Motif Name / Sequence / Function / Methylation status of individual plants
Year / Ra1 / Ra2 / Ea1 / Ea2 / Rb1 / Rb2 / Eb1 / Eb2 / Rc1 / Rc2 / Ec1 / Ec2
ARE / TGGTTT / cis-acting regulatory element essential for the anaerobic induction / 2007 /
2008 /
CAAT-box / CAAAT / common cis-acting element in promoter and enhancer regions / 2007 / /
2008 / /
CATT-motif / CATT / part of a light responsive element / 2007 / / / /
2008 / / / / /
CCAAT-box / CAACGG / MYBHv1 binding site / 2007
2008
CGTCA-motif / CGTCA / cis-acting regulatory element involved in the MeJA-responsiveness / 2007 / / / /
2008 / / / /
LTR / CCGAAA / cis-acting element involved in low-temperature responsiveness / 2007 / / / / / / / /
2008 / / / / / / / / / / /
TATA-box / TTTTA / core promoter element around / 2007
2008
TC-rich repeats / ATTTTCTTCA / cis-acting element involved in defense and stress responsiveness / 2007 / / / /
2008 / / / /
TCCC-motif / TCTCCCT / part of a light responsive element / 2007 / / /
2008 / / /

Table-3- Methylation status of regulatory motifs

HMGR- 288 bp

HMGS-229bp

Motif Name / Sequence / Function / Methylation status of individual plants
Year / Ra1 / Ra2 / Ea1 / Ea2 / Rb1 / Rb2 / Eb1 / Eb2 / Rc1 / Rc2 / Ec1 / Ec2
CAAT-box / CAATT / common cis-acting element in promoter and enhancer regions / 2008 / /
TATA-box / TACAAAA / core promoter element / 2008
AT-rich element / ATAGAAATCAA / binding site of AT-rich DNA binding protein (ATBP-1) / 2008
GARE-motif / AAACAGA / gibberellin-responsive element / 2008 / / /
HSE / AAAAAATTTC / cis-acting element involved in heat stress responsiveness / 2008 / / / / / / / / / /

FDP – 169 bp

Motif Name / Sequence / Function / Methylation status of individual plants
Year / Ra1 / Ra2 / Ea1 / Ea2 / Rb1 / Rb2 / Eb1 / Eb2 / Rc1 / Rc2 / Ec1 / Ec2
CAAT / CAAT / common cis-acting element in promoter and enhancer regions / 2008 / /
CGTCA / CGTCA / cis-acting regulatory element involved in the MeJA-responsiveness / 2008 / /
TGACG / TGACG / cis-acting regulatory element involved in the MeJA-responsive / 2008

REF – 348 bp

Motif Name / Sequence / Function / Methylation status of individual plants
Year / Ra1 / Ra2 / Ea1 / Ea2 / Rb1 / Rb2 / Eb1 / Eb2 / Rc1 / Rc2 / Ec1 / Ec2
ACE / AAAACGTTTA / cis-acting element involved in light responsiveness / 2008 / / / / / /
ARE / TGGTTT / cis-acting regulatory element essential for the anaerobic induction / 2008
Box I / TTTCAAA / light responsive element / 2008 /
CAAT-box / CAAAT / common cis-acting element in promoter and enhancer regions / 2008
G-Box / CACGTT / cis-acting regulatory element involved in light responsiveness / 2008
P-box / CCTTTTG / gibberellin-responsive element / 2008 /
TATA-box / TCTATAAAta / core promoter element / 2008
TCA-element / CAGAAAAGGA / cis-acting element involved in salicylic acid responsiveness / 2008 / / / / / / / /

COI1 - 167 bp

Motif Name / Sequence / Function / Methylation status of individual plants
Year / Ra1 / Ra2 / Ea1 / Ea2 / Rb1 / Rb2 / Eb1 / Eb2 / Rc1 / Rc2 / Ec1 / Ec2
ACE / ACTACGTTGG / cis-acting element involved in light responsiveness / 2007 / /
2008 / /
CAAT-box / CAAT / common cis-acting element in promoter and enhancer regions / 2007 / / / /
2008 / / / /
E2Fb / TTTGCCGC / unknown / 2007 / /
2008 / / / /
Skn- 1_motif / GTCAT / cis-acting regulatory element required for endosperm expression / 2007
2008
TATA-Box / TATA / core promoter element / 2007 / / / / / / / /
2008 / / / / / / / /
TATCCAT/C-motif / TATCCAT / unknown / 2007 / / / / / / / / / /
2008 / / / / / / /

-(Represents the attachment of a methyl group within the regulatory binding site)

Table.3. Methylation status of regulatory motifs.

Methylation status of core DNA binding motifs within HMGR1 HMGS, FDP, REF & COI1 gene partial promoter regions of each of the control and test plant during 2007 & 2008. R: Control-plants grown at RRII campus, E: Test- plants grown at Elappara, a: RRII 105, b: RRIM 600, c: PB260. (Data for HMGS, FDP & REF promoter is available only for 2008).