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The Katherine's guardianship papers were filed in court on Monday, and a hearing for permanent custody status has been set for Aug 3.
Jackson left behind three children: Michael Joseph Jackson Jr., known as Prince Michael, 12; Paris Michael Katherine Jackson, 11; and Prince Michael II, 7. The youngest son was born to a surrogate mother.
Deborah Rowe, is claiming a right to the two oldest children, according to her attorney.
Londell McMillan, the Jacksons' attorney, said the family hasn't heard from Rowe about custody.
The documents for guardianship state that the two oldest children have no relationship with Rowe.
"They have a long established relationship with their paternal grandmother and are comfortable in her care," the documents state.
The filings show that Katherine Jackson is also petitioning to take over the children's estate. Its value is listed as "unknown" in the filing.
Experts say the person who has the strongest legal claim to Jackson's two oldest children is Rowe. As for the youngest child, Jackson's wishes will be more influential. It remains unclear who Jackson designated as potential guardians for his children. Those details - likely contained in the 50-year-old singer's will - have not been released.
TMZ.com is reporting that there is a will that has surfaced, and that may answer questions about who will have custody of Jackson's children.
A co-author of a Jackson biography said Jackson wanted the nanny to have guardianship of the children.
The battle of the children is expected to be long and convoluted, and it won't be decided any time soon in the courts.
New details are also emerging about Jackson's mysterious death from the doctor who was with him in his final moments.
Dr. Conrad Murray is speaking out through attorneys, refuting rumors that he injected the pop star with pain killers. Murray's attorney also said any drugs that were prescribed did not contribute to the star's death.
A second autopsy, performed at the family's request, may yield some answers into Jackson's death sooner than the autopsy by the L.A. County Coroner's Office.
Murray's attorney Ed Cheroff said the singer was in bed and not breathing, but still had a faint pulse, when Murray found him last Thursday.
"The doctor compressed his chest with one hand, braced his back with the other hand. He checked to make sure there was blood flow, there was, that he was getting blood. In fact, at the time that he was, that emergency personnel came, he still had a weak pulse," Cheroff said.
There are questions about medications Jackson might have been taking, such as painkillers Oxycontin and Demerol. Cheroff said that if Jackson was taking them, they were not prescribed by Murray.
Funeral arrangements are still in the works.
The Rev. Al Sharpton and Michael Jackson's family met on Monday to talk about a possible global memorial for the King of Pop. Sharpton flew in from Atlanta to LAX on Sunday.
He said they would like to hold tributes to Jackson in key cities around the world.
Joe Jackson said he and his wife Katherine have the authority over Jackson's affairs, and said they also have legal authority over Jackson's three children, who have been living at the family compound in Encino since Jackson's death.
Sharpton said Jackson should be remembered for his impact on the music industry.
"They seemed very determined to at all costs preserve Michael's legacy. It is, to me, such a misjudgment by many, to try and concentrate on whatever they perceive as Michael's excesses, and not his legacy. This man changed the world. He changed pop culture," Sharpton said.
The family says they are awaiting a second autopsy before making solid plans for the star's funeral. The family says Michael will not likely be buried at Neverland Ranch and that the ceremony would be private. However, they hope to remember Michael publicly as well.
Jackson was going to embark on a series of concerts in London.
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The Associated Press contributed to this story.