One region within block 2 that was particularly sensitive to mutation contains consensus binding sequences for the factors HNF1 and INSM1, which have been previously implicated in development and function of pancreatic islets [33].
The consensus DNA binding sequences for these bHLH proteins form the typical E boxes (CANNTG).
Sequencing a total of 512 single product colony-PCR reactions, we successfully obtained 235 potential binding sequences for the mouse library, and 197 for the zebrafish library.
Briefly, a PWM compiles information content (log odd values) for each nucleotide position using existing information on known binding sequences for the protein of interest.
These results indicate that these additional DNA fragments provided binding sequences for the degenerate or vector-specific primers (Additional file 3: Figure S2B, C).
Among the common promoter elements found, 4 were similar to known binding sequences for the S. cerevisiae transcription factors Rap1p, Adr1p and Hcm1p.
We identified binding sequences for the CCAAT/enhancer binding protein (C/EBP) and GATA, as well as a signal transducer and activator of transcription-3 (Stat3) consensus sequence overlapping the C/EBP site, using 5'- deletion analysis and a gene reporter assay.
Input sequences are screened for consensus binding sequences for the SR proteins SF2/ASF, SC35, SRp40 and SRp55, developed using the SELEX (systematic evolution of ligands by exponential enrichment) procedure [ 11, 21, 22].
The Oligo-histidine tag should serve as a high affinity binding sequence for the purification of any fusion protein via metal chelating adsorbents.
These motifs are not exact strings: while most binding sites for a given factor resemble a "consensus string" (for example, ACGCGT, the most common binding sequence for the MBP1 protein in budding yeast), mismatches and variations often occur.
