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Table 2 Prediction of candidate genes and promoter regions for the CRISPR/Cas9 system

From: Advances in genome editing technology and its promising application in evolutionary and ecological studies

Species Gene Promoter
Total numbers Predicted numbers Ratio (%) Total numbers Predicted
numbers
Ratio (%)
Anas.platyrhynchos 15634 12753 81.57 15561 12959 83.28
Anopheles.gambiae 12810 9079 70.87 12810 9866 77.02
Apis.mellifera 10675 7644 71.61 10663 6096 57.17
Arabidopsis.thaliana 27416 12978 47.34 27416 8866 32.34
Bombyx.mori 14623 12087 82.66 14622 11679 79.87
Bos.taurus 19994 14657 73.31 19994 16138 80.71
Caenorhabditis.elegans 20532 9759 47.53 20532 10270 50.02
Camponotus.floridanus 16705 10804 64.68 16605 9969 60.04
Canis.familiaris 19856 14489 72.97 19856 16172 81.45
Columba.livia 16652 12223 73.4 16637 14177 85.21
Crassostrea.gigas 26089 15767 60.44 26081 12811 49.12
Danio.rerio 26245 16500 62.87 26244 13476 51.35
Drosophila.melanogaster 13937 9061 65.01 13937 8825 63.32
Equus.caballus 20449 14108 68.99 20447 16520 80.79
Gallus.gallus 16516 12305 74.5 16516 14159 85.73
Glycine.max 42909 18433 42.96 42909 13433 31.31
Harpegnathos.saltator 18429 9741 52.86 18384 11617 63.19
Heliconius.melpomene 12669 10673 84.25 12663 10146 80.12
Heter.glaber 22558 14949 66.27 22556 16823 74.58
Macaca.fascicularis 21283 15322 71.99 21278 16712 78.54
Macaca.mulatta 21905 15115 69 21894 17238 78.73
Oryza.sativa 35679 10223 28.65 35679 15028 42.12
Schistosoma.mansoni 10772 7117 66.07 10769 9206 85.49
Sus.scrofa 21630 13560 62.69 21624 15960 73.81
Tupaia.belangeri 15471 12741 82.35 15471 12906 83.42
Xenopus.tropicalis 18442 14188 76.93 18431 14048 76.22
  1. Note: 26 organisms were selected for in silico prediction of CRISPR/Cas9 candidate editable genes and promoter regions. Promoter regions are defined as the 2 kb region upstream and downstream of genes. A N20-NGG sequence pattern is used to identify the CRISPR/Cas9 target sits. Then, these target sites are BLAST against both gene and promoter regions to eliminate off-target sites using strict criteria, where a candidate editable site is defined when only the seed region (12 bps adjacent to PAM) is unique.
  2. BLAST, Basic Local Alignment Search Tool; CRISPR, Clustered Regularly Interspaced Short Palindromic Repeats; PAM, Protospacer Adjacent Motif.