Getting CSE in KIIT with a rank of 39251 will be difficult. In 2021, the required cutoff for CSE at KIIT was 5044. KIIT only takes into account your score in KIITEEE and your board percentage for admission.
However, if you get admission to a different branch, there is still an option for changing the branch to another department. If you have the required GPA in the first semester, then you can put it in the application for changing the branch to whatever they wish for. You can talk to the seniors and know the procedure.