Given a nilpotent endomorphism, we consider the manifold of invariant subspaces having a fixed Segre characteristic. In [Linear Algebra Appl., 332–334 (2001) 569], the implicit form of a miniversal deformation of an invariant subspace with respect to the usual equivalence relation between subspaces is obtained. Here we obtain the explicit form of this deformation when the invariant subspace is marked, and we use it to calculate the dimension of the orbit and in particular to characterize the stable marked subspaces (those with open orbit).Moreover, we study the rank of the endomorphisms in the quotient space by the subspaces in the miniversal deformation of the giving subspace.