Gene symbol and full name for latest col-0 annotation


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Dear ARAPORT Team,

I am looking for gene aliases file similar to following (TAIR10). Just wanted to check if there is any latest version of this in araport?

Thanks and regards, Reetu

You can obtain Arabidopsis gene Symbols and Aliases from ThaleMine and Araport11 GFF3 file(s) or from TAIR public data release file(s)

Hi Reetu,

TAIR is the official authority on Gene Symbols and Aliases, where they maintain a registry of the latest assigned symbols. Araport11 release files are prepared using TAIR Public Data Release files.

For example, the latest release Araport11_Release_201606 was prepared from the TAIR Public Release TAIR_Data_20150331, since TAIR makes quarterly public data releases with a 1-year time delay (March 2015 data is made public in March 2016).

You should be able to find the Gene Aliases stored in 9th column attributes (symbol and Alias) of the Araport11 GFF3 file Araport11_GFF3_genes_transposons.201606.gff.gz, as well as on any of the ThaleMine Gene Report pages, example: AT2G01830.

Since then, TAIR has made another public release, TAIR_Data_20150630. If you wish, you can retrieve this data directly from TAIR as well, from their public release directory, where you will find the following files:

  • gene_aliases_${RELDATE}.txt
  • Locus_Published_${RELDATE}.txt.gz
  • TAIR10_functional_descriptions_${RELDATE}.txt.gz
  • ATH_GO_GOSLIM.txt.gz
  • po_anatomy_gene_arabidopsis_tair.assoc.gz
  • po_temporal_gene_arabidopsis_tair.assoc.gz

The data of your interest should be in the gene_aliases_${RELDATE}.txt file.

Hope this helps!

Thank you,

Vivek Krishnakumar
On Behalf of the Araport Team