The nucleotides in human HS3 of the beta-globin locus control region (LCR) were assigned as functional based on protein binding results assayed by in vivo footprints, expanded to include all the nucleotides involved in known binding sites. The primary data are from Strauss and Orkin (1992). I started with these results, which gives start and stop positions for clusters of protected sites, thus internal nonreactive nucleotides are included. However, nucleotides beyond the bounds of the protected or enhanced sites could be important for binding the protein(s). Thus if a particular protein, such as GATA1 or EKLF, has been shown to act at a particular region, the entire consensus binding site is included in the following list. These data are largely consistent with the extensive mutagenesis results (Philipsen et al., 1993; Philipsen et al., 1990). However, the mutations in those papers were too large to be used for establishing this list of functional sites.
Clusters of protected sites (combining data from top and bottom strands)
expanded to include all of the consensus binding site:
The coordinates are for the sequence file starting 5' to HS5. Coordinates
in the GenBank file HUMHBB can be obtained by subtracting 2687.
References