Separate base usages of genes located on the leading and lagging strands in Chlamydia muridarum revealed by the Z curve method

Table 3 Codon usage for genes located on the leading and lagging strands in the C. muridarum genome

AA		Leading		Significant ^a	Lagging
		N	RSCU		N	RSCU
Phe	TTT	6116	1.45	>>	4543	1.24
	TTC	2333	0.55	<<	2806	0.76
Leu	TTA	6382	2.01	>>	4608	1.61
	TTG	4653	1.46	>>	1955	0.68
	CTT	3866	1.21	<<	4497	1.57
	CTC	1099	0.35	<<	2230	0.78
	CTA	1748	0.55	<<	2616	0.91
	CTG	1348	0.42	--	1266	0.44
Ile	ATT	6568	1.78	>>	5719	1.60
	ATC	2264	0.61	<<	3227	0.91
	ATA	2225	0.60	>>	1747	0.49
Met	ATG	3833	1.00	--	2565	1.00
Val	GTT	5637	1.73	>>	3056	1.59
	GTC	1470	0.45	<<	1515	0.79
	GTA	3172	0.97	<<	2012	1.05
	GTG	2766	0.85	>>	1104	0.57
Tyr	TAT	4137	1.52	>>	2842	1.27
	TAC	1321	0.48	<<	1628	0.73
TER	TAA	270	0.00	--	256	0.00
	TAG	161	0.00	--	89	0.00
His	CAT	2882	1.58	>>	2406	1.31
	CAC	776	0.42	<<	1276	0.69
Gln	CAA	4154	1.17	<<	4833	1.52
	CAG	2974	0.83	>>	1539	0.48
Asn	AAT	4480	1.52	>>	3811	1.29
	AAC	1418	0.48	<<	2085	0.71
Lys	AAA	6850	1.29	<<	6888	1.60
	AAG	3801	0.71	>>	1726	0.40
Asp	GAT	7033	1.66	>>	4364	1.43
	GAC	1462	0.34	<<	1758	0.57
Glu	GAA	7392	1.18	<<	6318	1.49
	GAG	5141	0.82	>>	2180	0.51
Ser	TCT	5851	2.58	--	5418	2.51
	TCC	1530	0.67	<<	2523	1.17
	TCA	1626	0.72	--	1640	0.76
	TCG	1193	0.53	>>	786	0.36
Pro	CCT	3633	2.16	>>	3588	1.99
	CCC	834	0.50	<<	1532	0.85
	CCA	1606	0.95	--	1648	0.91
	CCG	666	0.40	>>	454	0.25
Thr	ACT	2794	1.44	>>	2898	1.35
	ACC	1010	0.52	<<	1875	0.88
	ACA	2504	1.29	--	2849	1.33
	ACG	1466	0.75	>>	939	0.44
Ala	GCT	6448	2.01	>>	4661	1.82
	GCC	1459	0.45	<<	1797	0.70
	GCA	3191	0.99	<<	2826	1.11
	GCG	1753	0.55	>>	936	0.37
Cys	TGT	2044	1.41	>>	1266	1.08
	TGC	851	0.59	<<	1079	0.92
TER	TGA	69	0.00	--	65	0.00
Trp	TGG	1863	1.00	--	1275	1.00
Arg	CGT	2571	1.65	>>	1399	1.40
	CGC	915	0.59	<<	1351	1.35
	CGA	1844	1.18	<<	1362	1.36
	CGG	989	0.63	>>	336	0.34
Ser	AGT	2208	0.97	>>	1149	0.53
	AGC	1211	0.53	<<	1411	0.65
Arg	AGA	2228	1.43	>>	1284	1.28
	AGG	815	0.52	>>	271	0.27
Gly	GGT	2331	0.76	>>	1199	0.59
	GGC	1241	0.41	<<	1312	0.64
	GGA	5116	1.67	<<	4021	1.98
	GGG	3538	1.16	>>	1611	0.79

^a Results of Chi-squared test: << indicates that the leading strand genes used the condon more frequently than the lagging strand genes; >> indicates the lagging strand genes used the codon more frequently than the leading strand genes; -- indicates that there is no significant difference in usage of the codon on either strand. Significance is examined at the level of 5%.

ISSN: 1471-2164