The best general RNA database is Rfam (http://rfam.xfam.org) -- it's fairly complete and regularly updated. It includes a number of antisense RNA families, e.g. RF01695,  RF01419, RF02674, etc. The fasta file associated to the families within this database are here:

ftp://ftp.ebi.ac.uk/pub/databases/Rfam/CURRENT/fasta_files

with which one can and construct a BLAST database for searching sequences. A better approach is to download the covariance matrices files associated to each family:

ftp://ftp.ebi.ac.uk/pub/databases/Rfam/CURRENT/Rfam.tar.gz

and do the search with infernal: http://eddylab.org/infernal/

Now for the targets of your antisense RNA (asRNA), well, each RNA family within Rfam is well described, and normally will tell you about the targets. But in the case of the asRNA, aren't the targets simply reverse complement sequences of the asRNA? in that case you can simply search your asRNA sequences in the genome sequence of your organisms of interest with an aligner like blast, perhaps modifying some parameters like gap penalty, etc.

Finally you might also want to check a tool called copraRNA:

http://rna.informatik.uni-freiburg.de/CopraRNA/Input.jsp

I hope that helps. Best regards.

There is this 2006 paper with the algorithm to predict RNA targets for a given antisense oligo but they do not have the searchable tool online:

https://www.ncbi.nlm.nih.gov/pubmed/16597239

Here you could design antisense for your target:

Soligo:

http://sfold.wadsworth.org/cgi-bin/soligo.pl

OligoWalk:

http://rna1.urmc.rochester.edu/cgi-bin/server_exe/oligowalk/oligowalk_form.cgi

Any feedback? did some of the suggested methods, either by Igor or me, actually worked for you? maybe you did find another method? thanks.

Hello Salvador, 

First of all, that you so much for your reply. The information you provided is really interesting and I will surely use some of it for other of my projects.

But what I was looking for is more a tool to quickly find the corresponding gene targets of a list of antisense. I have the antisense ensembl ID, the  name, and the position in the chromosome, and I need the target. I can find one by one but I would like to know if there is a tool to do it quickly, an antisense-target data base  (I have a list of 2500 antisense).

For example: ENSG00000253374, RP11-257P3.3, AC023644.1, target FABP12

Hello Laura, 

Unfortunately I don't believe there exists a database for targets of asRNA given, say, a locus in every genome. However, if you have your 2500 asRNA as a fasta file, you can employ the procedures that I have suggested previously. Even the last tool, copraRNA, can be downloaded and executed locally to do an automatic analysis if your sequences are too many for using online tools. The same you can do with Rfam, etc.. 

I hope you find the database you need but maybe you can start trying these methods, just as an exploratory exercise if you want. 

Best regards.