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Table 7 LCR cis-motifs are proposed to be responsive to light or carbon

From: Genome-wide investigation of light and carbon signaling interactions in Arabidopsis

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

YGGGT TC

Y

N

N

N

N

GCCCG-motif

N/A

 

(3 genes)

Motif58

LCR3

0.0020

ANKNGRNNGSNH C

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

GNKNYGGW G

Y

N

N

N

N

PE3

Light response

           

RE1

Light response

           

ACE‡

Light response

           

RbcS-CMA7c

Light response

  

Motif51

LCR6

0.0287

A TTKTGVA

Y

N

N

N

N

HSE

Heat stress response

 

Cellular organization

Motif12

LCR7

0.0006

A NNCCANANHHMNNA

Y

N

N

N

N

H-box module‡

Light response

  

Motif13

LCR8

0.0102

GDGDTKG TG

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

GG TCNBNGWG

Y

N

N

N

N

G-box‡

Light response

  

Motif37

LCR10

0.0179

G NGRNNGNNNNWGNN Y

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

G DGDTDGTG

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

ANVNAANAAGHN G

Y

N

N

N

N

MPE

N/A

  

Motif21

LCR15

0.0427

ARAGAG A

Y

N

N

N

N

GAG-motif

Light response

           

3-AF1 binding site‡

Light response

  

Motif36

LCR16

0.0455

G GTYNNNGWG

Y

N

N

N

N

O2-site‡

Zein regulation

  1. *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).
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Genome Biology

ISSN: 1474-760X

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