Safir,
I wouldn't store any private tables in the same database as Jira is
stored. Not even if the data is directly related to your Jira
instance.
The solution Matt gives is the easiest way, using custom fields if you
need to, but if a lookup table, for example holding customer
information, is to be referenced, you'd better create a plugin (if
that's not yet available, I wouldn't know) and connect to your
external database from the plugin, not the other way around.
If you just need a totally un-related database-table on the same
server, then ask the database maintainer/owner for an account to your
private database, still away from the Jira db, and connect that in the
usual way from your application.
HTH