That j sound is a g
soft-gThe g of emarginate stands in front of an i and goes soft. It is the same g, in the same position, as the one in margin.
heard asemarjinate
spelledemarginate
saidee-MAR-jin-ut
emarginate. A g, followed by an i.
English gives g a soft j sound before e, i and y. Margin, ginger, gentle and gymnasium all work that way, and so does emarginate, which is really just margin wearing a prefix and a suffix. Writing the sound as a j is what you would do if you had only ever heard the word, and it is the single most common way this one goes wrong.
Nearby in the file
emargenate emarginat emerginate emarrginate emarginute emarginnate
The rest are on the word page. All 11 spellings of emarginate.