I have a question regarding the same-origin
policy.
My company has many subdomains and in one of them they would like an iframe with another subdomain
The things that define a domain in this context are protocol, port and domain so http://abc.com and https://abc.com are considered different domains by your browser (http vs https).
http://en.wikipedia.org/wiki/Same_origin_policy#Origin_determination_rules
https://x.company.org and https://y.company.org are also considered separate domains but they can both relax their domain setting to https://company.org and cross-communicate.
http://en.wikipedia.org/wiki/Same_origin_policy#document.domain_property
There's another option available to you now as HTML5 is in all the major browsers. Using the HTML5 postMessage you can communicate across domains, assuming the receiving domain wants to accept the message and respond.
http://html5demos.com/postmessage2