The GENCODE lncRNA data set is larger than other available lncRNA data sets, and it shows limited intersection with them. Forty-two percent (44 out of 96) of the lncRNA database lncRNAdb (Amaral et al. 2011) are represented in GENCODE lncRNAs. We checked the same strand overlap against recent lncRNA catalogs: GENCODE v7 lncRNAs contain 30% of Jia et al. (2010) lncRNAs, 39% of Cabili et al. lincRNAs (Cabili et al. 2011), and 12% of vlincs (Kapranov et al. 2007) (for more details, see Derrien et al. 2012). While this level of overlap between data sets shows how lncRNA annotation is improving, it also shows that substantial additional work is still required. There are likely to be a number of reasons for the limited overlap between the published lincRNAs and GENCODE, not least that a substantial fraction of transcript annotations are currently incomplete (see below). Another reason is that some of the published transcripts are single exons, which up to now have not been annotated in GENCODE unless there is additional support, for example, polyA features, conservation, submitted sequence, or publications.
