Question: difference in mm10 genomic coordinates in ensembl and igv
gravatar for ravast
4.7 years ago by
ravast10 wrote:


I have the genomic coordinates of mouse mm10 from ensembl biomart (Ensembl genes 80). I was using IGV  mouse mm10 for visualising some of the mouse genomic coordinates. Why there are differences in the position of genes when comparing the results, even though they are from the same mm10 build. For eg. Mycl  postion in IGV is chr4:122,994,099-123,004,480 and from ensembl its showing chr:4-122,995,652 -123,002,485. 

sequence genome • 1.6k views
ADD COMMENTlink written 4.7 years ago by ravast10
gravatar for Istvan Albert
4.7 years ago by
Istvan Albert ♦♦ 82k
University Park, USA
Istvan Albert ♦♦ 82k wrote:

there are different versions of gene annotations. Whereas the genomic build  may be the same or even the corresponding protein coding region may be the same the concept of a gene encompasses a larger interval that includes more regions. There are differences in the predictions.

ADD COMMENTlink written 4.7 years ago by Istvan Albert ♦♦ 82k
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