The sequence, masking, exons, and underlay files are provided to allow you to do your own comparisons, using our PipMaker server. Precomputed pips and dotplots are also provided, along with the alignments in text form. For some analyses, it is more convenient to use human as the reference sequence, but for others it is more convenient to use mouse. Thus both human vs. mouse and mouse vs. human comparisons are provided.
The HBB complex and surrounding genes (human chromosome 11p15.5, mouse chromosome 7, 50 cM)
For information about the meanings of the different settings used in computing the alignments (chaining, single coverage, one or two strands) see the PipMaker server: http://pipmaker.bx.psu.edu/pipmaker/. The scoring schemes used for "single coverage" and "all matches" are set to produce minimal spurious alignments, whereas the "chaining" option is set to a higher sensitivity.
The human HBB complex sequence is a compilation of sequences. Most of the sequences flanking the beta-like globin genes and LCR were determined by Mike Bulger in the Groudine lab, and he generated this compilation. A "minimal tiling path" of GenBank sequences that in combination will make something close to this compilation (after removing overlaps) is accession numbers AF137396, AF064190, U01317, AF137131, X54282, AF289203 and AF289204.
THERE IS A ROUGHLY 6 KB GAP IN THE HUMAN SEQUENCE at position 344746. The gene HOR3'beta3 and the 3' breakpoint for the Chinese thalassemia deletion precede this gap, and the 3' breakpoint for HPFH1 and the gene HOR3'beta4 follow this gap.
This gap was resistant to cloning and sequencing in multiple attempts. The Celera contig also ends in roughly this region.