What are some anime or manga with prominent gay characters that

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Neon Genesis Evangelion

Also, Yuureitou, but it's more about transgenderism than homosexuality

Anyway, I doubt you'd find much of them unless you go for deep underground stuff...
Homosexuality is kinda... taboo in Japan. So aside from yaoi/yuri, I doubt you'd find many of them.

>>259915
Psycho-Pass

Kiniro mosaic

>>259915
Utena, at least the TV series
Wandering Son is more about gender identity than it is about gay romance
Both series defining focus is more about coming of age and growth than it is about homosexual romances. Personal favorites of mine too. They start kind of slow.

Mirai Nikki, the pretty much most competent character was also gay. There was one in Akame ga Kill as well but he doesn't get much screen time.

Samurai Flamenco

River's Edge
Not Simple

>>259915
No. 6 is basically shounen ai if romance wasn't the focus. It's still made for fujoshi, but the gay romance comes secondary to the plot.

One of the main characters in Gankutsuou is gay. The whole thing is pretty gay in general, but this character is a certified homosexual.

There's a pretty new manga out called Shimanami Tasogare that's basically about an LGBT support group.

I haven't seen it myself, but I think Moyashimon has LGBT themes. And I also haven't seen Genshikan, but I think one of the seasons has a transgender protagonist.