About the retired genes in Ensembl gene in table browser

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Feng Tian

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Aug 15, 2016, 10:47:57 AM8/15/16
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I downloaded the chicken (galGal3) Ensembl gene from UCSC table browser.
But I found in the downloaded file there are some transcripts were "retired" in Ensembl website.
I think these transcripts should be removed.
For example:
http://mar2016.archive.ensembl.org/Gallus_gallus/Transcript/Idhistory?t=ENSGALT00000000265

Is it possible that the ensembl gene in table browser will be updated?

Thanks

--------------------------
Feng Tian
Center for Bioinformatics
Center for Life Sciences
Peking University

Christopher Lee

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Aug 23, 2016, 1:52:25 PM8/23/16
to Feng Tian, genome

Hi Feng,

Thank you for your question about galGal3 Ensembl transcripts. In the link you shared, note that the version is listed as 70. Version 70 of Ensembl Genes is the last available version for galGal3:
http://uswest.ensembl.org/info/website/archives/assembly.html

If you would like to see more recent updates to the Ensembl Genes (Version 81) please use galGal4:
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=galGal4&c=chr5&g=ensGene

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further
questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived
on a publicly-accessible forum. If your question includes sensitive data, you may send it instead
to genom...@soe.ucsc.edu.

Christopher Lee
UCSC Genomics Institute


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