By identifying genomic sequence regions conserved among several species, 
comparative genomics offers opportunities to discover putatively functional 
elements without any prior knowledge of what these functions might be. 
Comparative analyses across mammals estimated 4-5% of the human genome to be 
functionally constrained, a much larger fraction than the 1-2% occupied by 
annotated protein-coding or RNA genes. Such functionally constrained yet 
unannotated regions have been referred to as conserved non-coding sequences 
(CNCs) or ultra-conserved elements (UCEs), which remain largely uncharacterized 
but probably form a highly heterogeneous group of elements including enhancers, 
promoters, motifs, and others. To facilitate the study of such CNCs/UCEs, we 
present our resource of Conserved Elements from Genomic Alignments (CEGA), 
accessible from http://cega.ezlab.org. Harnessing the power of multiple species 
comparisons to detect genomic elements under purifying selection, CEGA provides 
a comprehensive set of CNCs identified at different radiations along the 
vertebrate lineage. Evolutionary constraint is identified using threshold-free 
phylogenetic modeling of unbiased and sensitive global alignments of genomic 
synteny blocks identified using protein orthology. We identified CNCs 
independently for five vertebrate clades, each referring to a different last 
common ancestor and therefore to an overlapping but varying set of CNCs with 24 
488 in vertebrates, 241 575 in amniotes, 709 743 in Eutheria, 642 701 in 
Boreoeutheria and 612 364 in Euarchontoglires, spanning from 6 Mbp in 
vertebrates to 119 Mbp in Euarchontoglires. The dynamic CEGA web interface 
displays alignments, genomic locations, as well as biologically relevant data to 
help prioritize and select CNCs of interest for further functional 
investigations.