You should look at Thalemine from Araport. They have the latest Arabidopsis annotations (most other sites are still using the TAIR10 which is a bit outdated now (Reference)).
Here's their search page.
Alternatively, you can do it via the API which they give templates for. Here is one I bodged from their script for pulling ontologies in bulk rather than one at a time:
$ thalemine_query genelist.txt
# This is an automatically generated script to run your query
# to use it you will require the intermine python client.
# To install the client, run the following command from a terminal:
# sudo easy_install intermine
# For further documentation you can visit:
# The following two lines will be needed in every python script:
from intermine.webservice import Service
service = Service("https://apps.araport.org:443/thalemine/service")
# Read file with list of genes for searching.
gene_list_file = sys.argv
gene_list = open(gene_list_file, "rU")
# Get a new query on the class (table) you will be querying:
for gene in gene_list:
gene = '"' + gene.rstrip() + '"'
query = service.new_query("Gene")
# The view specifies the output columns
"primaryIdentifier", "symbol", "name", "pathways.identifier",
# Uncomment and edit the line below (the default) to select a custom sort order:
# query.add_sort_order("Gene.primaryIdentifier", "ASC")
# You can edit the constraint values below
query.add_constraint("Gene", "LOOKUP", gene , "A. thaliana", code = "A")
# Uncomment and edit the code below to specify your own custom logic:
for row in query.rows():
print row["primaryIdentifier"], row["symbol"], row["name"], row["pathways.identifier"], \