Table 7

LCR cis-motifs are proposed to be responsive to light or carbon

Basis for motif discovery

Motifs discovered

Over represented in InterAct

InterAct

Funcat

Name

LCR

p-value*

Sequence^†

111

110

011

121

000

Example of element

Validated/proposed function (PlantCARE database)

111

Metabolism

Motif55^§

N/A

0.0001

GGHNGGNDCR

Y

N

Y

N

N

GCCCG-motif

N/A

C-metabolism

RE1

Repressing element

Unnamed 1

TEF 1 factor binding site

Unnamed 17

N/A

Starch biosynthesis

Motif45

LCR1

0.0013

SDHTHGTGDKTG

Y

N

N

N

N

None

N/A

Motif23

LCR2

0.0020

YGGGTTC

Y

N

N

N

N

GCCCG-motif

N/A

(3 genes)

Motif58

LCR3

0.0020

ANKNGRNNGSNHC

Y

N

N

N

N

Chs-unit 1

Light response

Motif5^§

N/A

0.0066

GNKNCGGWG

Y

Y

N

N

N

PE3

Light response

RE1

Light response

RbcS-CMA7c

Light response

Motif2

LCR4

0.0161

CAAAAWT

Y

N

N

N

N

DREP-module^‡

Light response

Motif10

LCR5

0.0281

GNKNYGGWG

Y

N

N

N

N

PE3

Light response

RE1

Light response

ACE^‡

Light response

RbcS-CMA7c

Light response

Motif51

LCR6

0.0287

ATTKTGVA

Y

N

N

N

N

HSE

Heat stress response

Cellular organization

Motif12

LCR7

0.0006

ANNCCANANHHMNNA

Y

N

N

N

N

H-box module^‡

Light response

Motif13

LCR8

0.0102

GDGDTKGTG

Y

N

N

N

N

GT-1 motif^‡

Light response

Cell wall

ACE^‡

Light response

RbcS-CMA7c

Light response

(5 genes)

Motif20

LCR9

0.0135

GGTCNBNGWG

Y

N

N

N

N

G-box^‡

Light response

Motif37

LCR10

0.0179

GNGRNNGNNNNWGNNY

Y

N

N

N

N

Endosperm-box^‡

Endosperm regulation

Motif6

LCR11

0.0207

GHTTNGAWTBDG

Y

N

N

N

N

None

N/A

Motif24

LCR12

0.0239

GDGDTDGTG

Y

N

N

N

N

Endosperm-box^‡

Endosperm regulation

Motif16

LCR13

0.0256

GARANNNARA

Y

N

N

N

N

CAG-motif

Light response

Prolamin-box^‡

Endosperm regulation

MPE

N/A

Motif11

LCR14

0.0427

ANVNAANAAGHNG

Y

N

N

N

N

MPE

N/A

Motif21

LCR15

0.0427

ARAGAGA

Y

N

N

N

N

GAG-motif

Light response

3-AF1 binding site^‡

Light response

Motif36

LCR16

0.0455

GGTYNNNGWG

Y

N

N

N

N

O2-site^‡

Zein regulation

*p-value designates the significance level of genes with a motif being over-represented among all InterAct 111 genes used in our analysis. For each motif, p-values were calculated for genes containing: any copy number, less than two copies, more than one copy, more than three copies, more than five copies, and more than eight copies. The p-value with the greatest significance is shown here. ^†Sequences used to query the PlantCARE database are underlined. ^‡Elements that have known binding factors. ^§Motifs originally found that did not pass the further statistical tests that they were not overrepresented in additional InterAct classes (see text for more details).

Thum et al. Genome Biology 2004 5:R10   doi:10.1186/gb-2004-5-2-r10