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OpenJDK is also the base for Oracle's supported Java packages. If you download JDK 6 or JDK 7 it is for the most part OpenJDK you're downloading.
That being said there is only one way to find out of your particular JavaFX applet works with OpenJDK: try it.
EDIT: judging by this linked article it seems that the people behind Ubuntu are blowing an incredible amount of smoke for nothing: