This question was addressed in vitro by performing a fluorescent variant of EMSA (fEMSA), in which nuclear extracts of DTT-treated HepG2 cells were combined with a DNA probe containing the consensus binding sequence recognized by C/EBPα [22].
However, computational scanning of the target exonic sequence for previously reported SELEX consensus RNA binding sequence recognized by B52 [40], [40], failed to reveal any match to this sequence, suggesting that B52 interacts with a set of distinct RNA sequences to regulate the eyeless splicing event.
We used this TSS information to identify transcription factor binding sites and putative promoter sequences recognized by seven of the 15 known S. meliloti σ factors σ, σ, σH1, σH2, σE1, σE2, and σE9).
For overrepresented sequences, preferences for sequences recognized by ubiquitous DNA-binding proteins and ubiquitous repetitive elements must be considered.
Second, both proteins display efficient binding to collagens [7], [9] Third, the collagen sequences recognized by LAIR-1 and LAIR-2 (as determined using the collagen tool-kits) overlap to a significant extent and collagen-binding is in both cases more efficient when the sequences are enriched in Glycine-Proline-Hydroxyproline (GPO -triplets [10].
Currently, little is understood about the sequences recognized by H. pylori Fur that dictate binding of the protein at target promoters.
DNA sequences recognized by TFs consist of consensus regions.
The binding sites and target sequence recognized by RelBE-like proteins are unknown in M. tuberculosis.
The bacterial Hsp90 homologue lacks the C-terminal acidic sequence recognized by the TPR binding motif of eukaryotic Hsp90 co-chaperones [9], [23].
