Table 1 Selected candidate reference genes used in the Real-time RTqPCR assay indicating name, GenBank accession number or reference, function, annealing temperature (Ta), PCR efficiency, regression coefficient and primers used for the expression study.
From: Evaluation of suitable reference genes for gene expression studies in bovine muscular tissue
Gene | Full gene name | GenBank accession number or reference | Function | Ta | PCR efficiency | Regression coefficient (r2) | Forward primer | Reverse primer |
|---|---|---|---|---|---|---|---|---|
18S | 18S ribosomal RNA | DQ222453.1 | Ribosomal eukaryotic small subunit | 57°C | 101.1% | 0.983 | CGGCTACCACATCCTATGAA | TGGAGCTGGAATTACCGCGG |
ACTB | β-actin | Goossens et al., 2005 | Cytosqueletal structural protein | 59°C | 97.0% | 0.982 | CCTCACGGAACGTGGTTACA | TCCTTGATGTCACGCACAATTT |
B2M | β-2-microglobulin | NM_173893.2 | Beta-chain of major histocompatibility complex class I molecules | 59°C | 99.1% | 0.981 | AGTAAGCCGCAGTGGAGGT | CGCAAAACACCCTGAAGACT |
CASC3 | cancer susceptibility candidate 3 | XM_610173.2 | Linked to development of breast cancer | 57°C | 97.8% | 0.95 | TACATCCCCACCAGACACC | GGAGCAGAAAAGTAAGTAGGAGCA |
EEF1A2 | eukaryotic translation elongation factor 1 alpha 2 | BC108110.1 | Translation elongation factor activity | 59°C | 99.3% | 0.972 | GCAGCCATTGTGGAGATG | ACTTGCCCGCCTTCTGTG |
GAPDH | glyceraldehyde-3-phosphate dehydrogenase | NM_001034034.1 | Oxidoreductase in glycolysis and gluconeogenesis | 59°C | 99.6% | 0.979 | TGCACCACCAACTGCTTGGC | GGCATGGACGGTGGTCATGAG |
HMBS | hydroxymethylbilane synthase | BC112573.1 | Heme synthesis, porphyrin metabolism | 59°C | 95.4% | 0.988 | CTTTGGAGAGGAATGAAGTGG | AATGGTGAAGCCAGGAGGAA |
RPII | polymerase (RNA) II (DNA directed) polypeptide A (220 kD) | NM_000937.2 | DNA-directed RNA polymerase II subunit | 59°C | 103.6% | 0.988 | ACCCACTAGCCCCACCTACT | GCTCACCCTCAGTTCTCGTC |
SF3A1 | splicing factor 3 subunit 1 | XM_878187.1 | Structural component of the splicing system | 57°C | 95.0% | 0.981 | GCGGGAGGAAGAAGTAGGAG | TCAGCAAGAGGGACACAAA |
UBC | Ubiquitin C | Chitko-McKown et al, 2004 | Protein degradation | 59°C | 103.4% | 0.976 | TCCCTACCTGCATCATGTGC | GGAATTTGGGCCAGTGCTC |