12-year-old Brisbane girl 'raped by a man found her mother dead in bed'.

Warning: this post contains graphic details. 

A 12-year-old girl sought comfort from her mother after being raped only to find her dead in bed with a sheet twisted around her neck, a court has heard.

Jacob Michael Smith, 40, is accused of killing the 34-year-old woman before raping her daughter at their Brisbane home on August 26, 2014.

He pleaded not guilty on Monday in the Supreme Court in Brisbane to one count each of murder, rape, attempted rape, assault occasioning bodily harm, and two charges of stealing.

During his opening address, prosecutor Phil McCarthy said the girl, her younger sister and their mother had been sleeping on mattresses on the lounge room floor on the evening of the attack as they recovered from a bout of gastro.

The court heard the girl was woken by Smith around 2.30am and taken into her mother’s bedroom, where she was raped and assaulted.

Smith then allegedly swapped his own pants for a pair of the girl’s tracksuit pants, stole the mother’s phone and numerous other items from the home, and fled.

Mr McCarthy said the scared girl then returned to the lounge room and tried to crawl into bed with her mum, only to find her face cold and blue, and a sheet twisted around her neck.

He said the girl later told police: "I tried waking her up and yelling at her but she wasn't responding... and I woke up (my sister) and said Mummy's dead".

While he was on the run Smith allegedly used the mother's phone and Facebook account to message and call friends, telling them he was "in trouble".

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When an ex-girlfriend picked him up from a Brisbane fast food outlet, he told her had "done something stupid and he'd killed someone".

He then allegedly told her that the girl's mother, who had attracted the ire of his current girlfriend because of her flirty manner, "had it coming".

Police arrested Smith a short time later hiding in the backyard of a friend's Gold Coast home.

Mr McCarthy said an autopsy found Smith's DNA was found under the mum's left fingernail, and that his fingerprints were also found on items stolen from her home that evening.

The older daughter also had injuries consistent with being raped, and Smith's DNA was found on a scratch on her body.

Up to 48 witnesses are expected to give evidence in the trial, scheduled to run for around 10 days.

If you or someone you know is dealing with domestic violence, please call 1800 RESPECT. If you are in immediate danger, please call 000.