Skip to main content

Table 2 Duplicate gene homeology/paralogy between BAC pairs

From: Gene duplication and paleopolyploidy in soybean and the implications for whole genome sequencing

BAC homeologs Putative function # of exons Coding lengtha Nucleotide identity Protein identity Protein similarity Ks Ka Date (Mya)
gmw1-74i13 gmw1-52d3 b b b 89.8 88.0 90.7 0.1490 0.0335 12.2
gmw1-105h23 gmw1-15k6 d d d 90.7 88.9 90.4 0.1061 0.0326 8.70
UMb001-24d13 DNA binding 6 1338 92.7 88.7 92.2 0.1177 0.0468 9.65
UMb001-5f5 DNA binding 7 1473       
UMb001-24d13 Gamma response I 9 987 95.9 95.7 96.3 0.1405 0.0152 11.52
UMb001-5f5 Gamma response I 9 984       
UMb001-24d13 Selenium binding 4 1881 56.3 54.6 56.4 0.1709 0.0575 14.01
UMb001-5f5 Selenium binding 5 585       
gmw1-103e11 A. thaliana-like NAP 7 510 96.4 95.8 97.2 0.0933 0.0188 7.65
gmw1-5g16 A. thaliana-like NAP 7 1002       
gmw1-103e11 Beta-fructofuranosidase 6 1944 94.4 92.7 94.1 0.0716 0.0276 5.87
gmw1-5g16 Beta-fructofuranosidase 6 1956       
gmw1-103e11 Galactinol synthase 4 732 90.5 93.5 94.7 0.3208 0.0316 26.30
gmw1-5g16 Galactinol synthase 3/4 669/987       
gmw1-103e11 RAD-like protein 6/7 564/900 96.9 92.9 97.6 0.0432 0.0442 3.54
gmw1-5g16 RAD-like protein 5 240       
gmw2-133d1 GTPase 14 3183 96.9 98.1 99.1 0.1055 0.0084 8.65
gmw1-93l19 GTPase 16 3480       
gmw2-133d1 Cellulose synthase 9 2211 67.6 65.1 67.0 0.1109 0.0438 9.09
gmw1-93l19 Cellulose synthase 5 924       
gmw2-133d1 Chain A protein 1 1608 81.1 76.4 80.1 0.1856 0.077 15.21
gmw1-93l19 Chain A protein 1 1452       
gmw1-13o17 Raffinose synthase 5 2277 66.4 71.5 81.5 2.5495 0.2051 208.98
gmw1-8g7 Raffinose synthase 6 2190       
gmw1-57d24 Phospholipase C 8 1308 80.5 78.7 87.6 0.5457 0.114 44.73
gmw1-58k3 Phospholipase C 8 1299       
gmw1-57d24 COMT 5 747 79.7 79.0 88.3 0.6442 0.1204 52.80
gmw1-58k3 COMT 4/5 615/354       
gmw1-58k3 COMT 4/5 615/354 73.6 76.3 87.7 1.7076 0.1667 139.97
gmw1-27d20 COMT 5 744       
gmw1-58k3 Otubain 6 1992 53.7 42.5 53.3 4.024 0.3023 329.84
gmw1-27d20 Otubain 7 1860       
gmw1-57d24 CBS 6/8 399/687 74.9 73.7 89.5 2.0095 0.1562 164.71
gmw1-27d20 CBS 8 678       
gmw1-57d24 COMT 5 747 74.1 81.6 91.0 1.5875 0.1196 130.12
gmw1-27d20 COMT 5 744       
  Average    86.6 85.4 88.8 0.4239 0.0577 34.75
  Recalculated average 1 d    89.8 88.2 90.1 0.1179 0.0341 9.665
  Recalculated average 2 e    71.8 71.9 82.7 1.8668 0.1691 153
  1. a Coding length in base pairs based upon CDS (from start to stop not including introns).
  2. b The values for homeologs between gmw1-74i13 and gmw1-52d3 are previously reported (Schlueter et al. 2006). Identity, similarity, Ks, Ka and Dates shown are average across BACs.
  3. c The values for homeologs between gmw1-105h23 and gmw1-15k6 are previously reported (Schlueter et al. 2007). Identity, similarity, Ks, Ka and Dates shown are average across BACs.
  4. d Recalculated average not including the highly divergent homeologs from gmw1-13o17, gmw1-8g7, gmw1-57d24, gmw1-58k3 and gmw1-27d20.
  5. e Recalculated average for just the highly divergent homeologs from gmw1-13o17, gmw1-8g7, gmw1-57d24, gmw1-58k3 and gmw1-27d24.