Don't beat yourself too much over it. Once you get in, you have ample opportunities to rise above your JEE rank. Just be sure you get into a branch you are interested in.. Somewhat.
4/5 years later, your JEE rank will be insignificant compared to what you did in your college and what you learnt.
[
I graduated from IIT Kharagpur a few weeks back. AIR 3148 in JEE '06. Sad rank, but I think I made it out okay... ]