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
are available through our
multiple alignment server.
PostScript files can be displayed with Aladdin's
viewer, while the PDF versions below can be viewed with Adobe's
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
- 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
- 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
- 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).
This paper also includes an extensive review of the LCR, and can be
Locus control regions of mammalian beta-globin gene clusters: combining
phylogenetic analyses and experimental results to gain functional insights.
Gene 205: 73-94.
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