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. 2004 Aug;14(8):1474–1482. doi: 10.1101/gr.2673204

Table 1.

Gene Features Predicted Along Homoeologous AT and DT BACs Surrounding the CesA1 Gene in Allopolyploid Cotton

Length (bp)b
Total length, exonsb
Total length, introns
Length (a.a.)
Divergencec
Gene Putative functiona DT AT Exons DT AT Introns DT AT DT AT Ks Ka Ksil
1 ABC transporterd 244 244 * 244 244 * 0 0 81 81 0.035 0.000 0.035
2 GTP-binding protein 1909 1925 2 657 657 1 1252 1268 218 218 0.054 0.006 0.047
3 WRKY TF 1024 1013 3 822 819 2 202 194 273 274 0.064 0.014 0.041
4 Arabidopsis hypothetical protein 994 992 3 471 471 2 523 521 156 156 0.020 0.017 0.061
5 No BLAST homoeology 519 519 1 519 519 0 0 0 172 172 0.084 0.026 0.084
6 G-protein B 2376 2376 9 1068 1068 8 1308 1308 355 355 0.043 0.012 0.029
7 CesA 4080 4083 12 2925 2925 11 1155 1158 974 974 0.041 0.004 0.033
8 LeuRR 1308 1308 1 1308 1308 0 0 0 435 435 0.020 0.012 0.020
9 PRR/Se-binding protein 2628 2628 3 2418 2418 2 210 210 805 805 0.019 0.013 0.018
10 Ribosomal protein L11 1273 1275 4 519 519 3 754 756 172 172 0.008 0.000 0.029
11 LeuRR transmembrane or kinase 3189 3197 11 1857 1857 10 1332 1340 618 618 0.042 0.006 0.031
12 Growth regulator 2631 2637 10 1797 1800 9 834 837 598 599 0.050 0.015 0.037
13 Permease 2633 2629 13 1575 1575 12 1058 1054 524 524 0.016 0.006 0.021
14 Arabidopsis expressed protein 4349 4325 8 1287 1278 7 3062 3047 425 422 0.037 0.014 0.029
Weighted average 0.037 0.010 0.032
a

Putative function is assigned by BLAST homoeology to genes in GenBank. The locations of genes along the BAC contigs are represented in Figure 2.

b

Total length including stop codon.

c

Ks, Ka, and Ksil denote rate of substitution across all sites, substitutions at nonsynonymous sites, and synonymous sites within codons plus all noncoding positions, respectively.

d

This predicted gene is fragmented in the BAC; a start codon was identified, but no intronic sequences or stop codon was found. This gene would presumably be full length, were it not fragmented in the generation of the BAC library. An asterisk (*) signifies that the number of exons and introns is not known.