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Liverpool players – including Northern Ireland’s Conor Bradley - joined the mourners in Jota’s hometown of Gondomar near Porto to pay their last respects.
The father of three, who had recently married his long-term partner Rute Cardoso, was killed alongside his brother Andre Silva after their car burst into flames following a suspected tyre blowout in the early hours of Thursday.
Ms Cardoso was embraced by mourners outside the church.
Afterwards, she tenderly touched the coffin as it was led from the church.
Other family members were visibly emotional as they arrived at Igreja Matriz de Gondomar church.
They were joined by Reds manager Arne Slot, captain Virgil Van Dijk and team-mates including Bradley, Andy Robertson, Ryan Gravenberch, Cody Gakpo, Curtis Jones, Darwin Nunez and Joe Gomez.
Liverpool fans pay tribute to Diogo Jota outside Anfield
Also at the funeral for the Portuguese international were his national team-mates Bruno Fernandes, of Manchester United; Ruben Dias and Bernardo Silva, of Manchester City; Joao Felix and Renato Veiga of Chelsea; Nelson Semedo from Wolves; Joao Moutinho, Rui Patricio and Ruben Neves, as well as former Liverpool player Fabinho.
Also present were Porto FC president Andre Villas-Boas and Portugal national team manager Roberto Martinez.
Some of the players carried wreaths shaped like football shirts as they arrived at the church.
Van Dijk carried a floral tribute with Jota's number 20, while Robertson carried one with the number 30 for Andre Silva.
Jordan Henderson pays emotional tribute to Diogo Jota outside Anfield
Liverpool have postponed the players’ return for pre-season training following Jota’s death.
Slot said the “sense of shock is absolute”, adding: “He was a loved one to all of us.”
On Friday former Liverpool captain Jordan Henderson looked visibly upset as he returned to Anfield with flowers and a club scarf.
A sea of floral tributes has been left outside the ground.
In an emotional tribute, Bradley said Jota was "an incredible footballer but an even better person”.
“When I first moved up from the academy you were always there for me and always helped me settle in with the lads which I’ll be forever grateful for,” he said.
“My thoughts are with your wife, children and family for losing both Diogo and Andre.
I can’t imagine how tough this is for you all, as I know how tough this feels for me today.
“Love you Jots, and I’m sure we will meet again.”
In Belfast, Liverpool supporters gathered to lay flowers outside the club’s city centre merchandise store.
The store was closed on Friday as a mark of respect, with cards and flowers laid in his honour.
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