Table 1. Primer properties and in silico evaluation.
| Gene a (Gene ID) | Gene full name | Acc # | isoformsb | PGsc (#) | Primer sequence | Exon | Location | amplicon size (bp) | mFOLD at Ta d (kcal/mol) | |||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| All | D | PC | PCD | |||||||||
| ACTB (ID: 60) |
actin beta | NM_001101 | 19 | 9 | 11 | 5 | 18 | F 5'-CACCAACTGGGACGACAT-3' | 3 | 420–437 | 189 | -1.43 |
| R 5'-ACAGCCTGGATAGCAACG-3' | 4 | 591–608 | ||||||||||
| B2M (ID: 567) |
beta-2-microglobulin | NM_004048 | 14 | 7 | 3 | 3 | 0 | F 5'-TAGCTGTGCTCGCGCT-3' | 1 | 50–65 | 224 | -0.22 |
| R 5'-AGACCAGTCCTTGCTGAAAGA-3' | 2 | 253–273 | ||||||||||
| GAPDH (ID: 2597) |
glyceraldehyde-3-phosphate dehydrogenase | NM_002046 | 11 | 10 | 6 | 5 | 64 | F 5'-GGATTTGGTCGTATTGGG-3' | 3 | 104–121 | 205 | 0.13 |
| R 5'-GGAAGATGGTGATGGGATT-3' | 4 | 290–308 | ||||||||||
| GUSB (ID: 2990) |
glucuronidase beta | NM_000181 | 14 | 5 | 2 | 2 | 18 | F 5'-GGGCCGTTGTTGTGGG-3' | 1 | 168–183 | 218 | -3.60 |
| R 5'-TCATTGAAGCTGGAGGGAAC-3' | 2 | 366–385 | ||||||||||
| HMBS (ID: 3145) |
hydroxymethylbilane synthase | NM_000190 | 26 | 16 | 11 | 8 | 0 | F 5'-CCATGTCTGGTAACGGCA-3' | 1 | 156–173 | 142 | 0.47 |
| R 5'-GGGTACGAGGCTTTCAATGT-3' | 3 | 278–297 | ||||||||||
| HPRT1(15) (ID: 3251) |
hypoxanthine phosphoribosyltransferase 1 | NM_000194 | 3 | 3 | 1 | 1 | 3 | F 5'-GACCAGTCAACAGGGGACAT-3' | 4 | 489–508 | 132 | 0.73 |
| R 5'-CCTGACCAAGGAAAGCAAAG-3' | 6 | 601–620 | ||||||||||
| PPIA(11) (ID: 5478) |
peptidylprolyl isomerase A | NM_021130 | 10 | 6 | 5 | 4 | 79 | F 5'-GTCAACCCCACCGTGTTCTT-3' | 1 | 93–112 | 97 | -1.20 |
| R 5'-CTGCTGTCTTTGGGACCTTGT-3' | 2 | 169–189 | ||||||||||
| PUM1 (ID: 9698) |
pumilio RNA binding family member 1 | NM_001020658 | 23 | 9 | 13 | 8 | 0 | F 5'-CAGGACATTCACAGACACCA-3' | 14 | 2371–2390 | 196 | -2.19 |
| R 5'-CGCAAACGAGAGGAAGAGA-3' | 15 | 2548–2566 | ||||||||||
| RPL13A (ID: 23521) |
ribosomal protein L13a | NM_012423 | 14 | 9 | 3 | 2 | 25 | F 5'-GGATAAGAAACCCTGCGACAA-3' | 1 | 25–45 | 187 | -2.46 |
| R 5'-GCCAGAAATGTTGATGCCTTC-3' | 3 | 191–211 | ||||||||||
| RPLP0(11) (ID: 6175) |
ribosomal protein lateral stalk subunit P0 | NM_053275 | 27 | 10 | 12 | 5 | 12 | F 5'-CAGCAGGTGTTCGACAATGG-3' | 6 | 805–824 | 214 | -0.91 |
| R 5'-GTGGGAAGGTGTAATCCGTCT-3' | 7 | 998–1018 | ||||||||||
| TBP (ID: 6908) |
TATA-box binding protein | NM_003194 | 8 | 6 | 7 | 5 | 0 | F 5'-ATCAGAACAACAGCCTGCC-3' | 2 | 284–302 | 113 | -0.13 |
| R 5'-GGTCAGTCCAGTGCCATAAG-3' | 3 | 377–396 | ||||||||||
| TFRC (ID: 7037) |
transferrin receptor | NM_003234 | 15 | 2 | 4 | 2 | 0 | F 5'-CTGGCTCGGCAAGTAGATG-3' | 3 | 356–374 | 234 | 0.00 |
| R 5'-TGCCAGTCTCTCACACTCA-3' | 4 | 571–589 | ||||||||||
| YWHAZ (ID: 7534) |
tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein zeta | NM_145690 | 23 | 14 | 18 | 11 | 11 | F 5'-TCATCTTGGAGGGTCGTCT-3' | 2 | 381–399 | 180 | -0.04 |
| R 5'-GACTTTGCTCTCTGCTTGTG-3' | 3 | 541–560 | ||||||||||
| ENG (ID: 2022) |
endoglin | NM_001114753 | 5 | 2 | 3 | 2 | 0 | F 5'-CCCAAAACCGGCACCCTCA-3' | 12 | 238 | ||
| R 5'-TGGGGGAACGCGTGTGC-3' | 14/15 | |||||||||||
| NT5E (ID: 4907) |
5'-nucleotidase ecto | NM_002526 | 5 | 1 | 5 | 1 | 0 | F 5'-GGCTGCTGTATTGCCCTTTG-3' | 7 | 175 | ||
| R 5'-TACTCTGTCTCCAGGTTTTCGG-3' | 8 | |||||||||||
| THY1 (ID: 7070) |
Thy-1 cell surface antigen |
NM_006288 |
10 | 8 | 5 | 3 | 0 | F 5'-AGCATCGCTCTCCTGCTAAC-3' | 2 | 230 | ||
| R 5'-CTGGTGAAGTTGGTTCGGGA-3' | 3 | |||||||||||
Details of primers used in this manuscript.
aPreviously published primer sets are referenced. All others have been newly designed.
bAccording to Ensemble.com (D = detectable with designed primers; PC = Protein Coding; PCD = Detectable PC with designed primers)
cPGs = Known pseudogenes. According to NCBI Gene database
dIn case of multiple possible structures the most negative value is given; Bold = in primer annealing region 3’/5’.