Motif analysis for the regulation of transcripts predicted to be up-regulated in stumpy forms. Oligonucleotide frequency analysis of the 300 nt downstream of genes identified as being up-regulated in stumpy forms with respect to other points in the differentiation programme. Two motifs were identified as being statistically overrepresented, of which SM1 (TCTTAC) was also elevated among the most strongly regulated genes in the stumpy expressed cohort. Positional analysis of the 3'UTR of those transcripts with this motif demonstrated a location bias 151-200 nt downstream of the stop codon of the associated gene. In contrast the position of the motif among genes not up-regulated in stumpy forms demonstrated no discernable positional bias.
Kabani et al. BMC Genomics 2009 10:427 doi:10.1186/1471-2164-10-427