Poor rat has pain inside windpipe (7)
I believe the answer is:
trachea
'windpipe' is the definition.
(synonyms)
'poor rat has pain' is the wordplay.
'poor' indicates an anagram.
'has' means one lot of letters goes inside another.
'pain' becomes 'ache' (ache is a kind of pain).
'rat' anagrammed gives 'tra'.
'tra' placed around 'ache' is 'TRACHEA'.
'inside' is the link.
(Other definitions for trachea that I've seen before include "The formal windpipe" , "body part" , "Tube carrying air to the lungs" , "It connects the larynx and bronchi" , "air passage" .)