Table 2.
The list of reference genes for rice, defined in this and previous studies.
| Gene | Probe Set Identifier | TIGR Identifier | Description | Mean | SD | CV | MV | Source |
|---|---|---|---|---|---|---|---|---|
| 1 | Os.10676.1.S1_a_at | LOC_Os06g11170.1 | Nucleic acid binding protein | 991.9 | 210.2 | 0.21 | 0.25 | This study |
| 2 | Os.8912.1.S1_at | LOC_Os06g48970.1 | Protein kinase | 453.3 | 96.8 | 0.21 | 0.50 | This study |
| 3 | Os.6.1.S1_a_at | LOC_Os11g43900.1 | Tumor protein homolog | 13137.5 | 3692.7 | 0.28 | 0.66 | This study |
| Os.6.1.S1_x_at | Tumor protein homolog | 13870.8 | 3368.4 | 0.24 | This study | |||
| - | Os.12625.2.S1_x_at | No TIGR identifier | NA | 18285.5 | 4473.7 | 0.24 | - | This study |
| 4 | Os.12237.2.S1_a_at | LOC_Os06g47230.1 | Expressed protein | 18251.2 | 4481.0 | 0.25 | 0.30 | This study |
| Os.12237.1.S1_a_at | Expressed protein | 22019.9 | 5294.2 | 0.24 | This study | |||
| 5 | Os.46231.2.S1_x_at | LOC_Os03g46770.1 | RNA-binding protein | 17176.5 | 4280.7 | 0.25 | 0.68 | This study |
| Os.46231.1.S1_a_at | RNA-binding protein | 22461.1 | 5636.0 | 0.25 | This study | |||
| 6 | Os.6860.1.S1_at | LOC_Os11g21990.1 | Eukaryotic initiation factor 5C | 6969.6 | 1967.0 | 0.28 | 0.54 | This study |
| 7 | Os.7945.1.S1_at | LOC_Os07g34589.1 | Translation factor SUI1 | 24678.2 | 7030.8 | 0.28 | 0.61 | This study |
| 8 | Os.12409.1.S1_at | LOC_Os07g02340.1 | Expressed protein | 11392.3 | 3488.8 | 0.31 | 0.44 | This study |
| 9 | Os.37924.1.S1_x_at | LOC_Os11g26910.1 | SKP1-like protein 1A | 8488.5 | 2713.8 | 0.32 | 0.85 | This study |
| 10 | Os.12382.1.S1_at | LOC_Os12g32950.1 | Membrane protein | 6550.4 | 2258.4 | 0.34 | 0.59 | This study |
| 11 | Os.8092.1.S1_at | LOC_Os05g48960.1 | Splicing factor U2af | 4051.7 | 1403.7 | 0.35 | 0.49 | This study |
| 12 | Os.12151.1.S1_at | LOC_Os06g43650.1 | Expressed protein | 4504.6 | 1581.7 | 0.35 | 0.39 | This study |
| 13 | AFFX-Os-actin-3_s_at | LOC_Os03g50890.1 | Actin | 9556.3 | 5719.5 | 0.60 | 0.97 | [7]; commonly used reference gene |
| 14 | Os.11355.1.S1_at | LOC_Os05g36290.1 | Actin1 | 1842.8 | 1471.3 | 0.80 | 0.79 | [7]; commonly used reference gene |
| 15 | Os.9504.1.S1_at | LOC_Os07g38730.1 | Alpha-tubulin | 5400.3 | 3466.6 | 0.64 | 0.76 | [7]; commonly used reference gene |
| 16 | Os.10139.1.S1_s_at | LOC_Os06g46770.1 | Polyubiquitin | 15085.3 | 6524.3 | 0.43 | 0.47 | [7]; commonly used reference gene |
| 17 | Os.7899.1.S1_at | LOC_Os02g16040.1 | Ubiquitin | 2598.8 | 1135.4 | 0.44 | 0.63 | [20]; commonly used reference gene |
| 18 | Os.22781.1.S1_at | LOC_Os02g38920.1 | GAPDH | 11640.8 | 8346.8 | 0.72 | 1.09 | [20]; commonly used reference gene |
| 19 | Os.10158.1.S1_at | LOC_Os07g43730.1 | EF1 | 5619.9 | 2549.3 | 0.45 | 0.52 | [20]; commonly used reference gene |
| 20 | Os.10385.1.S1_at | LOC_Os03g55270.1 | TIP41-like | 482.7 | 274.5 | 0.57 | 0.42 | [7] |
| 21 | Os.5500.1.S1_s_at | LOC_Os08g23180.1 | Arabinogalactan protein | 4957.5 | 3114.1 | 0.63 | 0.90 | [22] |
| 22 | Os.12835.2.S1_a_at | LOC_Os07g42300.1 | EF1d | 6073.3 | 3003.7 | 0.49 | 0.82 | [22] |
| 23 | Os.19618.1.S1_at | LOC_Os01g39260.1 | FtsH protease | 1487.4 | 725.5 | 0.49 | 0.57 | [22] |
| 24 | Os.7952.1.S1_at | LOC_Os03g25980.1 | Nucleotide tract-binding protein | 607.8 | 241.8 | 0.40 | 0.56 | (Orthologue) [10] |
| 25 | Os.22806.1.S1_s_at | LOC_Os02g46510.1 | AP-2 complex subunit | 1550.2 | 744.5 | 0.48 | 0.64 | (Orthologue) [10] |
| 26 | Os.13910.1.S1_at | LOC_Os03g21210.1 | endo-1,4-beta-glucanase | 900.7 | 1063.3 | 1.18 | 0.72 | (Orthologue) [10] |
The gene number, Affymetrix probeset identifiers, TIGR identifiers, gene descriptions (TIGR), mean expression and standard deviation (SD) based on GC-RMA normalised data. The coefficient of variance (CV) is also indicated for each probeset/gene. The M values calculated based the QRT-PCR data; using geNORM software is also shown. Source indicates the studies from which these genes were selected.