[BioC] chrome coordinates are not same between Ensembl and Affy's annotation file
James W. MacDonald
jmacdon at med.umich.edu
Thu Sep 24 20:52:44 CEST 2009
Hi Shirley,
shirley zhang wrote:
> Dear List,
>
> I have been trying to draw the genome graphs for some genes in human.
> I found that the coordinates of some genes are not close between
> Ensembl and Affy's annotation (Affymetrix Human Exon array). For
> example, gene SFRS1:
>
> SFRS1 (ENSG00000136450): Chromosome 17: 56,078,284-56,084,707
> reverse strand (Ensemble 55)
>
> SFRS1Transcript Cluster ID: 3764103 Human Exon 1.0 ST):
> chr17:53421412-53439635 (-)
>
> Can anybody tell me what happens?
Sure. Things change. If you query the UCSC genome browser using NCBI
build 36, you get
SFRS1 (uc002ivj.1) at chr17:53433279-53439706 - splicing factor,
arginine/serine-rich 1 isoform
SFRS1 (uc002ivi.1) at chr17:53433279-53439706 - splicing factor,
arginine/serine-rich 1 isoform
If you then try the newer build (GRCh37) you get
SFRS1 at chr17:56078282-56084707 - (NM_006924) splicing factor,
arginine/serine-rich 1 isoform
SFRS1 at chr17:56078282-56084707 - (NM_001078166) splicing factor,
arginine/serine-rich 1 isoform
The affy annotation is based on older information than Ensembl.
Best,
Jim
>
> Thanks,
> Shirley
>
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--
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
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