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Table 3 Prediction of candidate genes and promoter regions for the TALEN 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

15105

96.62

15561

14523

93.33

Anopheles.gambiae

12810

10760

84

12810

11547

90.14

Apis.mellifera

10675

7718

72.3

10663

6778

63.57

Arabidopsis.thaliana

27416

21937

80.02

27416

24224

88.36

Bombyx.mori

14623

13592

92.95

14622

13303

90.98

Bos.taurus

19994

18992

94.99

19994

19445

97.25

Caenorhabditis.elegans

20532

10634

51.79

20532

11098

54.05

Camponotus.floridanus

16705

12882

77.11

16605

12452

74.99

Canis.familiaris

19856

18786

94.61

19856

19164

96.51

Columba.livia

16652

14719

88.39

16637

15601

93.77

Crassostrea.gigas

26089

22773

87.29

26081

23249

89.14

Danio.rerio

26245

23180

88.32

26244

24295

92.57

Drosophila.melanogaster

13937

10281

73.77

13937

11241

80.66

Equus.caballus

20449

18631

91.11

20447

19721

96.45

Gallus.gallus

16516

14912

90.29

16516

15445

93.52

Glycine.max

42909

36403

84.84

42909

40997

95.54

Harpegnathos.saltator

18429

12766

69.27

18384

13933

75.79

Heliconius.melpomene

12669

11049

87.21

12663

10595

83.67

Heter.glaber

22558

21214

94.04

22556

21839

96.82

Macaca.fascicularis

21283

20405

95.87

21278

20846

97.97

Macaca.mulatta

21905

20248

92.44

21894

21292

97.25

Oryza.sativa

35679

28939

81.11

35679

31818

89.18

Schistosoma.mansoni

10772

9750

90.51

10769

9961

92.5

Sus.scrofa

21630

19611

90.67

21624

20321

93.97

Tupaia.belangeri

15471

14883

96.2

15471

14716

95.12

Xenopus.tropicalis

18442

17460

94.68

18431

17860

96.9

  1. Note: 26 organisms were selected for in silico prediction of TALEN 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; TALEN, Transcription Activator-Like Effector Nuclease.
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