Hello Girish,
Of course you have to select OBC category in the JIPMER Application Form 2019. You can apply for the JIPMER 2019 till 12th April 2019, the application form is available from 6th March 2019.
For more information, please go through the link given below
https://medicine.careers360.com/articles/jipmer-application-form
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All the best.

JIPMER being a national level examination , your caste certificate based on a national level shall be taken into consideration. Here as you have mentioned OBC, it shalll be OBC in JIPMER.