Go through the following link. Hope this will solve your issue.

http://www.targetscan.org/ 

Dear Manish

Thank you for your consideration.

As I said, I need a tool that predicts miRNAs interacting with my sequence based on its features. But programs like targetscan do the opposite! and are used in case of miRNA target genes finding.

In my case, some tools like miRWalk made it possible by "walking" the genes of just 3 genomes, but not mine (Arabidopsis). Usable in the wide ranges of organism, microinspector server seems is not working.

However, I wonder If there is not any program for this goal!

Dear

Please find interesting paper: miRWalk – Database: Prediction of possible miRNA binding sites by “walking” the genes of three genomes. Journal of Biomedical Informatics. Volume 44, Issue 5, October 2011, Pages 839–847

http://www.sciencedirect.com/science/article/pii/S1532046411000785

Dear Marius

miRWalk made it possible, but In my organism (Arabidopsis) it does not work!

The question misses a fundamental information, the organism on which you want to do the analysis. Plant and animal mirnas have rules for pairing on targets (and effects of the regulation) that are very different therefore tools working for instance in mammals, do not work properly in plants and viceversa. Anyway, at some point it pops out that you work on Arabidopsis. In plants you can use SeqTar giving as input a set of mirna sequences (for TAIR you ca get all the known mirnas from mirbase) and a blank degradome file if you do not want to use/have this and your favorite transcript or even, I think cleaveland. Seqtar will give you possible alignments on your transcripts by any of the mirnas in the input.

Hi Zahra

The database which is helpful for your case is psRNATarget, a plant small RNA target analysis server. 

Link: http://plantgrn.noble.org/psRNATarget/

 Dear Matteo

Thanks a lot. I think SeqTar may be  far from my purpose! As I need a tool that give me a list of candidate miRNA(s) that exhibit propensity to bind and interact with my gene of interest e.g. PR2 in Arabidopsis. I am really wondering if SeqTar do the same.

Your answer is appreciated.

Dear Reyhaneh

Thanks in advance for helping me out. Your commented server is exactly what I need.

Dear Zahra, yes you can do this with SeqTar. It would require degradome data but you can input an empty file I think. then the input transcript will be the one you are interested in and the sRNAs all the sequences you have. SeqTar will not, however, check if the sRNA it is using as possible regulators are indeed miRNAs (it does not check e.g. structure of the region surrounding the sRNAs in the genome for hairpins etc). You also have cleaveland for a similar purpose.

Dear Matteo, thanks for your consideration. I will try SeqTar in the way you explained. Hope it works.