Alternative polyadenylation (APA) is an important layer of gene regulation that 
produces mRNAs that have different 3' ends and/or encode diverse protein 
isoforms. Up to 70% of annotated genes in plants undergo APA. Increasing numbers 
of poly(A) sites collected in various plant species demand new methods and tools 
to access and mine these data. We have created an open-access web service called 
PlantAPA (http://bmi.xmu.edu.cn/plantapa) to visualize and analyze genome-wide 
poly(A) sites in plants. PlantAPA provides various interactive and dynamic 
graphics and seamlessly integrates a genome browser that can profile 
heterogeneous cleavage sites and quantify expression patterns of poly(A) sites 
across different conditions. Particularly, through PlantAPA, users can analyze 
poly(A) sites in extended 3' UTR regions, intergenic regions, and ambiguous 
regions owing to alternative transcription or RNA processing. In addition, it 
also provides tools for analyzing poly(A) site selections, 3' UTR lengthening or 
shortening, non-canonical APA site switching, and differential gene expression 
between conditions, making it more powerful for the study of APA-mediated gene 
expression regulation. More importantly, PlantAPA offers a bioinformatics 
pipeline that allows users to upload their own short reads or ESTs for poly(A) 
site extraction, enabling users to further explore poly(A) site selection using 
stored PlantAPA poly(A) sites together with their own poly(A) site datasets. To 
date, PlantAPA hosts the largest database of APA sites in plants, including 
Oryza sativa, Arabidopsis thaliana, Medicago truncatula, and Chlamydomonas 
reinhardtii. As a user-friendly web service, PlantAPA will be a valuable 
addition to the community of biologists studying APA mechanisms and gene 
expression regulation in plants.