Dear Hannah, Please find Michael's answer from the Ensembl Helpdesk team:
> The problem here is that the Ensembl pipeline has predicted one transcript > that has an exon, which is miles away from the rest of the gene model. The > following Transcript-Summary pages shows a distance of 2.49 Mb in the > ideogram. > > http://www.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;g=ENSG00000143799;r=1:224102741-226595780;t=ENST00000432338 > > Looking at the Supporting Evidence page, this distant exon is just built on a > single protein sequence Q6PJL0. > > http://www.ensembl.org/Homo_sapiens/Transcript/SupportingEvidence?db=core;g=ENSG00000143799;r=1:224102741-226595780;t=ENST00000432338 > > http://www.uniprot.org/uniprot/Q6PJL0 > > Looking at the exon page it turns out that the intron is 2,473,583 base pairs > long (!!!) and the exon itself (last one on the page) is most likely a PolyA > tail of some sort and therefore rather questionable. > > http://www.ensembl.org/Homo_sapiens/Transcript/Exons?db=core;g=ENSG00000143799;r=1:224102741-226595780;t=ENST00000432338 If you have further questions regarding this issue please contact the Ensembl Helpdesk team : http://www.ensembl.org/Help/Contact Hope this helps, Best Regards, Thomas Maurel On 15 Mar 2012, at 13:53, Arek Kasprzyk wrote: > Hi Hannah, > you need an expert advice on it. I cc'ed Thomas and Rhoda from Ensembl. > Hopefully they will be able to help you > > a > > On Mon, Mar 12, 2012 at 4:40 PM, Cheung, Hannah (TXCCC) <[email protected]> > wrote: > Hi, > > > > Why is there a discrepancy in the location of PARP1 gene? > > > > In Ensembl Biomart GRCh37.p6, the gene start at : chr1: 224102741-226595780 > while on UCSC browser, the start and stop locations are: > > chr1:226,548,392-226,595,801 for GRCh37 build hg19. > > > > Hannah Cheung > > > ______________________________________________________________________ > CONFIDENTIALITY NOTICE: > The information in this e-mail may be confidential and/or > privileged. If you are not the intended recipient or an > authorized representative of the intended recipient, you > are hereby notified that any review, dissemination, or > copying of this e-mail and its attachments, if any, or > the information contained herein is prohibited. If you > have received this e-mail in error, please immediately > notify the sender by return e-mail and delete this e-mail > from your computer system. Thank you. > ______________________________________________________________________ > > _______________________________________________ > Users mailing list > [email protected] > https://lists.biomart.org/mailman/listinfo/users > > > > > -- > Arek Kasprzyk, MD, MSc, PhD > BioMart Project Lead > -- Thomas Maurel Bioinformatician - Ensembl Production Team European Bioinformatics Institute (EMBL-EBI) Wellcome Trust Genome Campus, Hinxton Cambridge - CB10 1SD - UK
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