	0.7	61
	UUC	0.36	40	1.3	113
Leu	UUA*	2.67	323	0.34	35
	UUG*	1.21	146	0.5	51
	CUU	0.47	57	0.63	65
	CUC	0.29	35	1.83	189
	CUA*	0.94	114	0.53	55
	CUG	0.41	50	2.17	223
Ile	AUU	0.85	193	0.77	55
	AUC	0.29	66	1.72	122
	AUA*	1.86	425	0.51	36
Val	GUU	0.65	80	0.63	44
	GUC	0.36	44	1.38	96
	GUA*	2.17	267	0.32	22
	GUG	0.82	101	1.68	117
Tyr	UAU*	1.74	270	0.44	34
	UAC	0.26	41	1.56	121
His	CAU*	1.5	144	0.64	63
	CAC	0.5	48	1.36	134
Gln	CAA*	1.49	383	0.47	71
	CAG	0.51	131	1.53	228
Asn	AAU*	1.67	317	0.54	38
	AAC	0.33	62	1.46	104
Lys	AAA*	1.38	481	0.68	93
	AAG	0.62	218	1.32	182
Asp	GAU*	1.51	259	0.53	54
	GAC	0.49	85	1.47	149
Glu	GAA*	1.5	474	0.61	99
	GAG	0.5	159	1.39	228
Ser	UCU*	1.18	77	0.76	49
	UCC	0.56	37	2.1	136
	UCA*	1.88	123	0.51	33
	UCG	0.2	13	0.71	46
	AGU*	1.53	100	0.37	24
	AGC	0.66	43	1.56	101
Pro	CCU*	1.47	162	0.68	81
	CCC	0.52	57	2.04	243
	CCA*	1.78	196	0.75	89
	CCG	0.24	26	0.54	64
Thr	ACU*	1.29	156	0.67	57
	ACC	0.42	51	2.1	178
	ACA*	2.09	252	0.67	57
	ACG	0.2	24	0.55	47
Ala	GCU*	1.09	130	0.7	69
	GCC	0.58	69	2.11	207
	GCA*	2.07	246	0.67	66
	GCG	0.26	31	0.51	50
Cys	UGU*	1.69	133	0.5	27
	UGC	0.31	24	1.5	81
Arg	CGU	0.03	2	0.53	26
	CGC	0.09	6	1.64	81
	CGA	0.42	28	0.65	32
	CGG	0.12	8	2.03	100
	AGA*	3.71	250	0.45	22
	AGG*	1.63	110	0.71	35
Gly	GGU	0.49	73	0.42	37
	GGC	0.32	48	1.52	134
	GGA*	2.22	333	0.74	65
	GGG	0.97	145	1.33	117

#W, M, and stop codons are excluded. Those codons are significantly higher in highly expressed genes.