Multiple callers reported hearing gunshots around 1:30 a.m. near Sherman and Colgate drives, according to the Union City Police Department.
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Officers responded to the area and found the two boys with gunshot wounds in the west parking lot at Searles Elementary School.
A 14-year-old boy was pronounced dead at the scene. An 11-year-old boy died while being transported to a hospital, police said.
Police said the suspects shot into the victims' car multiple times.
The victims' names will not be released due to their ages.
John Thompson, superintendent of New Haven Unified School District, said no students from Searles Elementary School were involved in the incident.
"One victim was a student who attended school within the district. The other victim was a former New Haven Unified student," the district's statement said.
There will be support for students and staff on the campuses where these students attended when school resumes after the Thanksgiving break, the district said.
Police said there are no suspects in custody yet.
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Sherman Drive is closed between Colgate Drive and 15th Street due to an investigation. The street is expected to be closed for several hours.
Anyone with information about the incident was asked to call the Union City Police Department at 510-675-5227.