The shooting happened around 3 am Tuesday on Gerard Avenue and Carmel Road near Highway 99.
On Wednesday, authorities announced that an arrest warrant had been issued for 21-year-old Darrion Wayne Murphy.
Officials say he is now wanted for attempted murder.
Officers say surveillance video shows the suspect pointing a gun at the clerk who then takes cash out of the register.
Authorities say Murphy then shoots the victim before taking off on a bike.
The store clerk was taken to a trauma center.
Anyone with information on the incident or Murphy's location is urged to contact Merced police.