Merseyrail's City Line

Merseyrail's City Line is different from the rest of what is branded as Merseyrail. Unlike the Northern and Wirral lines, the City Line is not run by the Merseyrail Electrics company, nor does it use third-rail electrification. Instead, it is operated mainly by Northern Trains, using diesel and overhead electrification trains. 

A Northern class 323.

In addition, while the Wirral and Northern lines are almost entirely isolated from the rest of the National Rail network, the City Line is not. Intercity trains from TOCs such as Avanti West Coast and Transpennine Express use the lines as well, without stopping at most City Line stations. This means that at many stations, services are much less frequent than on the other two lines. Prescot, for example, gets one train an hour to Liverpool Lime Street and one to Blackpool North. While there had been plans in the 1960s and 70s to integrate some of the City Line into the rest of Merseyrail, this was never accomplished. 

Due to all these differences, you may be wondering - how come it's branded Merseyrail at all then?! This is because it is within the control of Merseytravel, who wish to keep all the railway services in the area under one established brand. Indeed, until the mid-2000s some of the diesel Pacer trains used on the City Line were in a Merseyrail livery - one can be seen at this link https://flic.kr/p/2kCV59A