[Genome] species conservation concerns

[Alexander Gow]

hi,
i am interested in looking at sequence conservation in the 
promoter/enhancer region of the mouse claudin 11 gene 
(chr3:31,338,500-31,341,000). when i have all vertebrate genes 
included in the alignment, i see a large block of conserved sequence 
in the proximal promoter region as would be expected. there are also 
several small regions of upstream conserved sequences although the 
vertical bars are quite small (0.1 or less). i am concerned that this 
pattern is invariant as i start to remove more  and more species from 
the alignment, but most concerned when i remove all species, and the 
pattern is invariant. to what is the mouse sequence being compared?

thanks for your thoughts on this issue.
sincerely
-- 
Alexander Gow, PhD
Associate Professor
Center for Molecular Medicine and Genetics,
Carman and Ann Adams Dept of Pediatrics,
Dept of Neurology,
3216 Scott Hall
540 E Canfield
Detroit MI 48201

voice:	313 577-9401
fax:	313 577-1632
email:	agow at genetics.wayne.edu