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So far I learned that these three words mean "below" or "bottom", is it right? If so, are they interchangeable? Could you give me some example and preferably some explanation about how to use them?

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下{した} is the more common of the three by a huge margin, and what you'll want to use at least 99% of the time. It's a completely basic word for "down", and has a huge variety of uses. It's the counterpart of 上{うえ}, the common word for "up".

下{しも} is a much, much rarer word, and I find it's mostly encountered in a small handful of set expressions, such as 風下{かざしも} "downwind", 川下{かわしも} "downstream" and 下{しも}ネタ "dirty jokes" (as in "jokes about the lower part of the body). It's the counterpart of 上{かみ}.

下{もと} is also restricted to certain specific uses, and is perhaps the furthest away from the basic meaning of "down". It's a variant of 本{もと} or 元{もと} meaning "origin", and generally refers to a location rather than a direction. Its uses include indicating the "root" or "base" of something (eg. 桜の木の下{もと}に "at the base of the cherry tree"), referring to a person as a location (eg. in the expression 親の下{もと}を離れる "to move home away from your parents") and referring to a higher power that one exists "under the authority" of (eg. 厳重な監視の下{もと}に置く "to place under strict surveillance"). This one doesn't have any "up" equivalent that I can think of.

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  • It's 親の元. Maybe you could also include the difference between もとに・もとで・もと. Otherwise I agree with you answer. Commented Oct 18, 2017 at 8:44
  • Actually, I wasn't sure about which もと kanji is more natural for 親のもとを離れる myself, but I looked on Goo Jisho and the phrase is specifically listed under the entry for 下 (dictionary.goo.ne.jp/jn/219559/meaning/m0u/%E3%82%82%E3%81%A8). Maybe both are acceptable?
    – Ben Roffey
    Commented Oct 18, 2017 at 9:46
  • @永劫回帰: I thought it was 親の許?
    – istrasci
    Commented Oct 18, 2017 at 15:11
  • 桜の 下{もと} seems like a really arbitrary reading to someone who hasn't read much of anything in Japanese like me. Am I going to raise any eyebrow if I just pronounce it as しも (the lower part)? Incidentally, this is the idiom that lead me here: 灯台 下{もと} 暗し, "can't see the forest for the trees."
    – Yeti Ape
    Commented Jun 7, 2018 at 23:22

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