Over the last decade, evidence from numerous high-throughput array experiments has indicated that evolution of the developmental processes regulating complex organisms can be attributed to the noncoding regions and not only to the protein-coding regions of the genome (Bertone et al. 2004; Mattick 2004; Kapranov et al. 2007; Clark et al. 2011). The GENCODE gene set has always attempted to catalog this noncoding transcription utilizing a combination of computational analysis, human and mammalian cDNAs/ESTs alignments, and extensive manual curation to validate their noncoding potential. GENCODE 7 contains 9640 lncRNA loci, representing 15,512 transcripts, which is the largest manually curated catalog of human lncRNAs currently publicly available. All the lncRNA loci in the catalog originate from the manual annotation pipeline and are initially classified as noncoding due to the lack of homology with any protein, no reasonable-sized open reading frame (ORF; not subject to NMD), and no high conservation, confirmed by PhyloCSF (see later section), through the majority of exons. The transcripts are not required to be polyadenylated but 16.8% are, and chromatin marks have been identified for 13.9% (Derrien et
