Although Union Pacific Corp. expected to have three of its five weather-damaged routes back in operation by this afternoon, the remaining rail lines will be out of commission indefinitely.

The two routes, originating from the rail yards east of downtown Los Angeles heading east to Salt Lake City and north to Oakland, remained flooded by the spate of recent storms.

Union Pacific officials originally planned to have all of its Southern California routes open by today, but damage proved greater than expected.

“We know we have a lot more work to do up there than we originally anticipated,” said John Bromley, spokesman for Union Pacific.

On a positive note, the routes from West Colton to downtown L.A. as well as the Cajon Pass rail line from the San Bernardino area to Northern California were expected to re-open today.

That follows yesterday’s re-opening of the rail line from West Colton to Yuma, Ariz. and onto El Paso, Texas, which had been operating at a limited capacity since Sunday, when the other four routes were shut down.

Despite the re-openings, Union Pacific won’t accept new freight for four or five days after each rail line is restored in order to remove the backlog of cargo stacking up at the ports of L.A. and Long Beach.

Burlington Northern Santa Fe Corp., whose two lines from L.A. to Chicago were not damaged by the storms, had been allowing Union Pacific to re-route a small portion of its freight on Burlington tracks.

But Bromley said today’s re-opening of the Cajon Pass route would no longer necessitate relying on Burlington Northern.