How to preprocess Bootstrap region
Here the solution, if somebody is interested:

create new section in your theme, call it e.g. bottom-section and use this preprocess hook to move the content of the bottom pane to bottom-section section

function theme_preprocess_panels_pane(&amp;$variables) {
  if ($variables['pane']-&gt;panel == 'bottom') {
    // Move to a region
    drupal_add_region_content('bottom-section', $variables['content']['#markup']);
    // Delete the pane from the panel
    $variables = array();
  }
}