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Current style of Pennsylvania signals The current layout is to have all yellow signals with 12-inch indicators on mast arms with a black back plate. The turn signal will cycle green arrow, yellow arrow, then red.  During the flash mode, turn signals will be entirely out as Pennsylvania does not flash arrows.  In cities and boroughs, this convention is not always followed.  Where mast arm installations are not feasible, wire span installations use the same convention.

Philadelphia turn signal with red arrow Although not endorsed by PennDOT, sometimes you will come across a signal installation with turn signals that utilize red arrows.  These are usually ones installed independently by boroughs or cities.  Many installations in Philadelphia use turn signals with red arrows.
Pittsburgh turn signal with red arrow The second largest city, Pittsburgh, uses signals such as these and has at least one installation with red arrows.

Doghouse signal At some smaller intersections, the "doghouse" signal is utilized, since it does the job of two signals in the area of one.  These are also used at large intersections where a route will leave one alignment and turn onto another, to keep the traffic flowing.

Four head protected/permissive turn signal Sometimes this signal is used at intersections instead of the dog house for turn sequences.  A rare sight in most of Pennsylvania, this signal can be seen extensively in District 6, around the Philadelphia suburbs.  Installations such as PA 611 and Wyandotte Road in Willow Grove or US 40 and Fifth Avenue in Brownsville use these protected/permissive turn signals.

Five head protected/permissive turn signal Even more rare than the inline four indicator is the inline five indicator turn signal which operates on the same principal as the doghouse above.  I've only seen one used on a state highway and that is PA 271 at Washington Street in Johnstown, but there are two on the circular route that surrounds Westmoreland Mall in Greensburg.  One at the entrance ramp from US 30 and the other at the entrance from old US 30.

Strobe signals At some intersections you might come across signals with strobe bars in the red light housing.  These are mainly used where there is a high number of accidents due to "red light running."  These are used at US 30 at Beatty County Road in Greensburg, US 22 at Resort Plaza Drive in Blairsville, and Business US 22 at PA 791 in Wilkins Township to name a few.

Emergency Signal Where fire stations are located along busy highways, signals such as these may be placed.  You aren't seeing things, in standard mode a yellow indicator flashes in the place of the green indicator.  When an emergency vehicle needs access, the signal goes to yellow then red and back to flash.  I have also seen this type used at plant and truck terminal entrances as well as a railroad crossing.

Ramp Meter Although not extensively used in Pennsylvania, there are two places that use traffic signals as ramp meters:  I-476 in Philadelphia and US 22 in Allentown-Bethlehem.  Ramp meters have been talked about for years for being the solution to traffic jams in Pittsburgh caused by the Fort Pitt and Squirrel Hill Tunnels.  The signals are coordinated to allow only a certain number of cars onto the expressway so as to regulate the flow of traffic and to avoid congestion.  Usually when the signal turns green, only one car may enter the flow of traffic.  Other parts of the country have more extensive systems in operation, and can be explored on Adam Froehlig's Ramp Meters page.

Turnpike System signals The Turnpike Commission has signals like these at the toll plazas.  The signal on the left is used on the main Turnpike in all lanes.  Ticket customers will just see the green and red cycles, but E-ZPass users can get all three:  green for payment, yellow if the account balance is low, and red if there is an error.  The signal on the right is for the extensions.  If you fail to pay, the rotating light on top lights and a siren will sound.

E-ZPass Prism Sign With the introduction of E-ZPass on the mainline Turnpike, these installations have been installed over the respective lanes.  The signals sequence from flashing yellow (E-ZPass Only), green (E-ZPass and tickets), or red (closed).

Tunnel Warning Signal At the entrances to the Fort Pitt and Squirrel Hill Tunnels in Pittsburgh, you'll see these signals.  They will turn on if an overheight truck is heading to the portal or if there is congestion (which is every rush hour) before the tunnel to alert drivers to be prepared to stop.

Pennsylvania complies with the Federal Highway Administration's guidelines for signaling of highways.  Below are some exceptions that are not covered in the United States Manual of Uniform Traffic Control Devices.

Representation of old signals Early layouts had all the signals on wires.  The turn signal would cycle green arrow and red light (this was a protected turn), then yellow arrow, then red.  These are still in existence today, but are being replaced slowly.

Representation of old signals Some of the early turn signals would use a circular yellow indicator instead of an arrow.  There was an example of this in use at the intersection of Industrial Boulevard and PA 982 in Derry.

Representation of old McKeesport signals Older signals around the City of McKeesport area in Allegheny County have an unusual sequence.  They still maintain green-yellow-red progress, but add a small delay in between each indication.  Coming up to one that just changed yellow, one might think that the signal is in flash mode.  The signal at West Fifth Avenue and Romine Avenue still uses these old timers.

Representation of old Pittsburgh signals Older Pittsburgh signals used to use a weird sequence.  The signals would go green-green/yellow-yellow-red.  The odd green/yellow phase was meant as a pedestrian phase to alert them that the signal would be changing to red and not to cross.  However, motorists detested the sequence and felt it was too confusing, so it was axed in the mid-1980s.  Current Pittsburgh signals, and hold-overs from that era use the green-yellow-red sequence.

Links:
Traffic Signals - Pennsylvania Code