Question: Differences between genomic coordinates for CFTR in Ensembl GRCh37.p13 and NCBI GRCh37.p13
0
gravatar for andrew.prayle
4.4 years ago by
United Kingdom
andrew.prayle0 wrote:

Apologies if this is too simple.  I am interested in CFTR.  When I look it up in NCBI gene, with the following:

http://www.ncbi.nlm.nih.gov/gene/?term=cftr[sym]+AND+human[orgn]

I get the genomic coordinates using GRCg37.p13 on chromosome 7 to be 117120017..117308719 (NC_000007.13)

However, when I search Ensembl, also using GRCg37.p13 looking for CFTR I get the co-ordinates 117105838 - 117356025. 

What am I missing here?

Thanks

Andrew

 

ADD COMMENTlink modified 4.4 years ago by Emily_Ensembl20k • written 4.4 years ago by andrew.prayle0
3
gravatar for Emily_Ensembl
4.4 years ago by
Emily_Ensembl20k
EMBL-EBI
Emily_Ensembl20k wrote:

There are many more non-coding transcripts of CFTR annotated by Ensembl, which extend out the coordinates of the gene, as you can see in the graphics on Ensembl and NCBI.

ADD COMMENTlink written 4.4 years ago by Emily_Ensembl20k

Thanks!  So as the CFTR-001 is roughly the same co-ordinates, is this the same as the NCBI sequence? 

ADD REPLYlink written 4.4 years ago by andrew.prayle0
1

It has a CCDS, so the coding sequence at least is the same.

ADD REPLYlink written 4.4 years ago by Emily_Ensembl20k

Thanks!  Very useful to know.  

ADD REPLYlink written 4.4 years ago by andrew.prayle0
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