Mapping codon usage of the translation initiation region in porcine reproductive and respiratory syndrome virus genome

Su, Jun-hong; Ma, Xiao-xia; He, Ya-li; Li, Ji-dong; Ma, Xu-sheng; Dou, Yong-xi; Luo, Xue-nong; Cai, Xue-peng

doi:10.1186/1743-422X-8-476

Virology Journal

Table 3 Preferentially used codons in the target region in US and EU serotypes of PRRSV

From: Mapping codon usage of the translation initiation region in porcine reproductive and respiratory syndrome virus genome

	ORF1a		ORF2			ORF3
Codon	US	EU	US		EU	US	EU
^aGCA	^b1.69	^b1.43	0		0.91	0.15	0.64
GCC	1.00	0.98	1.42		2.16	0	0.91
^aGCG	^b2.25	^b1.34	0		0	^b2.17	0
GCU	0	0.76	1.03		0.83	2.94	1.88
^aAGA	0	0	0.5		^b1.37	0	0
AGG	1.22	0	0		0	3.72	0
^aCGA	^b2.42	0	0		0	0	0
CGC	0	0	0		0	0	2.05
CGG	3.07	5.63	3.79		1.14	0	0
^aCGU	0	0	0		^b1.07	0.47	^b2.90
AAC	0.43	0.90	1.86		0	0.12	1.01
^aAAU	^b1.72	0.68	0.40		0	^b1.35	1.00
^aGAC	0	^b1.56	0		0	0	0
GAU	2.31	0.37	0		1.26	0.38	0.25
UGC	1.08	1.62	1.25		0	0.36	0.18
^aUGU	0.92	0.50	^b1.01		^b1.51	^b1.44	^b1.43
^aCAA	^b1.89	^b1.08	0.50		0.86	0	0
CAG	0.17	0.92	0		1.21	0	2.15
^aGAA	0.55	0.28	0		0	^b1.50	0
GAG	1.30	1.38	0		1.14	0.27	1.30
^aGGA	0	0.39	0		^b2.46	0	0
GGC	1.40	1.63	3.13		0	1.51	3.82
GGG	2.00	1.16	0		0.29	0	0
GGU	0.15	0.48	1.40		1.25	2.58	0.42
^aCAC	0	0	0		^b1.58	0	0.72
CAU	0	0	0		0.21	1.41	1.32
^aAUA	^b8.26	0	^b2.55		^b3.19	0	0
AUC	0	0	0		0	0	2.58
AUU	0	0.59	0		0	4.31	0
^aCUA	^b2.32	0.24	0.32		0	0	^b4.42
CUC	1.90	1.87	0		0	1.84	0.77
CUG	0.92	0	0		0.65	1.39	0.43
CUU	1.01	1.34	0.66		0.24	0	1.02
^aUUA	0.28	0.22	0.64		^b3.54	0	0
UUG	0	0.80	1.99		2.04	0.74	1.29
^aAAA	0	0	^b1.27		^b2.64	0	0
AAG	0	0	0		0	0	0
^aUUC	^b1.01	0.48	0.17		^b1.09	0.99	0.95
UUU	1.01	1.46	1.14		0.78	1.02	1.07
CCA	0	0.98	1.50		1.04	0	4.51
CCC	2.27	0.11	0		0	0.39	0
^aCCG	0	^b2.43	^b1.36		^b1.07	^b3.79	0
CCU	1.01	0.81	0		3.21	0	0.24
^aAGC	0.42	^b1.56	0		0.43	^b2.02	^b1.26
^aAGU	^b6.36	^b8.28	^b4.94		^b4.13	0	^b1.87
UCA	1.89	1.68	0.28		0.41	0	1.17
UCC	0.21	0.98	0.09		0.60	0.83	0.59
^aUCG	0	0	^b1.58		^b1.70	0	^b1.30
UCU	2.79	1.33	1.16		0.63	2.21	1.22
^aACA	^b1.97	^b1.48	^b6.17		0	^b1.24	0.70
ACC	0.89	0.58	0		0	0	0.70
^aACG	^b2.22	^b1.49	0		^b1.83	^b1.74	^b2.11
^aACU	0	^b1.06	0		0	0.96	0.82
UAC	1.33	0	0		1.36	1.32	2.03
^aUAU	0.37	0.30	^b1.77		0.53	0	0.11
^aGUA	0	^b2.67	0		^b4.79	0	0
GUC	0.77	1.77	3.78		0.33	0.11	0.33
GUG	1.71	0.31	0		2.04	1.88	0
GUU	0.76	0.53	2.96		0	1.08	4.14
	ORF4		ORF5		ORF6		ORF7
Codon	US	EU	US	EU	US	EU	US	EU
^aGCA	^b1.25	0.16	0	0	0	^b1.60	0	^b1.09
GCC	0.55	0.96	1.91	3.08	0.65	1.69	1.22	1.75
^aGCG	^b1.27	^b1.09	0.85	0.57	^b1.60	0	0	0
GCU	0.98	1.20	1.35	0	2.24	0.21	1.50	0.74
^aAGA	0	0	0	^b3.69	0	0	^b2.78	0.71
AGG	0	0	0	0.15	0	0	0.17	2.19
^aCGA	0	0	^b7.83	0	^b4.58	0.99	0	0.33
CGC	0	0	0	0	2.29	5.79	0	0.75
CGG	0	0	0	0	0	0.23	0	0.29
^aCGU	0	0	0	^b1.80	0	0	0	0
AAC	3.67	1.36	1.34	1.42	0	0.31	1.09	1.42
^aAAU	0	0.56	0	0.20	0.29	0.86	0.89	0.83
^aGAC	^b1.38	^b1.39	0.58	0.18	^b1.33	0.64	0.50	0
GAU	0.50	0.69	0	2.65	0.67	0.86	0.75	0
UGC	0.64	0.67	0.82	0.99	0.44	1.38	1.92	1.00
^aUGU	^b1.41	0.99	^b1.13	^b1.02	^b1.33	0.24	0	0.29
^aCAA	0.42	^b1.14	0.25	1.00	^b1.50	^b1.38	0.64	0.78
CAG	1.46	0.95	2	0	0.33	0	1.13	1.07
^aGAA	0.50	0	0	0	0.17	0.45	0	0
GAG	0.19	2.14	1.49	0.29	0	0	0	0
^aGGA	0	0	0	0	0	0.84	^b1.31	^b1.14
GGC	0.63	0	1.63	1.98	0.79	0.77	1.05	0.89
GGG	0	0	1.03	0.54	1.87	1.97	0.63	0.85
GGU	4.00	3.33	0.17	0	0	0.56	1.35	1.11
^aCAC	0	0	0	^b2.90	0.78	^b2.05	0	0
CAU	0	1.48	1.94	0	1.46	0	0	0
^aAUA	0	0	0	^b2.58	^b1.12	^b1.86	0	^b3.29
AUC	1.26	1.24	1.07	0.12	1.19	0.90	1.46	0
AUU	0.73	1.20	1.34	0.37	0.80	0.08	0	0
^aCUA	0	^b2.26	^b1.37	0	^b1.66	^b1.35	0	0
CUC	1.52	1.15	0.60	0	0.19	0.74	0	0
CUG	0	1.14	0.70	0.99	1.19	1.48	1.46	1.78
CUU	1.19	1.81	0.62	0.77	1.27	0.94	0	0
^aUUA	0	0.23	0.55	0	0.77	0.16	0	0
UUG	1.50	0.19	1.69	2.16	0.73	0.84	0.22	1.05
^aAAA	^b1.21	0.20	^b1.34	1.00	0	0.31	^b1.08	^b1.21
AAG	0.69	1.82	0.23	0.38	2.43	1.32	0.98	0.86
^aUUC	^b1.28	^b1.18	^b1.88	0.99	1.00	0.42	0	0
UUU	0.76	0.12	0.84	0.98	0.87	1.49	0	0
CCA	3.83	0	0	0.76	3.00	0	2.25	1.85
CCC	0.40	1.67	0	0	0	0.79	0	0.59
^aCCG	0	0.43	^b4.25	^b1.29	0	0	^b2.00	0.33
CCU	0	0.24	0.17	0	0	1.65	0	0.50
^aAGC	^b1.34	0	^b1.69	0.57	0.98	^b3.10	1.00	^b2.47
^aAGU	^b3.67	^b2.57	0	0	^b4.28	0	0	^b2.51
UCA	4.31	0.64	0	0	2.20	0	0	2.99
UCC	0.78	0	0.32	1.17	0.79	0	1.35	1.26
^aUCG	^b1.91	^b1.95	^b1.58	^b1.48	^b2.20	0	0	0
UCU	0.47	0.86	1.45	1.78	2.02	0.31	0	0
^aACA	0	0	0	^b1.32	0.17	^b1.76	0	^b1.63
ACC	1.78	1.41	0.98	0.67	0.83	0.56	0	0
^aACG	0	^b1.69	^b6.79	^b2.13	^b2.35	0	0	0
^aACU	0.78	0.21	0	0.53	0.18	0.43	0	0
UAC	0	0	1.80	1.11	0.67	1.05	0	0
^aUAU	0	0	0.48	0.90	^b1.50	0.55	0	0
^aGUA	0	0	0	0	0.98	0.27	0	0
GUC	0.92	1.04	0.34	0	0	0	1.72	2.96
GUG	0.52	0.10	2.79	0	2.10	2.29	0	0
GUU	2.25	1.77	0	0	0	0	0	0

^a presented the non-preferential codon.
^b presented that the non-preferential codon was more preferentially chosen in the translation initiation region than that of the whole coding sequence.

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ISSN: 1743-422X

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