Although the current definition of lncRNAs requires the transcript to be >200 bp (Wang and Chang 2011), the GENCODE ncRNA set contains 136 spliced transcripts <200 bp (all of them single transcript loci) to highlight that there is evidence of expression at that position in the genome. We currently group the transcripts into loci, which is different compared with other lncRNA analysis groups, for example, the Fantom Consortium (Katayama et al. 2005). Multiple lncRNA transcripts appear to start from the same transcription start site (TSS), for example, the DLX6-AS1 locus shown in Supplemental Figure 2. To estimate the completeness of the lncRNA transcripts, we took advantage of CAGE tags from 12 different cell lines and manually annotated polyA features to assess the TSS and 3′ end of transcripts (Djebali et al. 2012). The beginning and end of 15% and 16.8% of lncRNA are supported, respectively, indicating that the majority of transcripts are incomplete. Interestingly lncRNA transcripts have an unusual exon structure compared with protein-coding transcripts, with their distribution peaking at two and five exons, respectively (see Fig. 2). This lower
