Clearing notifications after reading emails

Maybe this is a dumb question, on 10.8.1 - 12 core Mac Pro, all notifications work just fine, but when I clicking on an email notification, read the email and reply to it, the notification still show on the notification center with a blue dot as if I never responded to it, how can I clear it from the list after reading or responding?
M

What type of email account are you using, POP or IMAP? Does it happen with more than one account?
If you have a POP account, that service downloads the emails and then automatically deletes them from the server. See this Apple doc for more info -> Using a POP account with multiple devices

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