HI,

Can someone give a good definition of the difference ?

Thanks

UCEs are short- and medium-sized stretches of DNA that are identical between different species. They are often non-coding.

Orthology refers always to coding sequences. It requires that function be conserved between different species, but there is no requirement for identical sequence.

While presumably there is a requirement for functional conservation in both cases, evolutionary pressure for sequence conservation is larger on UCEs than orthologs.