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. 2013 Sep 30;178(2):264–271. doi: 10.1016/j.virusres.2013.09.033

Table 1.

Conserved amino acid (aa) positions in the Avian coronavirus spike (S), nucleocapsid (N), non-structural protein 2 (NSP2) and papain-like protease (PLpro) genes coded by a preferred codon and the preferred codon for each aa in the Gallus gallus beta-actin (B-act), lung surfactant protein A (SFTPA1), intestinal cholecystokinin (CCK), oviduct ovomucin alpha subunit (Ovo) and kidney vitamin D receptor (ViTD rec) genes. Tryptophan and methionine, coded by a single codon, were excluded. Codon preference was indicated by relative synonymous codon usage (RSCU) >1. Positions are provided only for Avian coronavirus genes as G. gallus genes were used as the reference for comparison.

G gallus
 Avian coronavirus
aa B-act CCK Ovo SFTPA1 VitD rec S Position N Position Nsp2 Position PLPro Position
F UUC UUC UUU/UUC UUU UUC UUU 155 UUU 313, 390 UUU 52, 64, 101, 138, 200, 217 UUU 28, 54, 57, 102, 144, 211, 220, 270, 326, 369, 393
L CUC/CUG CUC/CUG CUG UUG/CUU/CUA/CUG CUC/CUG NC NC NC NC NC NC CUU 16, 47, 58, 94, 111, 129, 273, 288, 315, 413
I AUU/AUC AUC AUU/AUC AUU AUC NC NC AUU 319, 397 AUU 23, 199, 210 AUU 52, 133, 194, 226, 383, 429
V GUG GUG GUU/GUG GUU/GUG GUC/GUG NC NC NC NC GUU 154, 163, 226, 228, 235 GUU 191, 192, 317, 323, 324, 371, 394, 430, 435
S UCU/UCC/AGC UCC/AGC UCU/UCC/UCA/AGU/AGC UCU/AGU/AGC UCC/AGC NC NC UCA 340, 344 NC NC NC NC
P CCU/CCC CCC CCU/CCC/CCA CCU CCC NC NC CCA 338 NC NC CCU 178, 294, 338
T ACC/ACA ACA ACU/ACC/ACA ACU/ACA ACC/ACG NC NC NC NC ACU 123, 167, 241 NC NC
A GCC GCU/GCG GCU/GCC/GCA GCU/GCA GCC NC NC GCA 376 NC NC NC NC
Y UAC UAC UAU/UAC UAU/UAC UAC NC NC UAU 316 NC NC NC NC
H CAC CAC CAU/CAC CAU CAC NC NC NF NF NC NC CAU 143, 201
Q CAG CAG CAA/CAG CAA CAG NC NC CAG 312, 369, 387 NC NC NC NC
N AAC All RSCUs = 1 AAC AAU AAC NC NC AAU 315, 385, 407 NC NC AAU 27, 82, 97, 140, 186, 296, 343
K AAG AAG AAA AAA AAG NC NC NC NC AAA 6, 21, 86 NC NC
D GAU GAU GAU/GAC GAC GAC NC NC GAU 314, 374 NC NC GAU 5, 105, 160, 176, 182, 184, 217, 258, 281
E GAG All RSCUs = 1 GAA GAG GAG NC NC NC NC GAA 98, 136, 142, 165 GAA 130, 164, 185, 342
C UGC UGC UGU UGU UGC NC NC UGU 320, 323 UGU 68, 242 UGU 132, 154, 183, 202, 439
R CGU/AGA CGC/CGG/AGG AGA/AGG CGA/AGA CGC/CGG/AGG NC NC AGA 349 CGU 54, 111 NC NC
G GGU/GGC GGC GGA GGA GGC NC NC NC NC NC NC GGU 56, 86, 177, 319, 402

NC: no 100% conserved amino acids positions coded by the preferred codon; NF: amino acid not found in the sequence.