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].
