In elementary, due to not acting masculine enough, she was bullied. She was raised as a boy but always considered herself a girl. Ryoma, one of the one-shot protagonists in IS: Otoko demo Onna demo Nai Sei is intersex.There were NO survivors except for the two of them.
Then Sousou stepped into that, thought they were trying to gang-rape her, and his Superpowered Evil Side kicked in for the first time.
In Adolescence of Utena Saionji mistakes Utena for a boy until partway during a duel he cuts her shirt open.