Table 2.

Primers and probes for RACE and real-time PCR

Primers
Assay	Primer	Position	Sequence
RACE	5'RACE nested	48852556	CCTCTCACAGCTCATGTCTGAT
RACE	5'RACE	48852500	ACCACATCCAGGCACTGTTCTTC
RACE	3'RACE	48852519	GAACAGTGCCTGGATGTGGTGAC
PCR/Real-time	uPAR Fwd E1	48866085	CTGCTGCTGCTCCACACCT
PCR/Real-time	uPAR Rev E7	48845002	TGGGTGGTTACAGCCACTTT
PCR/Real-time	uPAR Rev E7b	48842344	ATCACATCTGCTGGGGCTAC
PCR/Real-time	uPAR Rev E2	48863624	ACTCTTCCACACGGCAATCCC
PCR/Real-time	uPAR Rev E7b (long UTR)	48842223	GCCTGTCCTTCCATGATGTT
Probes
Assay	TaqMan Probe	Location	Sequence ('denotes exon boundary)
Real-time PCR	Exon 1–2	Exon1–2	CCAGCCTCTTGGGGCCTGCGGT
Real-time PCR	Exon 5 del	Exon4–6	AGCTCCAGGA'CTTCTTCACCTTCC
Real-time PCR	Exon 3 del	Exon 2–4	CAGCCCGGC'CTTCCCACAAGCG
Real-time PCR	Exon 6 del +E7	Exon 5–7	TTCGGTT'TTGGGCCCTCGTTGCAT
Real-time PCR	Exon 6 del +E7b	Exon 5–7b	TTCCCCAGAGTGAGCGTT'TTGGGC
Real-time PCR	Exon 5+6 del +E7	Exon 4–7	TCCAGGAAGGTGAAGAAG'AACCGAAA
Real-time PCR	Exon 5+6 del; E7b	Exon 4–7b	CCCAGAGTGAGCGTT'CTTCTTCACC
Real-time PCR	Exon 4+5 del	Exon 3–6	TGCAACCAGGGCAACTCTG'TCCT

Primers listed for RACE were used with RACE-specific primers from GeneRacer kit (Invitrogen). Other primers were used to amplify full-length uPAR for both standard PCR and real-time assays. All TaqMan probes were labelled with Fam and TAMRA and were used with appropriate primers. Primer location is listed relative to chromosome 19 reference sequence for the start of the primer.