BAY SHORE, N.Y. (CBSNewYork) — Suffolk County police have arrested a Bay Shore High School teacher’s assistant for allegedly raping a student from the school.

As CBS2’s Jennifer McLogan reported, students leaving the school for home were filled with anxious, troubling questions.

Their 15-year-old classmate came forward to her parents and police, alleging she was the victim of rape at the hands of a popular teacher’s assistant.

Marcus Johnson, 27, pleaded not guilty at his arraignment Friday. He has been charged with second and third degree rape and endangering the welfare of a child,  police said.

Johnson is accused of having an inappropriate relationship with a 15-year-old female student. Prosecutors allege Johnson had sex with her once while she was 14 and another time since she turned 15.

Police say Johnson works with autistic students at the school, but say the victim is not one of his students.

On the campus of Bay Shore High School Friday morning, parents and students were in disbelief.

“That’s horrible,” parent Rana Ramjas told CBS2’s Janelle Burrell. “Absolutely horrible.”

“I got the chills because I just saw him yesterday,” said student Colleen Lopez. “It really is shocking because he would always be like that para-teacher that everyone would want to be friends with, get to know. You’d always see him interacting with students in the hallway. You’d say hi, he’d say hi back.”

“He was such a nice dude and that fact he would do such a thing,” said student Marley Davidson.

The arrest, many parents say, is prompting them to have what they admit will be an uncomfortable but necessary talk with their children.

“You just have to tell them to be careful,” Ramjas said. “You have to have conversations with your children so that they’re not in any danger.”

“I hope that, if in fact it’s true as to what happened, the teacher is punished to the full extent of the law,” said parent Dennis Gartland.

Johnson was arrested at the Westfield, South Shore Mall where he works another part time job as a clerk at Finish Line Sports.

After Johnson’s arraignment Friday, his attorney offered reporters no explanation.

The Bay Shore School District issued a statement saying it “became aware of an allegation involving an improper relationship occurring outside of school between a female high school student and a male paraprofessional.”

“The matter was promptly investigated by school officials and referred to the Suffolk County Police Department, resulting in an arrest,” the statement said.

Johnson is being held on $40,000 cash bail and the judge issued an order of protection warning Johnson that he must stay away from the alleged victim, Burrell reported

Detectives ask anyone with information to contact the Special Victims Section at 631-852-6531.