[Genome] Query: Restriction enzyme digest displays

[Kayla Smith]

Dillon,

We have a few different assemblies of the mouse genome, which will have 
different coordinates from each other.  Our most recent, mm8, 
corresponds to NCBI's Build 36, while mm7 corresponds to NCBI's Build 
35.  Could you be comparing DNA from two different builds?


The position of the itga1 gene in mm8 is chr13:116,080,957-116,222,842.
I see in mm8 that claI hits itga1 at the following positions:
chr13	116092758	116092764	ClaI	1000	+
chr13	116109387	116109393	ClaI	1000	+
chr13	116120677	116120683	ClaI	1000	+
chr13	116152058	116152064	ClaI	1000	+
chr13	116197694	116197700	ClaI	1000	+


The position of the itga1 gene in mm7 is chr13:112,132,199-112,273,942
And these are the positions claI hits itga1 in mm7:
chr13	112144000	112144006	ClaI	1000	+
chr13	112160370	112160376	ClaI	1000	+
chr13	112171660	112171666	ClaI	1000	+
chr13	112202969	112202975	ClaI	1000	+
chr13	112248561	112248567	ClaI	1000	+

I obtained this data using the "Restr Enzymes" track in the Genome 
Browser.  There is an option, when clicking into an individual 
restriction enzyme's details page to "Download BED of enzymes in this 
browser range", which you may find useful.

I hope this information is useful to you.  Please don't hesitate to 
write back if this didn't clear up your concerns about the discrepancy 
you are seeing.


Kayla Smith
UCSC Genome Bioinformatics Group
Dillon Leong wrote:
> 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
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