Table 2

Occurrences of a sequence motif overrepresented in wCNEs associated with pharyngeal genes

wCNE coordinates

Strand

Matching sequence

Position

Score

wCNE distance from TSS

Gene name


IV:3776258..3776298

+

TATTTAGCATCT

9

85.59

9,435

vab-2

IV:8369551..8369581

-

TTTTTTGCAACT

3

91.65

347

D2096.6

V:10673732..10673841

-

TGTTTGTCCACT

15

87.26

1,202

ceh-22*

V:13217316..13217419

+

TGTTTGGCAACT

23

100

3,588

F57B1.6

X:2215856..2215898

-

TGTTTTGAAATT

12

85.67

230

peb-1

X:6621897..6621968

-

TTTATGGCAACT

47

88.99

826

C25B8.4

X:7457940..7457992

+

TGTTTGACAATT

5

91.56

2,212

sox-2


We used the Weeder motif discovery program to search for overrepresented motifs in all wCNEs spatially associated with genes predicted to be expressed in the pharynx based on microarray data [31]. From this dataset, Weeder identified a motif very similar to the consensus binding site for PHA-4, the master specifier of pharyngeal cell identity (TRTTKRY, where R = A/G, K = T/G, and Y = T/C) [33, 34]. This table shows the coordinates (WormBase version WS140) of the wCNEs that contain matches to the overrepresented motif, the coordinates of the matches within the wCNEs, the Weeder scores of the matches to the motif, the distances (in bp) between the wCNEs and the transcription start site (TSS) of the associated genes and the names of the associated genes. The predicted site in the element 1.2 kb upstream of ceh-22 (marked with an asterisk) lies within a 30 bp pharyngeal muscle enhancer bound by PHA-4 [35].

Vavouri et al. Genome Biology 2007 8:R15   doi:10.1186/gb-2007-8-2-r15

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