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1) What is the script for Notifications and "You have new messages"?

2) Does Wikia take JQuery code?

3) How do I put a JQuery script above the Wikia header For example, where and how would I put this code:

<div class="toprightbox" style="display:none">
<span onclick="jQuery(this.parentNode).fadeOut();">
<img style="position:absolute; TOP:0px; RIGHT:3px; align="right"; width:50px; height:50px; src="" />
<script type="text/javascript">
// Popup window code
function newPopup(url) {
popupWindow =
<a href="JavaScript:newPopup('');">
<span style="color: #000000; font-size: 14pt">Contact Us</span>
<hr /><span style="color: #000000; font-size: 8pt">Having Problems completing the form, try refreshing by pressing F5!</span></a></center>


.toprightbox {
  position: absolute;
  top: 10px; right: 10px;
  background: #e1ebf2;
  color: #000000;
  text-shadow: 0px 0px 10px #000000;
  padding: 10px;
  -webkit-box-shadow: 0px 0px 10px #FFFFFF; -moz-box-shadow: 0px 0px 10px #FFFFFF;

—This unsigned comment is by Andromeda Vadum (wallcontribs) 21:53, 2012 March 31 (UTC). Please sign your posts with ~~~~!

I think I have answers to some of your questions.
#2. Wikia loads the jQuery library in the <head> section of all pages, so added jQuery code will work. However, <script> tags and onclick attributes placed directly in the body of an article generally will not work, since wikimarkup ignores that kind of html code. Instead, you can use <verbatim> tags to include the html/jQuery code inside an article, or you can add your jQuery code to MediaWiki:Common.js on the wiki where you want it to work so that it will be loaded in the <head> section of all pages.
#3. First of all, adding something above the Wikia header may be against the terms of use. Check out Help:Customization policy for information about what is or is not allowed. Secondly, inserting a link that directs visitors to an externally hosted contact form asking for a visitor's personal information would almost definitely be against the terms of use, but you should contact Wikia about it to be sure. Why don't you just use a link to Special:EmailUser/Andromeda Vadum instead? With that said, the insertion could be done by placing the following in the MediaWiki:Common.js:
$(document).ready(function() {
	$('#WikiHeader').before('content you want to insert');
--Gardimuer { ʈalk } 11:39, April 1, 2012 (UTC)
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