The following information is regarding TuneCore's Publishing Administration service
Yes! If your song is not distributed through TuneCore (or it's being sold on multiple releases, such as through a label or as a cover song by another artist), after you have signed up and paid for the TuneCore Publishing Administration service, simply click the "Getting Started" link on your Composition Manager where it asks "Need to register songs that were not distributed by TuneCore?" and complete and submit the form that appears.
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