FLC OF A BRITISH JETSTREAM 4100 BA41 OVERSHOT CLB ALT AFTER TKOF. FO MISSED RESETTING THE CLRED ALT IN THE ALERTER. ATC INTERVENED AND QUESTIONED THEM ON THEIR ASSIGNED ALT SINCE TURBOPROP ACFT USUALLY ARE GIVEN A LOWER ALT THAN THE SID INDICATES. THE FO ONLY REMEMBERED AMENDED ALT AFTER ATC'S INQUIRY.

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DURING TAXI OUT WITH FAA IN JUMP SEAT; I VERIFIED THE ALT IN THE ALT SELECT WINDOW WITH THE FO BY SAYING 'IS 5000 FT THE INITIAL?' FO RESPONDED; 'YES; 5000 FT IS THE INITIAL.' I BRIEFED TKOF TO BE MY LEG INCLUDING; AGAIN; THE INITIAL ALT OF 5000 FT. DIRECTLY AFTER TKOF; TWR INSTRUCTED US TO MAINTAIN VISUAL CONTACT WITH THE DC9 AND CONTACT DEP. CLBING THROUGH 4200 FT FOR 5000 FT DEP ASKED 'WHAT IS YOUR ASSIGNED ALT?' FO '5000 FT.' DEP; 'DO YOU HAVE THE DC9 IN SIGHT?' FO; 'AFFIRMATIVE.' DEP THEN GAVE US A ROUTINE TURNOUT AND CLRED US TO 14000 FT AND EXPLAINED TO US THAT CLRNC NORMALLY GIVES TURBOPROPS 3000 FT AND JETS 5000 FT. AFTER ARRIVING IN STL AND AFTER THE FAA JUMPSEATER LEFT THE AIRPLANE I ASKED THE FO WHAT SHE WROTE DOWN. SHE RESPONDED 3000 FT AND EXPLAINED THAT WE WERE CLRED VIA THE MEM 5 WHICH HAS PUBLISHED 5000 FT. WE HAD BLOWN THE AMENDED INITIAL ALT OF 3000 FT! I WAS NOT IN THE ACFT WHEN THE FO PICKED UP CLRNC SO I DID NOT HEAR CLRNC ISSUE 3000 FT. THE SID ONLY INCLUDES 5000 FT. IF CLRNC ROUTINELY ISSUES 3000 FT TO TURBOPROP ACFT; IT WOULD HELP TO JUST SAY THAT ON THE SID.