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Since there is possibility of "じゃありません" instead of "じゃないです" (which is logical, given "ありません" is polite "ない"), and it also seemed that I have seen "じゃ" used without "ない", I'd like to ask, what "じゃ" exactly means? It looks like some kind of particle which was used in old Japanese but is not used any more.

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It's a contraction of では (particle , which has various uses, and the topic marker ). It is not particularly related to classical Japanese, and is not used only with negation.

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But why is it used to sign letters? For instance, I once received a letter that ended, じゃ, (name). And why is it used to end sentences? –  ixtmixilix Feb 6 '12 at 17:39
    
Only the valediction じゃ is related to では; the copula じゃ is from a (only slightly different) etymology. –  Zhen Lin Feb 6 '12 at 18:11
    
@ixtmixilix That is ellipsis. The reader is expected to reconstruct what comes after it, which is omitted. –  sawa Feb 6 '12 at 18:48
    
@ZhenLin When you start analyzing into its parts, it is not even clear whether it is a copula or it includes a copula. comes from にて, and if you want to claim that is (or includes) a copula, then the only reasonable thing you can do is to claim that is the source of the copula. I don't know how much you can push that idea, but to me, it is more natural to consider that a nominal predicate in Japanese requires dative case and does not necessarily require a copula. For the part that nominal predicates require dative case, you can observe it the construction ...になる. –  sawa Feb 6 '12 at 18:52
    
@ZhenLin I realized that there is an entirely different じゃ, which is a copula, and is used by elder people or is a 役割語: わらわは織姫じゃ。 Are you mentioning that? Then, I don't know the origin of it (but probably it's from である, which in turn is from にてある), and what you wrote may be right. –  sawa Feb 6 '12 at 19:00

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