I am trying to express the gene in P. pastoris GS115 using PPIC9 vector. I have linearized the recombinant vector with stu 1 and electroporated in pichia. My clone showing band of 1300 bp (gene size) with my gene specific primer but with alpha factor primer it shows band of only 195 bp (PPIC9 back bone) instead of 195+1300 and even my untransformed pichia control is also showing this band. What could be the reason?

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