All Cufflinks assembled transcripts, whose 5’ends, regardless of strand, were located within the outer boundaries of CAGE enhancers or, on the same strand, within 200bp (upstream or downstream) of a GENCODE (v10) protein-coding TSS were considered for further analysis. For these Cufflinks transcripts we calculated their (intron-less) RNA length, (possibly intron-containing) genomic length as the genomic distance between their 5’ and 3’ ends, as well as their number of exons. Exons of Cufflinks transcripts with 5’ ends in enhancers were further checked for at least 50% (reciprocal) overlap with exons of GENCODE (v10) known, level 1, protein-coding genes and lincRNAs. We repeated the same analysis specifically for u-enhancers.
