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Islamists vowed further protests on Saturday to demand the army restore Egypt's first democratically elected leader, after a day of clashes which saw 30 people killed across the country.
"The masses will continue their civilised protests and peaceful sit-ins in Cairo until the military coup is reversed and the legitimate president is restored," a coalition of Islamist groups said in an early morning statement.
Ahead of the protests, central Cairo was already tense early Saturday.
Protesters opposed to deposed president Mohamed Morsi spent the night in Tahrir Square, with checkpoints manned by civilians after a night of deadly fighting nearby.
A bridge leading up to Cairo University -- where Morsi supporters had been camping out -- was littered with rocks and burned out tyres from confrontations between the two camps.
Throughout the city, there were reports of gunfire during the night, adding to the tension.
The Tamarod movement, which engineered the mass protests against Morsi that culminated in his overthrow by the army on Wednesday, urged its supporters to take the streets again on Sunday.
Tens of thousands of Morsi's supporters turned out on Friday to protest his ouster in the popularly backed military coup.
Equally large numbers of anti-Morsi protesters also flooded the streets of Cairo and the Mediterranean city of Alexandria, sparking pitched battles between members of the rival camps.
Police meanwhile pressed a round-up of top Islamists, announcing the arrest of Khairat al-Shater, widely seen as the most powerful man behind Morsi in the Muslim Brotherhood movement.
At least 12 people were killed in Alexandria as Morsi's supporters and opponents fought in the streets, the official MENA news agency said.
In Cairo's iconic Tahrir Square, at least two people were killed when Morsi supporters traded fire with his opponents, state television reported.
The clashes subsided when the army separated the protesters using armoured vehicles.
"We are not taking sides. Our mission is to secure the lives of protesters," military spokesman Colonel Ahmed Ali told AFP.
Four protesters were killed outside the Republican Guard headquarters after breaking away from a pro-Morsi demonstration, MENA reported.
In the restive north of the Sinai peninsula, armed Morsi supporters stormed the provincial headquarters in the town of El-Arish after a gunfight and raised the black banner of Al-Qaeda-inspired Islamist militants, an AFP correspondent said.
A spokesman for UN chief Ban Ki-moon quoted him calling for a peaceful end to the crisis. "There is no place for retribution or for the exclusion of any major party or community".
The United States too condemned the clashes and urged all leaders including the army to ensure the bloodletting ended.
"We condemn the violence that has taken place today in Egypt. We call on all Egyptian leaders to condemn the use of force and to prevent further violence among their supporters," State Department spokeswoman Jen Psaki said.
The Islamists accuse the military of conducting a brazen coup against Morsi, Egypt's first democratically elected president, after millions called for his ouster on the June 30 anniversary of his first turbulent year in power.
Friday's violence came as the supreme guide of Morsi's Brotherhood, Mohammed Badie, vowed that members of the Islamist movement would throng the streets in their millions until his presidency is restored.
Badie appeared at Cairo's Rabaa al-Adawiya mosque to screams of joy from jubilant supporters, following reports he had been detained after Wednesday's ouster of the president.
"Millions will remain in the squares until we carry our elected president, Mohamed Morsi, on our shoulders," Badie told the crowd, before leading chants of "Military coup!" and "Invalid!"
The armed forces have already sworn in Adly Mansour as interim president, and he issued his first decree on Friday, dissolving the Islamist-led parliament and appointing a new intelligence chief.
Morsi, who has not been seen since Wednesday, had issued a defiant call for supporters to protect his elected "legitimacy", in a recorded speech aired hours after his removal.
The military had said it supported the right to peaceful protest, but warned against violence and acts of civil disobedience.
Army chief General Abdel Fattah al-Sisi announced Morsi's overthrow on Wednesday night, citing his inability to end a deepening political crisis.
Military police rounded up senior Brotherhood members, although two were later released.
Morsi himself was "preventively detained", a senior officer told AFP.
A judicial source said the prosecution would on Monday begin questioning Brotherhood members, including Morsi, for "insulting the judiciary".
Morsi's rule was marked by accusations that he concentrated power in the hands of the Brotherhood.