Dividends:
Box 1a - ordinary dividends -list the full amount and enter the nominee amount. Goes to Sch B The nominee portion will go to the estate return -Form 1041, line 2a.
Box 1b - qualified dividends -only enter your father's share in the program for his return. The remainder goes to the estate return.
Boxes 2a and 2b - capital gain and unrecaptured 1250 gains - report your father's share on Sch D. The remainder goes on the estate return.
Boxes 11 and 12 - tax-exempt and AMT - report your father's share. The remainder to the estate return. The tax exempt items do need to be reported as they affect the distribution deduction. See 1041 Sch B, line 1.
CA: your federal tax exempt dividends are only tax free in CA if they come from CA municipal bonds. The supplement will show CA and federal amounts that can be exempted. Use those percentages to get the taxable amount. Prorate as best you can between the personal and estate.
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