[Genome] Query: Restriction enzyme digest displays

[Dillon Leong]

Dear Sir/Mdm,

I've been using genome browser (mouse) to design DNA digests for  
Southern Blots. Recently, I noticed a discrepancy which I hope you  
can help to clarify.

I downloaded the Refseq genomic sequence for mouse itga1 gene into a  
Microsoft Word file and searched for cleavage sites for restriction  
enzyme ClaI. I was sure to remove paragraph marks from the sequence.  
When I compared the cleavage pattern with that in genome browser, I  
found differences. The number of cleavage sites remained the same  
(=5), but the position of the sites and the resulting DNA fragment  
sizes were different.

I can't figure out why this is so, and I've redone my Word document  
to verify that I haven't made mistakes while transferring the  
sequence from Refseq. Would you please give it a go and see if you  
get the same result?

Best regards,
Dillon