cage : cap analysis of gene expression , a method based on selection of rnas containing the 5 cap modification and obtaining short sequences or tags near the 5 end of these rnas . encode : encyclopedia of dna elements , an nhgri - sponsored project aimed at empirically identifying functionally important element in the human genome sequence , http://www.genome.gov/10005107 . genomic dark matter : usually refers to the portion of a genome that does not correspond to exons ( coding or non - coding ) of annotated mrnas . outward  positioned primers to amplify toward the 5 and 3 end of an rna molecule from a point inside the molecule . rnaseq : a method to quantify and profile rna population in a cell based on massive sequencing of short ( typically less than 100 bases ) regions of a large number of rna molecules . typically , sequencing is conducted on cdna , rather than rna , thus cdnaseq would have been more appropriate . however , rnaseq is used for historical reasons . a note , since direct rna sequencing is now possible , a bona fide rnaseq analysis should somehow be distinguished from cdnaseq . single - molecule sequencing : a method where a single - molecule of a nucleic acid is sequenced directly as opposed methods that obtain sequence signal from a population of molecules . tiling array : a microarray platform designed to interrogate genomic sequence with a certain resolution set by the distance between the probes . opposite in concept to exon arrays where probes are designed only to the annotated regions of interest . vlinc : very long intergenic non - coding rna region , identified based on continuous rnaseq signal that spans genomic regions of 50  kb or longer ( often much longer ) in the area of genome where no annotated gene has been found . the authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest .