Table 2.
Primers for each DNA segment to probe possible combination of splice variants (exons a, b, c, SEC, and VASE), as well as for an exon outside of the splice sites for measuring total NCAM1
| Primer | Forward | Reverse |
|---|---|---|
| VASE | 5′-GACCCCATTCCCTCCAT CAC-3′ | 5′-GGCTACGCACCAC CATGTG-3′ |
| Exon a | 5′-GACGCAGCCAGTCCA TAGC-3′ | a |
| Exon b | 5′-CGTCTACCCCTGTTC CATTGTC-3′ | 5′-TCTGGTGGAGACAATG GAACAG-3′ |
| Exon c | 5′-TCCTGCCCTTGCAACCA 3′ | 5′-GGTTGCAAGGGCAG GAAGA-3′ |
| SEC exon | 5′-CCAAGCTGGTCTTCA TAATGCTCTA-3′ | 5′-TTTGATGCTTGAACACTAT GAACATG-3′ |
| Exon 3 | 5′-GGCGGCGCTCAATGG-3′ | b |
| Exon 8 | c | 5′-GATCAGGTTCACTTTAATA GAGTTTCCA-3′ |
| SNP9 for sequencing | 5′-CGCAGCCAGTCCGTAAG TAAAG-3′ | 5′-AAGCTGGACCGGCTAC TAGGA-3′ |
The numbering is shown in Fig. 1 according to accession M22094. SNP 9 was also genotyped by direct sequencing.
NCAM1, neural cell adhesion molecule 1; VASE, variable alternative spliced exon.
a
Only the forward primer could be designed because exon a is 14 bp.
b
Exon 3 is before the variable exons and only the forward primer was needed to PCR outside the exons. The reverse primer was designed within another exon.
c
Exon 8 is after the variable exons and only the reverse primer was needed to PCR outside the exons. The forward primer was designed within another exon.