Annotated images of multiple alignments: HSs in the beta-LCR

The following images show the alignment of mammalian beta-globin gene cluster sequences around hypersensitive sites (HSs) 1, 2, 3, 3.5, and 4 in the locus control region (LCR). PostScript and ASCII versions of a similar alignment are available through our multiple alignment server. PostScript files can be displayed with Aladdin's Ghostscript viewer, while the PDF versions below can be viewed with Adobe's Acrobat Reader.

	HS1:	PostScript	PDF
	HS2:	PostScript	PDF
	HS3:	PostScript	PDF
	HS3.5:	PostScript	PDF
	HS4:	PostScript	PDF

The annotated multiple alignments observe the following conventions.

• The human DNA sequence is presented on the top line, and its coordinate system begins at a HindIII site located 5' to HS5. GenBank entry HUMHBB begins at position 2688 in this coordinate system, so HUMHBB coordinates can be obtained by subtracting 2687 from the numbers in these figures.
• For the DNA sequences of nonhuman species, matches with the human sequence are shown as periods and mismatches are shown as the nonmatching nucleotide. Dashes represent gaps introduced to improve the alignment. Open boxes are drawn around conserved blocks of columns, or phylogenetic footprints, that are at least 6 gap-free columns long and contain at least 4 rows such that each row has no more than one mismatch compared to an unspecified consensus. A shaded box indicates a differential phylogenetic footprint.
• Protein binding sites are labeled with either the name of the protein or the binding site; in general, upper case characters denote an exact match with the consensus, whereas lower case characters indicate that the match is not perfect.
• DNase I hypersensitive sites are labeled with "HS" and their midpoints are underlined as single nucleotides, although the cleavage covers a longer DNA segment.
• Selected restriction endonuclease cleavage sites are underlined and labeled; the prefixes are r = rabbit, go = goat. Those that mark the ends of DNA fragments sufficient for position independent expression in transgenic mice (pos ind) are labeled as such.

The citation for these alignments is:

Hardison R, Slightom J, Gumucio D, Goodman M, Stojanovic N, and Miller W (1997).
Locus control regions of mammalian beta-globin gene clusters: combining phylogenetic analyses and experimental results to gain functional insights.
Gene 205: 73-94.