Bear, Rupert, initially appearing in annual? (5)
I believe the answer is:
brook
'bear' is the definition.
('brook' can be a synonym of 'bear')
'rupert initially appearing in annual?' is the wordplay.
'initially' indicates taking the first letters.
'appearing in' indicates putting letters inside.
'annual?' becomes 'book' (annual is a kind of book).
The initial letter of 'rupert' is 'r'.
'r' going into 'book' is 'BROOK'.
(Other definitions for brook that I've seen before include "running water" , "Stand for" , "Allow" , "Small fresh-water stream" , "Bear - small stream" .)