Orthomap is a web based tool for identifying bioinformatic orthologs between genomes.  You can provide a list of locus/isoform identifiers, which will return the best BLAST matches for the queries against the target genome.  You can then view the results online or download them for your convenience.  Orthomap supports queries for all major plant genomes.

Diurnal provides convenient access to circadian and diurnal gene expression data for several model plant species including Arabidopsis thaliana, Brachypodium Distachyon, Oryza sativa, and Populus trichocarpa.  All of the rhythmic genes have been modeled, which you can interactive view online, or you can download the statistical results for use in your own studies.

Element is a motif identification tool that takes a set or sets of inputed promoters and identifies all of the statistically overrepresented motifs in those sequences.  The results can then be viewed and manipulated online or downloaded for further analysis.  Element also supports searches across multiple genomes to identify motifs overrepresented across both.  It is also provided as a downloadable stand alone tool that can be run in your own local environment with custom background statistics.  

The Arabidopsis Splicing Database is a catalog of all splicing in the TAIR 10 annotation of Arabidopsis thaliana. Users can view the splicing patterns of any gene in the annotation, as well as alter the splicing pattern and view the predicted effect of the alteration. 

Access the Arabidopsis Splicing Database here.

Haystack is web-based tool for identifying most highly correlated model for a data series.  It operates by calculating the Pearson correlation pairwise between a user supplied data series and model.  The model with the largest correlation that passes the cutoff filters is added to the result set.   

Phaser is a web-based tool that allows users to quickly determine if a set of genes that have known diurnal/circadian data are rhythmic and overrepresented for a particular phase of peak expression.