Dear Mingliang,

Unfortunately there are no direct prediction pipelines for prediction of LNCRNA function in plants at this moment.

The best you can do is to predict function on basis of homology to known LNC RNAs. For this you can use the dataset available in CANTATA db [http://cantata.amu.edu.pl/]

Hope this helps

Cheers

Sayak

Hi Mingliang

I agree with previous answer about the homology of known lncRNAs. However do not be dissapointed if you did not find anything homologous to your specific lncRNA, since those guys have the tendency to be very specific of group and species. I am not a plant person, but in animals it is really amazing how these guys are so specific from genetically defined groups.

Whatever the case, if you have coding expression data, another possible strategy to guess the function of lncRNAs is to check for the genes that are close together with it within the genome (let's say around 100 kb to your lncRNA) and see if they are UP or DOWN compared to your lncRNA. This could pinpoint cis-regulatory effects (or at least guess). Of course that you will always miss the trans-regulatory effects exerted far away in the genome.

In conclusion.. it is very difficult to guess the function of a lncRNA either in plants or animals just by its sequence. The best way would be to knock-down the gene (by CRISPR or LNA gapmers), and see phenotypic effects if possible.

Good luck. Best

Paco

Here are some useful recent advancement on that front....

http://www.cuilab.cn/lnctar,

https://www.lncrnablog.com/lncrnas2pathways-identifying-the-pathways-influenced-by-a-set-of-lncrnas-of-interest-based-on-a-global-network-propagation-method/