hi,

see the eligibility criteria for gate exam is candidates need to have bachelors degree of 4 years in technology or in relevant field or 2 years  masters course in relevant discipline. however students who are in final year of their bachelors or masters course are eligible to apply. so I suggest you to give your masters course as latest degree. since you have bachelors course of 3 years duration I guess, you have to give msc course as your latest qualification.