Stone put underground, shifting the odd bits around (4)
I believe the answer is:
ruby
'stone' is the definition.
(I know that ruby is a type of transparent gem)
I don't understand how the rest of the clue works.
(Other definitions for ruby that I've seen before include "killed an assassin" , "Deep red variety of corundum" , "A red jewel" , "Jack perhaps" , "Vivid red" .)