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Table 2 Examples of gene families that are known to be associated with traits in rice and their TEs insertions numbers

From: Domestication of rice has reduced the occurrence of transposable elements within gene coding regions

PFAMa   Cultivated rice Wild rice
  O.sat O.ind O.gla O.ruf O.niv O.bar
PF08323 Glycosyl Transferaes family 5 13b 8c 21d 9 8 16 9 11 17 12 15 19 14 15 15 17 12 17
PF00646 F-box protein 56 21 51 56 29 48 33 4 22 26 153 26 23 113 24 27 106 17
PF03254 Xyloglucan fucosyltransferase 21 6 17 15 12 19 18 7 15 5 43 3 3 41 2 1 46 1
PF00194 Carbonic anhydrase 4 2 1 0 1 1 2 1 2 6 19 2 4 33 3 2 15 3
PF04616 Glycoside Hydrolase family 43 2 1 3 6 5 4 4 1 2 4 7 2 4 7 2 7 6 3
PF01486 MADS-box family 0 0 1 1 0 1 0 0 1 2 4 1 2 4 1 2 4 1
PF01734 patatin protein family 3 5 9 9 5 8 4 3 6 7 21 4 9 34 3 5 12 3
PF03083 Flavin-containing monooxygenase 2 3 1 3 1 2 2 1 2 2 11 0 3 7 0 5 8 1
PF00743 Flavin-containing monooxygenase 10 2 3 8 1 3 1 1 0 4 18 1 4 14 1 3 12 0
PF05691 Glycoside hydrolase family 36 7 2 9 11 2 9 7 2 9 7 4 9 9 6 7 7 3 9
PF00141 Haem peroxidase 1 0 1 4 0 1 0 0 1 2 5 1 4 5 3 3 5 2
  1. aThe PFAM is a large collection of protein families, each represented by multiple sequence alignments and hidden Markov models
  2. TEs insertions numbers in
  3. b2kb upstream
  4. cgene regions and
  5. d2kb downstream of a gene