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 .
 the mysteries surrounding the 9798% of the human genome that does not encode proteins have long captivated imagination of scientists . 
 does the protein - coding , 23% of the genome carry the 9798% as a mere passenger and neutral  cargo  on the evolutionary path , or does the latter have biological function ? 
 on one side of the debate , many commentaries have referred to the non - coding portion of the genome as  selfish  or  junk 
  dna ( orgel and crick , 1980 ) , while on the other side , authors have argued that it contains the real blueprint for organismal development ( penman , 1995 ; mattick , 2003 ) , and the mechanisms of developmental complexity . 
 thus , this question could be referred to without much exaggeration as the most important issue in genetics today . 
Glossary
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