Is there any bioinformatics tools to find uncharacterized Long non-coding RNAs of genes of interest?

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Adriana Contreras

Nucleic Acids Res. 2013 Jan 7;41(1):e20. doi: 10.1093/nar/gks877. Epub 2012 Sep 24.

Noncoder: a web interface for exon array-based detection of long non-coding RNAs.

Gellert P1, Ponomareva Y, Braun T, Uchida S.

Dejun Li

The paper "ncFANs: a web server for functional annotation of long non-coding RNAs" might be helpful for you.