difference in mm10 genomic coordinates in ensembl and igv

Question

[ravast]

HI,

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 position in IGV is chr4:122,994,099-123,004,480 and from ensembl its showing chr:4-122,995,652 -123,002,485.

Answer 1

[Istvan Albert]

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.