Primers used for quantitative PCR
Gene	Amplicon	Forward primer	Reverse primer
Robo1	E6b-	gacagttcaagagccgccacattt	gatttccagttgcttcgcactg
	E6b+	cgctactttgacagttcaagttggg	gatttccagttgcttcgcactg
	Common exons	gggatcatacacttgtgtggcagaa	gatttccagttgcttcgcactg
Robo2	E6b-	ccctcactgtccgagctcctcc	ttgagcaacgatctgatctcttgg
	E6b+	ccgagttcgccctgttgctcc	ttgagcaacgatctgatctcttgg
	E21-	ggaacaacggtgggaaaggtgg	ggaggaggaggtaga
	E21+	gcaccaccagctctcacaacagc	ggaggaggaggtaga
	Common exons	agtggaagcctctgctaccctc	ttgagcaacgatctgatctcttgg
Nova1	Common exons	ctcgcggaaaaggccgcttg	gtactggccgtcttcgcccgt
Nova2	Common exons	cgacagagccaagcaggcca	acggtcaccacgcgctcttg
Hprt	Common exons	tgacactggtaaaacaatgca	tcaaatccaacaaagtctg
Primers used for semi-quantitative PCR (amplifying multiple isoforms)
Gene	Amplicon	Forward primer	Reverse primer
Robo1	Exon 6b	gggatcatacacttgtgtggcagaa	ctggtcccgaggttttacaacg
	Exon 18	gcaagaagagaaacggactcacca	cggcctccctccactgctg
	Exon 21	ccatggctggcagacacg	ctggatgagttgagtggtggc
Robo2	Exon 6b	agtggaagcctctgctaccctc	ttgagcaacgatctgatctcttgg
	Exon 21	ccacagtggaaaagctcagttca	ggaggaggaggtaga
	Exon 24b	cccaggcccctcagagcacta	gtgggccgctgcctttgaga
	Exon 26	acagccagtgttacctcatcgg	ctgatgagctgtgcccgcca
Foxp1	Exons 15 to 17 of Foxp1 with exons 16 and 16b sequences replaced by Robo1/2 exon 6b (also see below and Figure 3—figure supplement 1E).	gaatgtttgcttacttccgacgc	agtaggcgtggctgctctgc