Skip to main content

Table 1 Details of oligonucleotide sequences of primers and probes used to quantify hypoxia inducible factor 1α (HIF-1α) mRNA splice variants by real-time quantitative reverse transcription PCR assays

From: Hypoxia inducible factor 1α gene (HIF-1α) splice variants: potential prognostic biomarkers in breast cancer

Oligonucleotide

Position (exon)

5' Position

Sequence (5' to 3')

Primer/probe concentrations (nM)

Amplicon size

 

5

518

F: GTACCCTAACTAGCCGAGGAAGAA

300

 
 

6

597

R: GTGAATGTGGCCTGTGCAGT

300

 

HIF-1α (total)

5 to 6 junction

544

P: ATGAACATAAAGTCTGCAACATGGAAGGTATTG

200

80 bp

 

1

17

F: GCGCGAACGACAAGAAAAATAG

50

 
 

2

138

R: TGGCAACTGATGAGCAAGCT

300

 

HIF-1α TAG

2

74

P: ATGCAGCCAGATCTCGGCGAAGTAAA

200

122 bp

 

13 to 15 junction

2,182

F: TCACTTTTTCAAGCAGTAGGAATTATTTAG

600

 
 

15

2,330

R: TAATTCTTCACCCTGCAGTAGGTTT

600

 

HIF-1α 736

15

2,260

P: TGACCAGTTATGATTGTGAAGTTAATGCTCCTATACAAGG

200

149 bp

 

11

1,566

F: TGTGGATAGTGATATGGTCAATGAATT

300

 
 

13

1,699

R: TAGTATCTTTGGATTTAGTTCTTCCTCAGG

300

 

HIF-1α 557

11 to 13 junction

1,642

P: AAGCAAACCCATTTTCTACTCAGAACTACA

200

134 bp

 

10

1,490

F: AGACACCTAGTCCTTCCGATGG

600

 
 

13

1,580

R: AAGCTAGTATCTTTGGATTTAGTTCTTCCT

600

 

HIF-1α 516

10 to 13 junction

1,513

P: AGCACTAGACAAAGTTCACCTGAGAACTACAGT

200

91 bp

  1. The mRNA sequences of four alternatively spliced variants (HIF-1α TAG, HIF-1α 736, HIF-1α 557and HIF-1α 516) were constructed using the human HIF-1α transcript sequence NM_001530. bp = base pairs; F = forward primer; P = oligonucleotide probe; R = reverse primer.