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Table 2 Sequence Variations Detected Within the Hd6 Region Among Cultivated Varieties and Wild Rice Accessions

From: Molecular and Evolutionary Analysis of the Hd6 Photoperiod Sensitivity Gene Within Genus Oryza

Speciesa Variety or accession Entire region (bp) Exon (bp) Intron (bp)
Length Indel Substitutionb Length Indelc Substitution
O. sativa ssp. indica Kasalath 5,178 1,002 4,176
93–11 5,176 1,002 0 0 4,174 7 (5) 16
Shuusoushu 5,176 1,002 0 0 4,174 4 (3) 5
O. sativa ssp. japonica Nipponbare 5,176 1,002 0 1 (1) 4,174 4 (3) 15
Khau Mac Kho 5,176 1,002 0 0 4,174 4 (3) 15
O. rufipogon W0106 5,178 1,002 0 0 4,176 0 1
W0574 5,178 1,002 0 0 4,176 0 0
W1943 5,176 1,002 0 0 4,174 4 (3) 13
O. glaberrima IRGC104038 5,175 1,002 0 0 4,173 3 (2) 9
O. barthii W1588 5,182 1,002 0 0 4,180 6 (2) 11
O. glumaepatula IRGC105688 5,177 1,002 0 2 (1) 4,175 3 (2) 10
O. meridionalis W1625 5,180 1,002 0 1 4,178 64 (16) 59
O. longistaminata W1413 5,119 1,002 0 3 4,117 173 (22) 114
O. punctata IRGC105690 5,137 1,002 0 10 4,135 557 (58) 289
O. minuta (OM_Ba0079N19) IRGC101141 5,125 1,002 0 10 4,123 547 (59) 289
O. minuta (OM_Ba0144F13)   5,253 1,002 0 8 4,251 361 (45) 251
O. officinalis IRGC100896 5,245 1,002 0 10 (1) 4,243 371 (45) 249
O. alta IRGC105143 6,741 1,002 0 20 5,739 1,925 (59) 292
O. australiensis W0008 5,741 1,002 0 18 (1) 4,739 933 (55) 323
O. brachyantha IRGC101232 5,583 1,002 0 31 (1) 4,581 1,499 (105) 642
O. granulata IRGC102118 6,049 1,002 0 30 5,047 1,869 (112) 718
  1. Calculation of indels and substitutions of nucleotides is conducted by taking the Kasalath Hd6 as a reference
  2. a O. minuta has two distinct sequences obtained respectively from the different BAC clones with names given in parentheses
  3. bNumbers in parentheses represent nonsynonymous substitutions
  4. cNumbers in parentheses indicate the total sites of indel