Skip to main content

Table 1 Sequence of oligonucleotides used either to prepare double stranded DNA for EMSA or for RT-PCR and PCR:

From: An ABRE-binding factor, OSBZ8, is highly expressed in salt tolerant cultivars than in salt sensitive cultivars of indica rice

Name

Sequence

Size

Use

1. ABRE5

5'AGCTTGCCGGACACGTGGCGCTCTAG3'

26 mer

Annealed with ABRE3 to form 1X ABRE used in EMSA as probe or competitor

2. ABRE3

5'CTAGAGCGCCACGTGTCCGGCAAGCT3'

26 mer

ABRE probe in EMSA

3.4X ABRE

5'CCTCGAAAGCTTGCCACGTGGCGCCACGTGGCGCCACGTGGCGCCACGTGGATGACGCACAATCCCAC3'

68 mer

Annealed with 17 LS and filled in by Klenow to form double stranded DNA used as competitor in EMSA

4.2X ABRC

5'GTCAGAAAGCTTGCCACGTGGCTGCAGTG CCATTGCCACCGGATCAGCCACGTGGCTCCA GTGCTTGCCACCGGATGACGCACAATCCCAC3'

92 mer

Annealed with 17 LS and filled in by Klenow to form double stranded DNA and used as competitor in EMSA

5. 4X DRE

5'CCACTTGAAGCTTACTACCGACATGAGTTCACTACCGACATGAGTTCACTACCGACATGACGCACAATCCCAC3'

72 mer

Annealed with 17 LS and filled in by Klenow to form double stranded DNA and used as competitor in EMSA.

6. 2X ERE

5'AGCAAGCTTTTTTATTCCCAACAATAGAAAGTCTTGTTTTATTCCCAACAATAGAAAGTCTT GATGACGCACAATCCCAC 3'

80 mer

Annealed with 17 LS and filled in by Klenow to form double stranded DNA and used as competitor in EMSA

7. 17 LS

5'GTGGGATTGTGCGTCAT3'

17 mer

Preparation of ds Competitor

8.OSBZ85

5'TGTAGATCTCAACAATGGGAAATGACGAAGCTGTAGTTACTCA3'

43 mer

Amplification of OSBZ8 cDNA by RT-PCR

9.OSBZ83

5'GAGAGATCTTTACTTGAGGCTACAGCATCAGTCGC3'

36 mer

Amplification of OSBZ8 cDNA by RT-PCR

10.OSBZ85A

5'GGCGTGGAAACTGGTGGAGCT3'

21 mer

For sequencing of cDNA

11.OSBZ83A

5'CTTGAGAATTCTAAGCTCCACCAGTTTCCACGCC3'

34 mer

Amplification of 5'end of OSBZ8

12. RAB5

5'CGACAAGCTTCACGCGCACAGTACAC ACACAT-3'

32 mer

Amplification of Rab16A promoter and full length by PCR from genomic DNA

13. RAB3A

5'TAGAGCTCGGATCCTCTAGACTGCAGT CATGCTGTGGTGTGCAAGCAGG-3'

49 mer

Amplification of Rab16A promoter by PCR from genomic DNA

14. RAB3B

5'ATAGAGCTCTGGATCCTCAGTGCTGGCCGGGCAGCTT3'

37 mer

Amplification of Rab16A full length by PCR from genomic DNA