Dear Parth ,
A Caste Certificate is proof of one's belonging to a particular caste as specified in the Indian Constitution. The Government felt that the Scheduled Castes and Tribes need special encouragement and opportunities to progress at the same pace as the rest of the people in the country. So its doesn't matter where you live but if you are apply through domicile quota and you have Rajasthan certificate rather then Gujarat then it will trouble .
So as per my knowledge you will not face any difficulties at the time of admission if you have proper and accurate document .
Hope it will helpful
thanks
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