Small noncoding RNAs are automatically annotated from the Ensembl pipeline and included within the GENCODE gene set. The number has remained relatively stable at 8801 since release 4. Protein-coding and noncoding transcripts that contain a small ncRNA within at least one intron or exon will be annotated with the attribute ncrna_host. Thirty-three percent of small ncRNAs map within the boundaries of a GENCODE gene, the majority of which reside in introns. The GENCODE 7 release contains 1679 protein coding and 301 lncRNA genes with ncrna_host attributes, and there is a sixfold enrichment of small nuclear RNAs (snoRNAs) within exons of lncRNAs (Derrien et al. 2012).
