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2:06 PM
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St Mark's cathedral was packed with mourners paying their respects to the 88-year-old pope who died on Saturday.
He was the spiritual leader of Egypt's Copts, who make up 10% of the country's population and are the Middle East's largest Christian community.
Pope Shenouda's body was then flown to the Nile Delta northwest of Cairo and buried in a remote desert monastery.
Thousands of people greeted the motorcade carrying his body when it arrived just before sunset, and military police struggled to control the mourners trying to get into the monastery.
The patriarch spent more than three years in exile there in the 1980s when the late Egyptian President Anwar Sadat accused him of fomenting sectarian strife.
Two months ago he asked to be interred at St Bishoy monastery on his death - he was laid to rest in a white marble tomb with a cross on top.
The ceiling of the chamber is covered with pictures of Jesus Christ, the Virgin Mary and saints, and it also has small windows to let in some light.
Copts were given time off work to prepare for the funeral, and a national day of mourning has been declared.
Global tributes Continue reading the main story
Jon Leyne BBC News, Cairo Outside St Mark's Cathedral the monastic bell tolls the parting of Pope Shenouda. A guard of honour greets the long procession of dignitaries.
The chanting of priests is broadcast to the huge crowd gathered to pay their respects echoing round this Cairo neighbourhood. The gates of the cathedral were locked early in the day as the massive church filled up.
Many thousands of Coptic Christians stand in silence outside, some praying some weeping at the loss of a pope who led them through four turbulent decades.
Tens of thousands of people queued to see Pope Shenouda, whose body had been on display in the cathedral since his death.Dressed in embroidered vestments and a golden mitre and holding a gold-tipped staff, his body was laid in a coffin before being placed on a ceremonial throne.
"The Holy Pope was able to gain the love of even those who held different opinions and I believe this will be a difficult thing to replace," said a mourner named as Samir.
"But God protects the Church and he will find a suitable patriarch."
Thousands of mourners who were unable to get into the cathedral followed the service on a huge television screen outside.
The BBC's Jon Leyne in Cairo says the massive crowds bear witness to the huge love and respect for Pope Shenouda.
As the white coffin was carried out from the cathedral there were almost hysterical scenes, with some women wailing and fainting.
The Pope was seen as a leader who did his best to protect Coptic Christians at a time when Islamism was on the rise, our correspondent says.
Continue reading the main story
Born Nazeer Gayed 3 August 1923 in Asyut, Upper EgyptBecame a monk in 1954, as Father Antonios el-SyrianiEnthroned as pope of Alexandria in 1971, after death of Pope Cyril VIBanished to desert monastery after row with then President Anwar SadatReleased in 1985 by President Hosni MubarakBut his deep conservatism - including his opposition to divorce - was not always popular with younger Christians.There is no timetable yet for finding a successor, who will be elected by a conclave of senior bishops.
The first challenge for the new leader will be to reassure Copts of their place in a country whose largest political party is now the Islamist Muslim Brotherhood, our correspondent adds.
Tributes have come in from around the world, with Roman Catholic Pope Benedict XVI offering prayers and US President Barack Obama praising Pope Shenouda as an "advocate for tolerance and religious dialogue".
Egypt's military rulers expressed the hope on their Facebook page that his wish of "preserving the unity of Egypt and the unity of its social fabric" would be achieved.
And a senior Muslim cleric, the Grand Imam of the prestigious al-Azhar university Ahmed al-Tayeb, expressed sorrow and said he "greatly remembers his vision towards Jerusalem and its history".
