I have a sequence of miRNA and a large sequence of target mRNA of Arabidopsis and i want to find out the potential binding position of this miRNA within the mRNA sequence. Can anyone suggest/guide me how can i do it. Any suggestion will be well appreciated. Thanks in advance.
I don't know exactly about arabidopsis species, but generally, for human/rat/mice, there are databases (such as miRBase, TargetScan, miRDB, miRTAR, DIANA TarBase, etc) where u will find the miRNA and its respective targets which are being generated using bioinformatic docking method and further validated using 3'UTR reporter assay, western blot, and qRT-PCR. Those databases contain the seed sequence match also.
You can set up your own experiment and establish the miRNA-mRNA relation. first, overexpress the miRNA and do qRT-PCR of some possible genes based on literature review, the do western blot of selected one, and then finally do 3'UTR reporter assay of one gene which has shown strong positive results.
Dear Shankar
Please check psRNATarget ( http://plantgrn.noble.org/psRNATarget/ ), it is specific for plants.
To run your query " I have a sequence of miRNA and a large sequence of target mRNA of Arabidopsis " i think third option of server will be good "submit small RNA and Target"
Hello
Kindly, look at links :
https://academic.oup.com/nar/article/33/suppl_2/W696/2505446
http://sfold.wadsworth.org/publications/Starmirdb.pdf
Good Luck
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