gene copy number - how to find how many? (Jun/17/2008 )
Hello I have a doubt about gene copy number. How or where do I find out how many copies of a given gene are in the genome?
Even better, is beta-actin a single copy gene in mouse? 
Thanks !!!!!!!
hi,
you could blast the beta-actin sequence against the whole mouse genome and see how many times you find it. about the second question i have no idea...
thanks toejam, should definitely have thought of that myself...
will see what I find.
you could blast the beta-actin sequence against the whole mouse genome and see how many times you find it. about the second question i have no idea...
Hi again toejam. So i did the blast, and it comes with about 38 hits, but only one is the exact match, in chromosome 5 (which i knew already). Now my question, does that mean there's 38 copies (polymorphisms or whatever), or that there's only one. sooooo confused....
here's the link to my results in case it helps any. http://blast.ncbi.nlm.nih.gov/Blast.cgi
THANKS!!!!!
hello aad,
did you check where your matches are aligning? just to make sure it is not the same region. in the blast results you should also sheck the identity percentage, for some of them might be polymorpisms while others might be just artifacts i think.
to me it would make sense if there's more than one copy since this is a housekeeping gene, in case a copy has a mutation there would be the "backup". also, not because it has many copies it means all of them have to be necesarily active. i hope this makes it clearer.
did you check where your matches are aligning? just to make sure it is not the same region. in the blast results you should also sheck the identity percentage, for some of them might be polymorpisms while others might be just artifacts i think.
to me it would make sense if there's more than one copy since this is a housekeeping gene, in case a copy has a mutation there would be the "backup". also, not because it has many copies it means all of them have to be necesarily active. i hope this makes it clearer.
Thanks tj, I'll definitely have a closer look. I also expect b-actin to have more than one copy, but really cant get my head round it on how to find out.
why don't you perform a southern blot? the probe should bind to all the copies of b-actin in the genome.
I agree with TJ.
In silico queries are a good starting point, but it's necessary to achieve experimental proofs performing Southern analysis.
I'm afriad, that no referee is going to agree that your gene is in single copy just on the base of blast searches... 
I'm taking for granted that this b-actin gene has not been studied that much in the organism you are working on. If you can cite literature where someone already demostrated the conserved copy number of this gene, then things may be different...
you might find this interesting. looks like the functional b-actin gene in mouse is single copy after all....
http://www.pubmedcentral.nih.gov/articlere...gi?artid=363155
Hello
why dont you try southern blotting.
It is an easy way to find how many
copies you have in the genome 