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Oct 6 (Reuters) - GT Advanced Technologies Inc, a partner with Apple Inc in a sapphire glass plant in Arizona, said it had filed for voluntary bankruptcy protection.

Shares of the company fell more than 90 percent to 96 cents after a trading halt was lifted on the Nasdaq.

The company suffered a major setback last month when its scratch-resistant sapphire glass was left out of Apple's new large-screen iPhones.

"It would appear that something very fundamentally broke down in the relationship between Apple and GT Advanced," Raymond James analyst Pavel Molchanov said in an email.

Up to Friday's close, GT Advanced shares had slumped 36 percent since Sept. 9 when Apple unveiled its latest iPhones.

GT Advanced , whose subsidiaries also filed for bankruptcy, said it had $85 million of cash as of Sept. 29.

The company listed assets and liabilities in excess of $1 billion in its Chapter 11 petition.

The company, which filed for bankruptcy in a U.S. bankruptcy court in the District of New Hampshire, said it was seeking debtor-in-possession financing to get access to additional funds.

GT Advanced said it expected the court to authorize it to continue to conduct business as usual while it reorganized.

The company's shares had more than doubled in the nine months between last month's unveiling of the new iphones and Nov. 4, when the Arizona plan was first announced.

The stock traded as high as $20.54 in early July.

(Reporting by Swetha Gopinath in Bangalore; Editing by Sriraj Kalluvila)