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This result was consistent with the expectation that these genes contained a number of direct miRNA targets.
Mosquito and fly genes contained a relatively small number of exons (varying from 4 to 6) whereas those of S. mansoni and S. purpuratus were shown to be composed of 15 and 21 exons respectively.
We scanned the ChIP identified regions with internal Pol II peaks with the corresponding SVM model (CpG+ or CpG−) and we found that 11 of these 15 intragenic genes contained a highly likely TSS region (Table 3).
No significantly overrepresented motifs common to all sequences were found, however, 5' flanks of four genes contained a CGTTGAA heptamer.
The stop codons were nearly always located at positions where the full-ORF genes contained a glutamine residue codon.
These genes contained a significant proportion of genes predicted to function in cell-cell communication and signal transduction.
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Homeobox genes contain a conserved DNA-binding motif known as the homeodomain that consists of 60 amino acid residues.
Genes Expected Number is the expected number of genes containing a particular TFBS.
Genes Number is the number of genes containing a particular TFBS.
Additionally we were interested in all target genes containing a motif score below 7.3.
All genes contain a single central- or N-terminal-positioned PDZ domain.
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