I think it would be better if you specify the JAVA_HOME env variable in your .bash_profile file. If you have root access, you can set it into file /etc/bashrc so that it will be available to all users.
In Unix/Linux, environment variables aren't something you set globally and they apply everywhere. Most commonly you set them in one of the profile files (I prefer .bash_profile) for the account that will use them.
Also, in case you haven't been bitten yet, every time you open a new command shell and don't specify otherwise, you'll get a new environment. A lot of people get frustrated becuase they write a script that sets JAVA_HOME but after they call it, JAVA_HOME's not set, because they didn't export the value from the script's environment to the script invoker's environment.
JAVA_HOME isn't used by Java itself, but it's a very useful convention adopted by all the major Java applications. It makes it possible for different apps to run with different Java versions in the same machine.
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