Jesse Leal Rodriguez, 34, of Anaheim appeared via video for his arraignment inside a Riverside courtroom on Tuesday.
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He faces three counts of attempted murder.
More than 100 people reported their windows shot out by a BB or pellet gun over the past month on Southern California freeways.
Bail was set at $1 million for Rodriguez.
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The Riverside County District Attorney's office expects more charges to be filed against him as the investigation continues.
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Rodriguez was arrested last week in Riverside near the Tyler mall. His red Chevy Trailblazer matched the description of the suspect vehicle in a BB shooting earlier that day in Norco.
Rodriguez recently told the Press Enterprise newspaper that even though a BB gun was found inside his vehicle, he's not responsible for any of the 100-plus shootings reported since late April, most of them on the 91 Freeway.
However, Riverside County District Attorney Mike Hestrin says evidence suggests otherwise.
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"I'm very confident that this is the right individual for the charges that we've charged him with. We wouldn't have filed it if we didn't think we could prove it beyond a reasonable doubt, but beyond that we'll let the investigation play out the way it is, because we follow the evidence," Hestrin said.
Hestrin declined to speak about what evidence authorities have, nor what was found in the vehicle.
But Eyewitness News did ask him why the decision was made to charge Rodriguez with attempted murder, as opposed to assault with a deadly weapon, which was the charge he was initially arrested on.
"It's incredibly dangerous behavior because people are not expecting it, they're traveling 60, 70, or more maybe MPH, and someone gets startled by a window shattering while they're on the freeway and it can cause a major accident," Hestrin said. "People are going to lose their lives or be seriously hurt, so we're very relieved that didn't happen in this case, but incredibly dangerous."