I've started learning japanese not long ago, from what I've learned the
correct way to say "see you" is じゃ【ja】、また【mata】.

But I've just seen a show and a character said じゃね【ja ne】.

So I searched a bit and found that the translation is actually またね【mata ne】.

So could anyone clear this up for me? What are the differences, what is the
role of また【mata】 and じゃ【ja】?
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word-choice translation greetings
What is the correct way of saying "see you"?
So, the actual "correct" (i.e. expanded) phrase is :

> じゃあ、またね！ or じゃまたね！

Keep in mind that is only intended for casual conversations. Other greetings
are in order in other contexts (See below). This phrase itself is actually
already a
[shortening](http://ejje.weblio.jp/content/%E3%81%A7%E3%81%AF%E3%81%BE%E3%81%9F%E3%81%AD)
where 「じゃ」 replaces 「では」 wit the same meaning but more informal.

To separate it, think of "じゃ「あ」" as `then`, "また" is closer to `see you` and
"ね", albeit more [complicated](http://www.tofugu.com/2013/07/11/the-many-uses-
of-ne/), can be
[summarized](https://japanese.stackexchange.com/questions/23442/whats-the-
meaning-of-%E3%81%A7%E3%81%99%E3%81%AD-in-here) as:

> The ね is either implying a question where agreement is expected (...)

So as virmaior pointed out, "また" is probably the closest to `see you`. But you
would usually use it in a casual way, thus shortening the sentence to either:

  * じゃ、また
  * じゃ、ね

That means `see you around`, `see you soon`...

If you want to be more precise, add an event or a timeframe after また:

  * また来週{らいしゅう}! (See you next week)
  * また会｛あ｝おうね! (See you next time we meet)
  * また来{き}ます! (I'll be back, lit. see you when I come back)

You can then play around with other durations, and add/remove parts of the
original sentence as pointed out in the comments:

  * じゃあ、明日{あした}ね (Catch / See you tomorrow)
  * また今度{こんど} (Catch / See you next time)
  * また後{あと}で (Catch / See you afterwards)

Remember that, as almost always in japanese animation, these are familiar
examples (Do not use them in a business context) !
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Actually じゃ、また is the abbreviated form of

では[Indicate changing the subject of conversation]、また(again)今{こん}度{ど}(next
time)会{あ}いましょう(meet)

which, altogether, gives "See (you) again next time".
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As others have pointed out, there are many ways that one can say farewell.
However, you seem interested in the shortest, most common way to say it
casually. This is the phrase that you want:

じゃね！

To clarify, the phrase 「じゃ、またね！」is used in the same way we might say "Ok, see
you later!" in English. The また part carries the meaning of "later".

If you shorten that longer phrase to just 「じゃね！」 it can be used the same way
that an English speaker might say, "Later!" or, "See ya!"
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