Selected synopsis (emphasis by me):
Ryo Narushima (成嶋 亮 Narushima Ryō?), a talented highschooler who was about to enter Tokyo University, the most prestigious university in Japan, killed his parents before his successful life could begin. [...] The 16-year-old bookworm murderer was convicted and sent to a reformatory where he was gang raped by other boys. Kenji Kurokawa (黒川健児 Kurokawa Kenji?), a jailed man who nearly assassinated Japanese Prime Minister decades ago, was sent to the reformatory to teach the youngsters karate every week. [...] Ryo returns to society with the mindset of gaining strength so as to survive and never be a victim again.
Of interesting note is that
This story was inspired by the Kobe child murders of 1997 that a 14-year-old "Boy A" ("Shōnen A") killed and decapitated several children.
The plot and settings somehow reminded me of Rainbow, which tells the story of 7 teenage delinquents, their lives in the reformatory, and their encounters in the real world outside. One of the seven killed his father (if memory serves), another went searching for his sister, and yet another learned boxing while in the reformatory, all very similar to what the protagonist Ryo in Shamo did.