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Schalke condemned the action of the perpetrators in a post on Twitter and promised that the club will investigate the matter.
"We can only apologise for the behaviour of some of our fans towards Youssoufa#Moukokoat today's U19s match. Derby emotions aside, we completely condemn and oppose such insults," a tweet read.
Moukoko hit back at the Schalke fans with an Instagram post which read: "I am proud to be born with this skin colour and will always be proud."
Andteam-mate Lloyd-Addo Kuffour expressed his outrage in a post-match interview, saying:“It's a shame that some fans still haven't understood that we're in 2020.
"In football we have no place for racismand yet I'm very proud of the guys that we gave the right answer on the pitch."
Meanwhile, Dortmund's youth co-ordinator Lars Ricken was appalled by the vitriol aimed at the striker, but was proud of the team's response in Gelsenkirchen.
“The players have known each other for years from various selections and direct duels against each other. Again, despite all the intensity, it was actually a fair game the whole time."
Moukoko's hat-trick was his third in a row, having helped his side obliteratePreussen Munster U19s 5-0 in September before his one-man show in the 3-0 win againstWehen Wiesbaden U19s in the youth DFB-Pokal earlier this month.