The Wafaqul Madaris al-Arabia, an umbrella body of madrassas, is observing a countrywide "protest day" over the killings and violence in Rawalpindi last week.
The violence in Rawalpindi erupted when a Muharram procession organised by Shias was passing by a Sunni seminary. Both Shias and Sunnis were killed and over 50 were injured.
The Difa-e-Pakistan Council, a grouping of extremist organisations formed by Jamaat-ud-Dawah chief Hafiz Saeed, extended its support to the "peaceful protest".
Protest rallies were organised in several cities after the Friday prayers. Educational institutions in Rawalpindi were closed. The link road between the twin cities of Rawalpindi and Islamabad was closed.
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In Islamabad, protestors marched in a rally from the radical Lal Mosque to the National Press Club. The federal capital's "Red Zone", which houses parliament, Supreme Court, key government buildings and the diplomatic enclave, was shut down.
The government of Punjab province deployed army and paramilitary Pakistan Rangers in 13 districts as part of security arrangements.
In Lahore, police set up check points in several areas of the city. Police and army were deployed in several areas of Multan and private educational institutions were closed.
Pillion riding was banned in Faisalabad, where over 500 mosques and 25 imambargahs or Shia prayer halls were declared sensitive.
A rally organised in Quetta culminated at the press club. Several markets in the capital of Balochistan province were closed.
In the northwestern city of Peshawar, the Frontier Constabulary was called out to thwart any untoward incident.