Cannot get JavaScript set value in code behind

I have a (mainly) JQuery and JavaScript  aspx page with a mix of .net and html controls on it

On the page...A span's innerHTML and a  .net hiddsen field both get set

I know they are set because I can do an JavaScript alert and get the ID's by calling the script below

function setHiddenReplyID() {
    var myHidden = document.getElementById('<%= hdnPopupMessageID.ClientID %>');
    myHidden.Value = document.getElementById('sel').innerHTML;
    alert(document.getElementById('sel').innerHTML + "| " + myHidden.Value)
}

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However...
When I do a .Net Button Submit...
I cannot get either value

C# Code behind

string str = sel.InnerText.ToString();
int MessageID = int.Parse(hdnPopupMessageID.Value);

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These are the controls
<span id="sel" runat="server" class="inbox-receivedID" style="color:transparent;" ></span>
<asp:HiddenField ID="hdnPopupMessageID" runat="server"/>

I don't care which one I use...
I somply need that id accessible in code behind to pass into SQL Server