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Table 3 Comparison of sequence similarity and TFBS/miRNA target site divergence for putative cis-regulatory regions surrounding the opsin arrays of O. niloticus and M. zebra

From: Divergence in cis-regulatory sequences surrounding the opsin gene arrays of African cichlid fishes

Region Identity Dxy1 Length Length TFBS TFBS Est. p-value3
   (%) (%) On(bp) Mz(bp) Divt. Shrd Pdiv2 (%)  
CNE4 1 96.84 3.23 158 158 0 2 0.0 1.000
  2 96.22 3.88 240 239 2 6 25.0 0.130
  3 94.74 4.53 349 359 7 1 87.5 < 0.001*
  4 98.31 1.70 240 241 2 0 100.0 0.006
  5 96.14 3.97 207 207 1 0 100.0 0.080
  6 - - 300 - - - - -
  7 97.16 2.89 882 885 1 8 11.1 0.528
  8 88.46 4.86 779 799 3 9 25.0 0.065
  9 93.93 6.33 313 313 1 3 25.0 0.283
  10 97.64 2.40 127 127 0 0 - -
  11 95.97 4.14 124 124 1 1 50.0 0.154
  12 95.53 4.61 246 249 1 3 25.0 0.284
  13 97.66 2.37 214 214 1 9 10.0 0.566
  14 88.97 4.71 999 1404 1 9 10.0 0.566
  15 95.32 4.84 428 428 3 6 33.3 0.030
  16 91.21 9.35 182 191 0 2 0.0 1.000
  17 96.14 3.96 311 313 2 3 40.0 0.054
  18 93.25 7.07 1087 976 5 13 27.8 0.012
  19 - - 69 - - - - -
  20 98.88 1.13 358 38 1 13 7.1 1.000
Proximal
Promoter5
LWS 97.56 2.48 1000 1000 1 16 5.9 1.000
  RH2Aα 94.80 5.38 1000 1000 10 11 47.6 < 0.001*
  RH2Aβ 91.77 8.60 1000 1000 14 19 42.4 < 0.001*
  RH2B 61.35 9.40 1000 1000 15 7 68.1 < 0.001*
  SWS1 71.49 26.37 1000 1000 18 10 64.3 < 0.001*
  SWS2A 97.19 2.87 1000 1000 11 12 47.8 < 0.001*
  SWS2B 81.96 16.31 1000 1000 4 10 28.6 0.021
3'-UTR6 LWS 93.39 6.92 189 189 1 4 20.0 0.341
  RH2Aα 94.04 6.21 438 442 4 9 30.8 0.016
  RH2Aβ 93.26 7.06 465 460 4 11 26.7 0.027
  RH2B 93.15 7.18 310 319 4 4 50.0 0.002*
  SWS1 96.74 3.33 217 242 1 3 25.0 0.284
  SWS2A 98.37 1.64 123 123 0 1 0.0 1.000
  SWS2B 95.90 4.21 124 137 4 1 80.0 < 0.001*
  1. 1 Pairwise sequence divergence between O. niloticus and M. zebra, corrected for multiple hits.
  2. 2 Actual proportion of divergent TFBSs observed for O. niloticus and M. zebra.
  3. 3 P-values for the Exact binomial test at a null proportion divergence = 8%. Tests marked with an asterisk (*) are significant after Bonferroni correction for multiple comparisons.
  4. 4 See Additional file 6 for individual counts of each TFBS identified for the CNEs.
  5. 5 See Figure 3 for individual counts of each TFBS identified for the proximal promoters.
  6. 6 See Additional file 7 for individual counts of each microRNA target site identified for the 3'-UTRs.