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There is a gene in the human body that was originally named "Pokemon", but was renamed to "ZBTB7". The name change was sparked by The Pokemon Company threatening legal action against the center that discovered ZBTB7, as it is a cancer-causing gene.
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In the Japanese versions of Pokemon, the attack "Night Slash" is called "Blade Testing". This is a reference to an old practice that some immoral samurai held to test their new swords. They would wait alongside a road at night for a random passer-by, then attack them with the intention to kill. Night Slash also has a higher than average critical hit rate, which could be another nod to the story, as the passer by would be defenseless.
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It's rumored that the Pokemon Uxie, Mesprit, and Azelf represent the Triforce from The Legend of Zelda, as they are the Knowledge (Wisdom), Emotion (Courage) and Will-Power (Power) Pokemon. They were also created by the God Pokemon Arceus, and the Triforce was created by the Goddesses Din, Nayru and Farore.
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There's an old Japanese idiom that says, "A duck comes along carrying a leek". It means a happy convenience, as duck with leek is a popular meal. The Pokemon Farfetch'd is based on this saying. The anime also states they are rare due to them being delicious. It seems that Farfetch'd were designed to be eaten from the very beginning. Any notion of them being used as food was later toned down or dropped. Along with the word "leek", which is now called a stick or a stalk.
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Attachment Magikarp and Gyarados are based on a Chinese mythological story where a "Dragon's Gate" is located at the top of a waterfall cascading from a legendary mountain. The few carp that manage to leap over th gate are transformed into powerful dragons. This legend is directly referenced in Pokemon Snap when the player must knock Magikarp into a waterfall to evolve it into a Gyarados.
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In the Japanese releases, the normal type move "Self Destruct" is called "Suicide Bombing".
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When Paras evolves into Parasect, it's actually being engulfed by the fungi growing on its back. It takes over the Pokemon's body and does all the thinking. This essentially leave the Pokemon zombified and lifeless, as illustrated by its lack of pupils.
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There's evidence suggesting that the psychic type in Pokemon is weak to bug, ghost, and dark types because they are basic fears, and fear can manipulate the mind. This is further implied by the ability "Rattled" (or "Jitter" in Japanese) where the user's speed stat is raised one stage when hit by bug, dark, or ghost-type moves, implying they have been shook up, or scared.
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Attachment Pokemon was originally called "Capsule Monsters" but was renamed as the creators had trouble trademarking the name. They also tried to trademark "Capumon" and then "Pocked Monsters". Capsule Monsters was put on hold so Game Freak could develop Yoshi for the NES and Game Boy. The success of Yoshi helped Game Freak acquire the resources they needed to continue work on Pokemon, and could even be the reason we have Pokemon today. The name "Capsule Monsters" is inspired by Japanese gashapon machines. It appears PokeMarts were supposed to sell the capsules, as indicated by this concept art.
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There was a police investigation in Spain called "Operación Pokémon" (Operation Pokemon). It got its name from the almost endless amount of politicians that had committed fraud, so the police took the motto "Gotta catch 'em all!" from the Pokemon series.
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Attachment Niue, an island country in the South Pacific Ocean, made a set of usable $1 coins to commemorate the popularity of the Pokemon games. The Niue coat of arms is on one side, and a Pokemon on the other. The featured Pokemon were Pikachu, Meowth, Bulbasaur, Charmander, and Squirtle.
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In 2008, Japanese researchers discovered a new protein which helps carry electrical impulses from the eyes to the brain and named it 'Pikachurin.' According to the researchers, the decision was based on both the Pokemon and protein possessing 'lightning-fast moves and shocking electrical effects.'
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Attachment The Pokemon Jynx went through a slight redesign due to allegations of racism. The effects were first implemented in the international version of Pokemon Crystal, and can even be seen in the virtual console re-release of Pokemon Snap.
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Koffing and Weezing were originally named "NY" and "LA" respectively, referencing the polluted states of the cities New York and Los Angeles.
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Attachment The Pokemon games (starting with generation II) feature an in-game virus that Pokemon can catch called Pokerus. It can't be healed at a Pokemon center or with items, and can only be contracted by the Pokemon in question once. It has a 3 in 65,536 chance of generating on a Pokemon, either wild or bred. The virus causes Pokemon to gain double the effort values from battles.

The virus will eventually dissipate after two days, all the while remaining highly contagious, though placing an infected Pokemon in the PC will cause the virus to last indefinitely. After the virus is gone, a smiley face (a red dot in Generation II) will appear on the formerly infected Pokemon's status screen, and the positive effects will still remain, particularly the increase in effort values
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Despite looking black-faced, Jynx wasn't meant to be racist. It is actually based off the Japanese Myth, Yama-Uba. Yama-Uba was described as having bright blond hair and a torn red kimono much similar to the design of Jynx.
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There can be 4,294,967,296 different visual variations of Spinda, as Spinda's spots are determined by its personality value. The number is significantly higher if you also include shiny Pokemon.
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Even though the move "Explosion" is a normal type attack, the only normal type Pokemon who can learn it is Lickilicky (by TM, not level up).
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In 1st generation games, Lapras was able to learn Solarbeam from TM. This was taken out of later games.
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Attachment The name of Ghetsis, the main antagonist of Pokemon Black and White and their sequels, actually originates from his battle theme. His Japanese name, G-Cis, comes from the musical notes G and C#, which are the notes the timpani are tuned to in his battle theme. Ghetsis, his name in the English localizations, is a mistranslation. His last name, Harmonia, is Latin for "harmony", another musical term.
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