1. Can SO:0000325 rRNA_large_subunit_primary_transcript have the synonym "35S rRNA primary transcript"? It can be a narrow synonym if there are other large subunit primary transcripts of different sizes (the 35S is for budding and fission yeast; I don't know a thing about other species).
2. And would SO include any of the rRNA processing intermediates? I think it could get pretty complicated -- PMID:21385875 shows intermediates of 27S (2 forms, 27SA and 27SB, before and after a bit of trimming, probably by an exonuclease), 20S, 26S, and 7S. PMID:10690410 (a very good review) describes even more intermediates observed in budding yeast.
The term I would have a use for (phenotype ontology cross-product def) would be one for any of the 27S intermediates:
def: "Any RNA molecule of 27S that is derived by cleavage from the ribosomal RNA large subunit primary transcript, and contains the 5.8S and 25S rRNA sequences." [PomBase:mah, PMID:21385875, PMID:10690410]
relationship: derives_from SO:0000325 ! rRNA_large_subunit_primary_transcript
I guess the is_a parent could be transcript SO:0000673 -- it's neither primary nor fully mature ...