Long transcripts that do not encode protein have only rarely been the subject of 
experimental scrutiny. Presumably, this is owing to the current lack of evidence 
of their functionality, thereby leaving an impression that, instead, they 
represent "transcriptional noise." Here, we describe an analysis of 3122 long 
and full-length, noncoding RNAs ("macroRNAs") from the mouse, and compare their 
sequences and their promoters with orthologous sequence from human and from rat. 
We considered three independent signatures of purifying selection related to 
substitutions, sequence insertions and deletions, and splicing. We find that the 
evolution of the set of noncoding RNAs is not consistent with neutralist 
explanations. Rather, our results indicate that purifying selection has acted on 
the macroRNAs' promoters, primary sequence, and consensus splice site motifs. 
Promoters have experienced the greatest elimination of nucleotide substitutions, 
insertions, and deletions. The proportion of conserved sequence (4.1%-5.5%) in 
these macroRNAs is comparable to the density of exons within protein-coding 
transcripts (5.2%). These macroRNAs, taken together, thus possess the imprint of 
purifying selection, thereby indicating their functionality. Our findings should 
now provide an incentive for the experimental investigation of these macroRNAs' 
functions.