To add a little more detail:

The SP/IER line ran all along Stanford (as in Leland J, one of the CP/SP founders), from the present UP (ex-SP) mainline, gently curving onto Adeline (definitely look at a street map!), then continuing up Adeline to its gentle joining up to Shattuck. It continued along Shattuck to what was the original SP Berkeley depot, located downtown on that triangular-shaped block bounded by Shattuck, Center, and Berkeley Square. (See "Berkeley Branch Railroad" & "Berkeley Station" in Wikipedia, as a starting point for more research.)

(As you explore in (or on a map of) Emeryville, notice Spur Way and Emery Bay Dr, running from Stanford & Hollis to 53rd & Boyer. Another industrial lead?)

The Key System ran from Oakland, I believe along the entire length of Adeline, but certainly from a main tranfer point at San Pablo & Yerba Buena (between 40th & MacArthur). Thus, at one time, along portions of Adeline & Shattuck, there were 4 parallel tracks, as both Key & SP were double-tracked! There used to be an informative plaque at the northeast corner of Adeline & Ashby, briefly describing operations there.

As to Lowell, I believe David is correct -- this was part of Santa Fe's mainline into "Oakland" (actually, Emeryville, at a depot just west of San Pablo at about 40th), before it was cut back to Richmond. If you follow Lowell north of Stanford, to where it joins Sacramento, you can see clear remnants of the old ROW -- Lowell onto the median of Sacramento, then (at some point, I'm not sure where) it cut west, to then run along or parallel to West St, to University Av (where you can still see the old Santa Fe depot building (now part of a school or community center, south side of the street just east of Bonar -- you can see where the ROW crossed, because it is now the bike path), then on morth through El Cerrito into Richmond.