The standoff between security forces and protesters who had barricaded themselves inside Al-Fateh mosque near Ramses Square in central Cairo ended this evening when troops used teargas and entered the building.
All protesters were taken out of the mosque and many were arrested, security forces said.
The situation turned violent this afternoon when Islamists inside the mosque fired at security forces outside. Footage on television showed security forces on the ground trading fire with a gunman in the main minaret.
As the toll in yesterday's clashes rose to 173, the Brotherhood today called for a week of protests.
Brotherhood chief Mohamed Badie's son Ammar Badie was among dozens shot dead Cairo yesterday.
Since Wednesday, over 800 people have died in clashes that erupted after security forces stormed two camps set up by Morsi loyalists in Cairo to protest his ouster on July 3.
After yesterday's clashes, scores of protesters took those killed and wounded to Al-Fateh mosque and refused to leave. Security personnel entered the mosque to negotiate with protesters but the Brotherhood rejected a proposal to allow women to leave.
Speaking to Al Jazeera by phone from inside Al-Fateh mosque before it was stormed by security forces, Omaima Halawa - the daughter of the imam of Ireland's biggest mosque - had said there were about 700 people, including women and children, inside.
The Interior Ministry said 1,004 Morsi supporters were arrested after protests yesterday, dubbed the "Friday of Rage" by the Brotherhood.
Authorities also arrested the brother of al-Qaeda chief Ayman al-Zawahiri, a security official said. Mohammed al-Zawahiri, leader of the ultraconservative Jihadi Salafist group, was detained at a checkpoint in Giza.
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