Well, for that gene is only one transcript associated to the gene (AT3G53180.1 at Ensembl), looks longer than other species, but this is expected in plants (Compara tree). I don't know what analyzes do you want, so maybe it's better to keep the full sequence until you know what you doing.

You can try to in-silico predict the CDS, with a tool like TransDecoder, and see how the results match to reference entry. If the situation is quite desperate, you can take the following, very time-consuming move: look for Arabidopsis RNA-Seq data at SRA and try to extract/de-novo assemble isoforms for that gene with tools like Trinity or TopHat.