Hi Josh,
The numbers relate to the position on the coordinate system on which
the gene was built. In human that might be positions on a chromosome
but for some species this will be positions on a Gene Scaffold etc.
Hope that helps,
Regards,
Rhoda
On 4 Feb 2009, at 14:57, Syed Haider wrote:
Hi Josh,
fowardnig your email to Ensembl team, who are best to answer this
question.
Cheers
Syed
T Joshi wrote:
Hi,
I have question regarding the genomic position of the sequences we
obtain from NCBI36. I referred to the documentation on Ensembl
which states that the base pairs are numbered from the start of the
transcript. In the case when I obtain sequences for 3' UTR region,
I can also choose to select 3'UTR start and end positions.
My concern is with respect to the numbering of these base pairs.
Are start positions aligned to some reference, for example TSS or
stop codon ? Your help will be greatly appreciated
Thanks
Josh
Rhoda Kinsella Ph.D.
Ensembl Bioinformatician,
European Bioinformatics Institute (EMBL-EBI),
Wellcome Trust Genome Campus,
Hinxton
Cambridge CB10 1SD,
UK.
