Table 3

Primer sequences used for the amplification of the specified fragments

Sequence name

Forward primer

Reverse primer

Tench shha intron 2

GCIGGITTYGACTGGGTCTA (degenerative, used for isolation)

GAGTACCAGTGSAYICCIKC (degenerative, used for isolation)

Tench shha intron 2

GTAAGACCATGGCAGGATG (specific, used for subcloning)

TCGAGATAATAGCAATGGGT (specific, used for subcloning)

Tench shhb intron 2

GCIGGITTYGACTGGGTCTA (degenerative, used for isolation)

GAGTACCAGTGSAYICCIKC (degenerative, used for isolation)

Tench shhb intron 2

GTGAGAGCAATGTCACC (specific, used for subcloning)

GCGATAAAAGTAAAAAGAGAC (specific, used for subcloning)

Latimeria shh intron 2

TCAAAGCAGGTAAGCAGACG

AAGCAACCCCCTGATTTTG

Mouse shh intron 2

GTGGAAGCAGGTTTCGACTG

GAAAGACCAGGTGTTGAGTGC

Chick shh intron 2

CGGCTTCGACTGGGTCTAC

GCTGCCACTGAGTTTTCTGC

Zebrafish shhb ar-C

CCGAATAACAACAACTCGCAATC

CTGAGAAGATATACAAACACAA

Zebrafish shhb intron 2, nonconserved part

GTGAGCAAAAGCTGATATGC

GATTGCGAGTTGTTGTTATTCGG

2.7 kb zebrafish shhb, promoter

CATCTAAATCAACTGCAAGAACG

GACGTTTGAATTATCTCTTCTGGTC

In the degenerative oligonucleotides, in which the occurrence of all four nucleotides was equally possible, an inosine (I) was introduced to reduce degeneracy. On all specific primers, restriction enzyme sites were added (see Materials and methods for details).

Hadzhiev et al. Genome Biology 2007 8:R106   doi:10.1186/gb-2007-8-6-r106