Table 2

Sequence comparison of starch synthases from 30 accessions of A. thaliana
Domain Sites S η Nonsyn Indels h Hd π GC content
AtSSI gene 3946 126 128 9 26 21 0.966 0.0112 0.396
exons 1959 30 30 9 - 8 0.584 0.0047 0.467
introns 1987 96 98 - 26 21 0.966 0.0180 0.321
promoter 1422 68 71 - 24 22 0.972 0.0151 0.309
cTP 147 2 2 0 - 2 0.405 0.0055 0.515
GT5 780 8 8 4 - 4 0.499 0.0024 0.470
GT1 510 13 13 2 - 3 0.421 0.0097 0.474
AtSSII gene 3226 31 31 13 3 12 0.841 0.0014 0.423
exons 2379 19 19 13 - 10 0.782 0.0012 0.451
introns 847 12 12 - 3 7 0.611 0.0019 0.341
promoter 855 26 26 - 13 14 0.913 0.0063 0.304
cTP 165 4 4 3 - 3 0.131 0.0016 0.491
GT5 732 8 8 4 - 8 0.749 0.0025 0.444
GT1 495 0 0 0 - 1 0.000 0.0000 0.467
AtSSIII gene 4358 105 106 34 11 17 0.929 0.0056 0.403
exons 3099 63 64 34 1 14 0.899 0.0047 0.422
introns 1259 42 42 - 10 10 0.811 0.0078 0.357
promoter 937 8 8 - 4 7 0.676 0.0016 0.356
cTP 60 0 0 0 - 1 0.000 0.0000 0.517
GT5 597 15 15 6 - 6 0.680 0.0057 0.406
GT1 528 11 11 2 - 3 0.297 0.0047 0.444
AtSSIV gene 4874 72 73 17 15 23 0.977 0.0028 0.379
exons 3123 31 31 17 - 15 0.839 0.0018 0.413
introns 1751 41 42 - 15 18 0.952 0.0047 0.316
promoter 547 30 30 - 8 12 0.834 0.0125 0.366
cTP 126 2 2 2 - 3 0.393 0.0033 0.443
GT5 726 3 3 2 - 4 0.251 0.0004 0.429
GT1 525 2 2 1 - 3 0.246 0.0005 0.411
AtGBSS gene 2989 53 53 12 10 17 0.945 0.0045 0.403
exons 1833 28 28 12 - 14 0.857 0.0042 0.452
introns 1156 25 25 - 10 16 0.903 0.0050 0.319
promoter 906 37 38 - 11 15 0.894 0.0078 0.356
cTP 237 15 15 9 - 5 0.499 0.0223 0.406
GT5 786 7 7 3 - 8 0.630 0.0017 0.442
GT1 411 4 4 0 - 5 0.575 0.0019 0.486

Promoter = either the complete intergenic region or about 1 kb upstream the coding region; cTP = chloroplast transit peptide; GT5 domain = starch synthase catalytic domain; GT1 domain = glucosyl transferase group 1; S = polymorphic sites; η = total number of mutations; nonsyn = nonsynonymous sites; indels = number of insertions/deletions; h = number of haplotypes (=alleles); Hd = haplotype diversity; π = nucleotide diversity.

Schwarte et al.

Schwarte et al. BMC Research Notes 2013 6:84   doi:10.1186/1756-0500-6-84

Open Data