Skip to main content

Table 2 G-rich motif-sets identified by AlignACE, Weeder and MEME in the upstream regions of the group of 22 transcription machinery genes.

From: Identification of putative regulatory motifs in the upstream regions of co-expressed functional groups of genes in Plasmodium falciparum

AlignACE

  

AlignACE

  
 

GGG--AAAW-WAWA

  

KGWGGGS

 

PFB0715w;

GGGAAAAAACAAAA

122

PFB0290c;

TGGGGAG

150*

PFC0155c;

GGGAAAAAAAAAAA

398

PFE0465c;

TGTGGGG

32*

PFC0155c;

GGGTAAAAAAAAAA

1458

PFE0465c;

AGAGGGG

634*

PFF1390w;

GGGAAAAAAAAAAA

163*

PFF1390w;

TGTGGAC

122

PF11_0264;

GGGGGAAAAATAAA

588*

PFF1390w;

TGTAGGC

981

PF11_0445;

GGGTCACATTTATA

6*

PF07_0027;

TGTGGGG

81*

PF11_0445;

GGGTGAAAATAAAA

626

PF07_0027;

AGAGGGC

914*

PF11_0445;

GGGAAAAAAAAAAA

1147*

PF11_0264;

GGAGGGG

583*

PF14_0207;

GGGAAAAAATAATA

774*

PF11_0445;

TGTGGGG

2*

   

PF11_0445;

TGTGGAG

42*

AlignACE

  

PF13_0023;

GGTGGAG

1579*

 

G-GGGG-AAAAAWAAAAWWAWA

 

PF14_0207;

GGTTGGG

770*

PFC0155c;

GCGGGTCTACAAGAAAAATGAA

678

   

PFE0465c;

GGGGTGTAATGATAAAAAGGGA

35*

Weeder

  

PFE0465c;

GAGGGGAAAATAAAATAATAAA

635

 

TGGGGAGT

 

PFF1390w;

GTGGGAAAAAAAAAAAAAAAAA

161*

PFB0290c;

TGGGGAGT

151*

PF07_0027;

GAGGGCTCAAAAAAAAAAAAAA

915*

PFE0465c;

TGGGGTGT

35*

PF11_0264;

GGGGGGGAAAAATAAAATAATA

586*

PF07_0027;

TGGGGAGT

84*

PF11_0445;

GTGGGGTCACATTTATATTGAA

3*

PF13_0150;

TAGGGAGT

1488

PF11_0445;

AAGGGGAAAAAAAAAAATAAAA

1144*

   

PF13_0023;

GAGGGGGAAAGTATTAATTATT

1583*

MEME

  
     

AGTGGAAAAAA

AlignACE

  

PF13_0023;

1583

GGAGGGGGAAA*

 

G-GGGG-S--A

 

PF11_0264;

587

GGGGGGGAAAA*

PF11_0445;

GTGGGGTCACA

3*

PFF1390w;

161

GGTGGGAAAAA

PF11_0264;

GAGGGGGGGAA

584*

PFE0465c;

635

AGAGGGGAAAA*

PFE0465c;

GTGGGGTGTAA

33*

PF13_0150;

863

GGTGGAAAAAA

PF07_0027;

GTGGGGAGTGA

82*

PF07_0027;

85

GGGGAGTGAAA*

PF07_0027;

GAGGGCTCAAA

915*

PFL0330c;

1146

AGAGGAAGAAA

PF11_0445;

GTGGAGACTTA

43*

PF11_0445;

1146

AGGGGAAAAAA

PF13_0023;

GTGGAGGGGGA

1580*

PF14_0469;

646

AGTGAGAGAAA

PFF1390w;

GTGTGGACCAA

121*

PF14_0207;

771

GGTTGGGAAAA*

PFB0290c;

TTGGGGAGTTA

149*

PFC0805w;

254

AGTGGAAAAAA

   

PFA0505c;

106

AGAGGAAAAAA

AlignACE

  

PF10_0269;

368

GGAGAAAAAAA

 

GGGGRGKGR-A

 

PFB0715w;

1202

AGAGAAGAAAA

PF13_0023;

GGAGGGGGAAA

1582*

PF11_0358;

312

GAAGGAAGACA

PF11_0264;

GGAGGGGGGGA

583*

PFC0155c;

396

AATGGGAAAAA

PF07_0027;

GGGGAGTGAAA

84*

PFL0665c;

484

AGTGAAGACAA

PFE0465c;

GTGGGGTGTAA

33*

PF13_0341;

8

AGCGAAAAAAA

PFB0290c;

GGGGAGTTATA

151*

PF14_0241;

511

CATGGAAGAAA

PF11_0445;

GTGGGGTCACA

3*

PFI1130c;

767

GCTGAGTAAAA

  1. The motif-sets are related and together constitute a strong motif group.
  2. Given, for each motif in a set, are: the gene name, the motif that was identified in the upstream region of the gene, the position of the motif in the upstream region, and, sometimes, an *, which indicates that the motif overlaps with motif occurrences in one or more of the other motif-sets; at the top of each motif-set, a consensus sequence for the set is given; each motif-set has been used to obtain a sequence logo which is shown in Figure 1; all motifs in the table occur on the forward strand.