Table 2 Cadmium-upregulated cis-NATs identified in roots by ssRNA-Seq analysis
Root | ||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Antisense transcript | RAP | |||||||||||||||
Fold Change | RPKM | Fold Change | RPKM | |||||||||||||
Cd_50 μM | Control | Cd_50 μM | Cd_50 μM | Control | Cd_50 μM | |||||||||||
Transcript | Length (bp) | 1 h | 12 h | 24 h | 0 h | 1 h | 12 h | 24 h | 1 h | 12 h | 24 h | 0 h | 1 h | 12 h | 24 h | RAP Description |
Os02t0108500-01 | 985 | 38.5 | 233.6 | 204.4 | 1.6 | 99.9 | 610.9 | 534.6 | 1 | 1.6 | 2.6 | 0.0 | 0.0 | 0.6 | 1.6 | Non-protein coding transcript |
Os02t0181200-00 | 393 | 156 | 136.9 | 102.7 | 4.6 | 868.2 | 761.4 | 571.0 | 1 | 1 | 1 | 0.0 | 0.0 | 0.0 | 0.0 | Hypothetical protein |
Os01t0949800-01 | 857 | 9.1 | 49.5 | 60.3 | 0.0 | 8.1 | 48.5 | 59.3 | 0.1 | 0.1 | 0.1 | 455.2 | 42.7 | 32.2 | 35.9 | OsGSTU36 |
Os11t0474100-01 | 776 | 1.8 | 19.7 | 42.7 | 0 | 0.8 | 18.71 | 41.7 | 0.3 | 0.7 | 0.9 | 9.26 | 2.56 | 6.34 | 8.54 | Conserved hypothetical protein |
Os05t0568000-01 | 2355 | 16.9 | 89.2 | 40.4 | 0.0 | 15.9 | 88.2 | 39.4 | 3.6 | 1.3 | 0.8 | 91.3 | 331.7 | 116.3 | 73.0 | Fatty acid elongase (FAE)1 |
Os01t0795600-01 | 555 | 1.2 | 20.4 | 38.5 | 0.0 | 0.2 | 19.4 | 37.5 | 10.6 | 43.8 | 48.6 | 2.5 | 36.2 | 153.4 | 170.2 | Conserved hypothetical protein |
Os04t0407500-00 | 913 | 2.4 | 57.4 | 34.5 | 0.0 | 1.4 | 56.4 | 33.5 | 0.5 | 0.7 | 0.5 | 3.3 | 1.1 | 1.8 | 1.3 | Unknown protein |
Os09t0500151-00 | 492 | 3.5 | 31.7 | 33.8 | 0 | 2.52 | 30.7 | 32.75 | 0.7 | 0.7 | 0.7 | 0.41 | 0 | 0 | 0 | Hypothetical genes |
Os01t0661750-00 | 354 | 1.3 | 28.6 | 31.5 | 0.6 | 1.1 | 43.7 | 48.1 | 1 | 1 | 1 | 0.0 | 0.0 | 0.0 | 0.0 | Hypothetical conserved gene |
Os05t0182000-01 | 843 | 1.2 | 9.6 | 23.7 | 0.0 | 0.2 | 8.6 | 22.7 | 0.6 | 0.6 | 0.4 | 5.2 | 2.5 | 2.6 | 1.7 | Conserved hypothetical protein |
Os12t0153700-00 | 1119 | 0.8 | 6.2 | 22.1 | 0.71 | 0.44 | 9.52 | 36.81 | 1 | 1 | 1 | 0 | 0 | 0 | 0 | Peptidase aspartic, catalytic domain containing protein |
Os11t0536400-00 | 165 | 10 | 17.3 | 19.1 | 0 | 9.03 | 16.32 | 18.11 | 1 | 1 | 1 | 0 | 0 | 0 | 0 | Non-protein coding transcript |
Os07t0545800-01 | 2161 | 1.1 | 18.3 | 18.6 | 0 | 0.11 | 17.28 | 17.56 | 6.8 | 5.2 | 3.6 | 26.5 | 186.02 | 141.02 | 97.53 | GRAS domain family protein |
Os11t0429433-00 | 687 | 1 | 10.2 | 17.5 | 0 | 0 | 9.2 | 16.46 | 0.6 | 0.7 | 0.9 | 7.84 | 4.34 | 4.77 | 7 | Hypothetical gene |
Os08t0183700-00 | 276 | 1.5 | 6.1 | 17.5 | 0 | 0.45 | 5.09 | 16.48 | 1 | 1 | 1 | 0 | 0 | 0 | 0 | – |
Os10t0545800-01 | 1162 | 1.1 | 9.9 | 17.4 | 0 | 0.11 | 8.87 | 16.44 | 9.7 | 20.8 | 16.2 | 7.9 | 85.77 | 184.37 | 143.03 | Nucleic acid-binding, OB-fold domain containing protein |
Os01t0783600-01 | 866 | 8.5 | 24.7 | 17.4 | 0.5 | 11.5 | 35.0 | 24.5 | 0.5 | 0.3 | 0.2 | 18.7 | 8.0 | 5.4 | 3.0 | Frataxin |
Os08t0153750-00 | 472 | 1.7 | 11.5 | 16.8 | 4.23 | 7.63 | 59.28 | 86.72 | 1 | 1 | 1 | 0 | 0 | 0 | 0 | Hypothetical protein |
Os05t0142600-00 | 246 | 1 | 2.4 | 14.7 | 0.0 | 0.0 | 1.4 | 13.7 | 3.5 | 29.2 | 32.2 | 4.1 | 16.7 | 146.6 | 162.2 | Hypothetical protein |
Os02t0142060-01 | 877 | 1.3 | 8.5 | 14.6 | 0.0 | 0.3 | 7.5 | 13.6 | 0.3 | 0.4 | 0.3 | 3.2 | 0.4 | 0.7 | 0.2 | Conserved hypothetical protein |
Os12t0219300-00 | 303 | 2.3 | 8.2 | 13.9 | 1.98 | 5.73 | 23.57 | 40.31 | 1 | 1 | 1.9 | 0 | 0 | 0 | 0.86 | – |
Os03t0227500-01 | 474 | 1 | 8.4 | 13.6 | 0.0 | 0.0 | 7.4 | 12.6 | 0.9 | 0.7 | 0.9 | 3.4 | 2.9 | 2.0 | 2.7 | Hypothetical protein |
Os03t0231400-01 | 781 | 2.4 | 13 | 12.9 | 2.6 | 7.6 | 45.1 | 44.8 | 0.4 | 1.1 | 1.1 | 3.6 | 0.8 | 3.9 | 4.0 | Hypothetical protein |
Os05t0133900-02 | 2694 | 2.2 | 5.2 | 12.3 | 0.1 | 1.3 | 4.6 | 12.1 | 0.7 | 0.5 | 0.6 | 13.2 | 8.9 | 5.8 | 7.4 | DNA methyl transferase 106 |
Os01t0159800-01 | 1473 | 0.9 | 5.4 | 12.3 | 0.3 | 0.1 | 5.9 | 14.6 | 0.7 | 2.3 | 3.1 | 8.1 | 5.1 | 19.6 | 27.0 | DNA binding protein (bHLH) |
Os01t0223600-01 | 1730 | 1 | 12 | 11.4 | 0.2 | 0.3 | 13.7 | 13.0 | 0.6 | 0.3 | 0.3 | 42.9 | 25.3 | 13.8 | 11.3 | Pto kinase interactor 1-like protein |
Os05t0194500-01 | 1510 | 1.3 | 10.5 | 11.1 | 0.0 | 0.3 | 9.5 | 10.1 | 2.2 | 9.2 | 9.3 | 3.2 | 8.2 | 37.3 | 37.6 | DNA binding protein (NAM) |
Os03t0693400-01 | 787 | 1.6 | 6.1 | 10.9 | 0.0 | 0.6 | 5.1 | 9.9 | 0.7 | 0.5 | 0.8 | 33.7 | 23.5 | 17.9 | 27.6 | Unknown protein |
Os01t0955400-00 | 453 | 1 | 4.4 | 10.5 | 0.0 | 0.0 | 3.4 | 9.5 | 15.8 | 32.5 | 35.1 | 0.0 | 14.8 | 31.5 | 34.1 | OsCML23 |
Os09t0392700-01 | 844 | 1 | 2.8 | 10.4 | 0 | 0 | 1.8 | 9.39 | 0.6 | 1 | 1.9 | 2.84 | 1.32 | 2.77 | 6.16 | Hypothetical conserved gene |
Os03t0180100-01 | 885 | 1.3 | 9.1 | 10.3 | 0.0 | 0.3 | 8.1 | 9.3 | 1.8 | 1.3 | 1 | 12.9 | 23.7 | 17.3 | 13.1 | Unknown protein |
Os05t0553900-00 | 312 | 1 | 3.3 | 10.2 | 0.0 | 0.0 | 2.3 | 9.2 | 1 | 1 | 1.8 | 0.0 | 0.0 | 0.0 | 0.8 | – |
Os12t0433066-00 | 822 | 1.6 | 9.6 | 9.8 | 1.46 | 2.87 | 22.5 | 23.08 | 0.8 | 0.9 | 1 | 0.49 | 0.15 | 0.28 | 0.47 | Hypothetical gene |
Os06t0147100-01 | 698 | 2.4 | 11.4 | 9.5 | 0.57 | 2.84 | 16.94 | 13.96 | 0.4 | 1.4 | 2.1 | 104.06 | 37.52 | 143.4 | 220.61 | Conserved hypothetical protein |
Os11t0121000-00 | 947 | 1.4 | 10.9 | 9.4 | 0 | 0.39 | 9.89 | 8.37 | 1.5 | 1.4 | 1.6 | 2.95 | 4.98 | 4.57 | 5.35 | Hypothetical conserved gene |
Os06t0181800-00 | 1174 | 1 | 8.7 | 8.9 | 0 | 0 | 7.68 | 7.86 | 3.9 | 6.7 | 6.9 | 2.04 | 10.78 | 19.25 | 20.03 | Unknown protein |
Os05t0121600-00 | 985 | 1.1 | 5 | 8.9 | 0.0 | 0.1 | 4.0 | 7.9 | 1.3 | 0.9 | 0.8 | 111.0 | 140.9 | 99.8 | 88.5 | AP2/EREBP |
Os08t0104100-01 | 998 | 1.5 | 6.6 | 8.8 | 0 | 0.5 | 5.63 | 7.81 | 0.6 | 0.3 | 0.2 | 53.78 | 33.45 | 14.31 | 12.63 | Conserved hypothetical protein |
Os05t0209500-01 | 685 | 1 | 6 | 8.8 | 0.0 | 0.0 | 5.0 | 7.8 | 1.3 | 1.7 | 2 | 16.3 | 21.9 | 27.7 | 33.2 | Conserved hypothetical protein |
Os02t0819500-04 | 1080 | 1 | 13.8 | 8.8 | 0.0 | 0.0 | 12.8 | 7.8 | 0.6 | 0.6 | 0.8 | 56.7 | 31.5 | 33.7 | 45.0 | Cysteine-type peptidase |
Os08t0474600-01 | 1707 | 1 | 9.2 | 8.7 | 0 | 0 | 8.16 | 7.69 | 0.3 | 0.6 | 0.5 | 9.59 | 2.18 | 5.01 | 4.26 | Heat shock protein DnaJ |
Os07t0561650-00 | 504 | 1 | 6.1 | 8.5 | 0 | 0 | 5.11 | 7.48 | 1 | 1 | 1 | 0 | 0 | 0 | 0 | – |
Os09t0442600-01 | 2186 | 1.3 | 8 | 8.4 | 0 | 0.28 | 7.02 | 7.37 | 1.2 | 1.1 | 1.2 | 47.37 | 55.47 | 52.43 | 57.36 | Plastid (P)ppGpp synthase |
Os11t0307600-01 | 1013 | 1.3 | 7.5 | 8.3 | 0 | 0.25 | 6.47 | 7.31 | 0.3 | 0.2 | 0.3 | 12.61 | 3.31 | 2.2 | 2.69 | – |
Os01t0771200-01 | 963 | 0.5 | 4.7 | 8.3 | 1.5 | 0.1 | 10.6 | 19.4 | 1.3 | 2.3 | 2.7 | 28.6 | 37.5 | 65.7 | 80.0 | Mal d 1-associated protein |
Os06t0133400-01 | 490 | 1 | 5.3 | 8.2 | 0 | 0 | 4.3 | 7.16 | 16.8 | 18.2 | 23.6 | 17.92 | 317.62 | 343.09 | 445.26 | Conserved hypothetical protein |
Os01t0118700-01 | 2087 | 0.8 | 5.5 | 8.2 | 0.2 | 0.0 | 5.5 | 8.8 | 2.9 | 2.6 | 2.8 | 24.0 | 71.3 | 63.3 | 68.9 | HGA4 |
Os06t0580100-02 | 2283 | 1.1 | 6 | 8.1 | 0 | 0.05 | 5.03 | 7.11 | 0.3 | 0.4 | 0.5 | 46.67 | 12.45 | 18.15 | 23.85 | Hypothetical gene |
Os01t0908200-01 | 1446 | 1.1 | 5.5 | 8.1 | 0.0 | 0.1 | 4.5 | 7.1 | 1 | 0.3 | 0.4 | 60.0 | 58.9 | 19.5 | 21.4 | Zinc finger (TAZ-type) |
Os09t0251900-00 | 384 | 1 | 7.7 | 7.8 | 0 | 0 | 6.71 | 6.77 | 1 | 1 | 1 | 0 | 0 | 0 | 0 | – |