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Due to the fact that your partnership ended on 11/30/2012, your due date
was 3/15/2013 (the fourth month following the end of the partnerships tax
year). However, there is a IRS safe harbor rule that allows you to file form 1065 late if the following applies:
Rev. Proc. 84-35 --
1.) There are 10 or fewer partners.
2.) All partners are US individuals.
3.) All partners file their personal returns for the year on time (including extensions).
4.) The entity files as a partnership.
If all the above items apply, simply write back to the IRS and explain that the return was not late because of the items mentioned above.
If the safe harbor (Rev. Proc. 84-35) doesn't apply, I would mail a letter back to the IRS at the return address of the last notice you received and request that the penalty be removed based on the following issues:
1.) The partnership is now closed.
2.) The due date has always been 4/15/2013 and that the due date was 3/15/13 due to the extraordinary event of the partnership's termination.
3.) Assuming you have not had issues with late filed partnership returns, a statement regarding the partnerships history of timely filed returns.
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