The girls were tied to their mother's saree and the three didn't have any injury marks on their bodies, they said, adding it was a suspected case of suicide.
The woman was allegedly raped by the youth on Wednesday night when she was sleeping.
Lalji Gautam (51) was attacked by members of his rival group at Dudwa Dharampuri village on Monday night and died on Tuesday at his house.
A case was registered against the accused based on a complaint lodged by the girl's mother, police said, adding the minor has been sent for medical examination.
The girl has been rushed to Kanpur for specialised treatment as she has received severe burn injuries, police said.
There were multiple injuries on the body indicating it was a murder,” said Shahjahanpur SP S Anand, adding that some of the classmates of the victim were taken into custody.
The girl was rescued from his house on Saturday morning, Lalauli police station SHO Sandeep Kumar Tiwari said.
UP: Raped by two men 27 years ago, woman files complaint against both after her son asks for father's name
Referring to the police report lodged on the basis of the woman's complaint, SP Kumar said after the accused, his younger brother also raped the woman who was 12 at that time.
The girl was allegedly taken to a nearby forest area by force by a Class 10 student of the same school and was raped.
The victim said she was forced to stay silent after being threatened that the video would be put out on social media.
CM Yogi Adityanath has issued directives to invoke the NSA against all four accused
When their son came home on Thursday morning and enquired about his mother, the accused told him about the incident and fled, police said.
According to Shahjahanpur SP S Anand, the girl alleged that Manish, brother-in-law of her friend Pinki, and his two accomplices first tried to rape her in a field but she escaped.
The body of Virendra Yadav alias Rahul (24) was found outside the village on Thursday morning.
Acting on the complaint, the police on Friday arrested the accused belonging to Basantpur in Shahjahanpur district, Station House Officer Ram Adhar said.