BACKGROUND: Only a small portion of human long non-coding RNAs (lncRNAs) appear 
to be conserved outside of mammals, but the events underlying the birth of new 
lncRNAs in mammals remain largely unknown. One potential source is remnants of 
protein-coding genes that transitioned into lncRNAs.
RESULTS: We systematically compare lncRNA and protein-coding loci across 
vertebrates, and estimate that up to 5% of conserved mammalian lncRNAs are 
derived from lost protein-coding genes. These lncRNAs have specific 
characteristics, such as broader expression domains, that set them apart from 
other lncRNAs. Fourteen lncRNAs have sequence similarity with the loci of the 
contemporary homologs of the lost protein-coding genes. We propose that 
selection acting on enhancer sequences is mostly responsible for retention of 
these regions. As an example of an RNA element from a protein-coding ancestor 
that was retained in the lncRNA, we describe in detail a short translated ORF in 
the JPX lncRNA that was derived from an upstream ORF in a protein-coding gene 
and retains some of its functionality.
CONCLUSIONS: We estimate that ~ 55 annotated conserved human lncRNAs are derived 
from parts of ancestral protein-coding genes, and loss of coding potential is 
thus a non-negligible source of new lncRNAs. Some lncRNAs inherited regulatory 
elements influencing transcription and translation from their protein-coding 
ancestors and those elements can influence the expression breadth and 
functionality of these lncRNAs.