Signs of boat in manuscript (5)
I believe the answer is:
marks
'signs' is the definition.
(mark is a kind of sign)
'boat in manuscript' is the wordplay.
'boat' becomes 'ark' (ark is a kind of boat).
'in' indicates putting letters inside.
'manuscript' becomes 'ms' (abbreviation for manuscript).
'ark' placed within 'ms' is 'MARKS'.
'of' acts as a link.
(Other definitions for marks that I've seen before include "points" , "Grades assigned to school work" , "See 8" , "Goals" , "Visible signs" .)