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Ensembl genomes - are these sequences "wild type"


Best Answer Trof, 01 August 2013 - 09:35 AM

Wild type what? Usually scientists are only working with inbred mouse strains. These vary in several polymorphisms, you can search them by strains in Mouse Genome Database (MGD) Project. Nowadays most usual strains are genome sequenced and annotated in dbSNP and Ensembl. I'm affraid a real "wild" mouse won't be there, only the laboratory strains.

 

However reference sequences for mouse or Ensembl sequences may be from different stains, probably, but they are extremely unlikely to contain any cancerogenous or otherwise disease-causing mutations (unless specified). You may see the variations in the cDNA, exon or protein view. I only have experience with human variations, but there are additional info about them.

I tried to click on one variation and under Populatin genetics it displayed genotypes of all the strains from Mouse genome project.

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#1 Ahrenhase

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Posted 31 July 2013 - 03:58 PM

So I'm trying to determine variations in the mouse genome from a cancer cell line I"m using.  For this, I am using Ensembl's mouse genome browser.  Do their sequences represent "wild type" or just one genome they sequenced?



#2 Trof

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Posted 01 August 2013 - 09:35 AM   Best Answer

Wild type what? Usually scientists are only working with inbred mouse strains. These vary in several polymorphisms, you can search them by strains in Mouse Genome Database (MGD) Project. Nowadays most usual strains are genome sequenced and annotated in dbSNP and Ensembl. I'm affraid a real "wild" mouse won't be there, only the laboratory strains.

 

However reference sequences for mouse or Ensembl sequences may be from different stains, probably, but they are extremely unlikely to contain any cancerogenous or otherwise disease-causing mutations (unless specified). You may see the variations in the cDNA, exon or protein view. I only have experience with human variations, but there are additional info about them.

I tried to click on one variation and under Populatin genetics it displayed genotypes of all the strains from Mouse genome project.


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#3 Ahrenhase

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Posted 01 August 2013 - 11:53 AM

Sorry for the poorly worded question.  So it looks like Ensembl generates their base sequence GRCm38 of C57B6J - that's what I was referring to as WT.  Thanks for that last link, that's pretty much what I was looking for. 


Edited by Ahrenhase, 01 August 2013 - 11:53 AM.





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