- CDS or CDS -- 3′ UTR, the decoy site is assigned to the region in which the majority of the site is contained. The length of the 5′ UTR, CDS, and 3′ UTR of 286 transcripts is tallied respectively, and then the number of decoy sites for each feature is normalized to 1 kb sequence length. (**B**) Predicted decoy sites are classified into the 'bulge' type if there are bulges corresponding to miRNA bases 10--11, otherwise, they are classified into the 'mismatch' type, decoys of which have at least one mismatch to miRNA base 10 or 11.](pone.0021330.g007){#pone-0021330-g007}

10.1371/journal.pone.0021330.t001

###### Distribution of predicted decoys in functional categories.

![](pone.0021330.t001){#pone-0021330-t001-1}

  Category                   Loci     Transcripts   Decoy Sites
  ------------------------ --------- ------------- -------------
  Protein Coding              230         286           292
  Short Peptide                1           1             1
  Pseudogene                   5           5             5
  ⊤Transposable Elements      22          22            23
  Known Decoy (IPS1)           1           1             1
  Other RNA                    1           2             2
  **Total**                 **260**     **317**       **364**

miRNA decoy sites are predicted from *Arabidopsis* loci in different functional categories, including protein coding genes.

Discussion {#s3}
==========

Typically, plants are genetically engineered to express single exogenous genes for traits, such as resistance to herbicides and insects [@pone.0021330-James1]. A global challenge is increasing agricultural productivity for a growing population. This challenge may be met by creating more productive crops through the addition of traits, including improved tolerance to abiotic stresses such as drought, or increased yield potential. Such traits are usually controlled by a number of environmentally regulated genes, and complex trait engineering may require finely regulated or coordinately modified expression o