BACKGROUND: Long considered to be the building block of life, it is now apparent 
that protein is only one of many functional products generated by the eukaryotic 
genome. Indeed, more of the human genome is transcribed into noncoding sequence 
than into protein-coding sequence. Nevertheless, whilst we have developed a deep 
understanding of the relationships between evolutionary constraint and function 
for protein-coding sequence, little is known about these relationships for 
non-coding transcribed sequence. This dearth of information is partially 
attributable to a lack of established non-protein-coding RNA (ncRNA) orthologs 
among birds and mammals within sequence and expression databases.
RESULTS: Here, we performed a multi-disciplinary study of four highly conserved 
and brain-expressed transcripts selected from a list of mouse long intergenic 
noncoding RNA (lncRNA) loci that generally show pronounced evolutionary 
constraint within their putative promoter regions and across exon-intron 
boundaries. We identify some of the first lncRNA orthologs present in birds 
(chicken), marsupial (opossum), and eutherian mammals (mouse), and investigate 
whether they exhibit conservation of brain expression. In contrast to 
conventional protein-coding genes, the sequences, transcriptional start sites, 
exon structures, and lengths for these non-coding genes are all highly variable.
CONCLUSIONS: The biological relevance of lncRNAs would be highly questionable if 
they were limited to closely related phyla. Instead, their preservation across 
diverse amniotes, their apparent conservation in exon structure, and 
similarities in their pattern of brain expression during embryonic and early 
postnatal stages together indicate that these are functional RNA molecules, of 
which some have roles in vertebrate brain development.