Dungar first of all as you are doing BE in IT so you will need to give GATE exam in your IT branch only and yes there is a provision of opting a different specialization branch for doing M.Tech from IITs on the basis of your GATE score but whether you can get a CS branch specialization branch with an IT GATE score cannot be said surely because it depends on the various branches department whether they want to accept a different branch score or not. There is no fixed provision and it varies from college to college, department to department within the college.

As IT and CS branches are quite similar and in many of the IITs for both these branches the department is also same so you have a very good chance to get CS branch with your GATe score in IT paper but in order IIT Bombay CS branch your score needs to be best of the best. Work hard and get maximum marks in your GATE exam.

Feel free to ask if you have any more queries. All the best!!