Table 3

Sequences of oligos used for amplification in qRT-PCR

Oligo Name

Oligo Sequence

mRNA/cDNA section amplified (bp from ATG)

Total length of mRNA (bp)


Igl 5' F

GCTGTTCCACATTGTGCATCAGTTTCAAATG

85–450 (Igl1), 85–459 (Igl2)

3306 (Igl1), 3318 (Igl2)

Igl 5' R

TTCTGCATGATCTTCTGTAGTTGCATTATCACATAAC

Igl 3' F

TGAAGGCACTTCTACAGAAGATAATAAAAT

2967–3166 (Igl1), 2979–3178 (Igl2)

Igl 3' R

TATGTCTTGAACATGGAATACATGATC

Igl1 F

TCTTGTAATAAGTTCCCGGAGCA

634–841 (Igl1)

Igl1 R

CATCAGAAACAGTACATCTTTTATTACATG

Igl2 F

GTACTAAATACCCAGATCATTGTTCAAA

643–841 (Igl2)

Igl2 R

CATCAGAAACAGTACATCTTTTATTACATG

URE3-BP 5' F

CCTGTAGCTAATTTCTGTTTATGGAATC

10–155

663

URE3-BP 5' R

CTTGTATATTGATCTAATGGGATAGTGTTAAG

URE3-BP Middle F

GATGAGAATTTTTGATACTGATTTTAATGGAC

276–454

URE3-BP Middle R

GATTAATATAGAATCCAAGTTGTTGAAGAG

URE3-BP 3' F

CTGTGATCTTAATTGTTGGATTG

504–658

URE3-BP 3' R

CCAAGAGGGAAGTAACAACGT

Actin F

GCACTTGTTGTAGATAATGGATCAGGAATG

variable (detects all family members/alleles)

variable

Actin R

ACCCATACCAGCCATAACTGAAACG

Jacob F

CAAAGGAGTTCAAATGGGATGTGTTAG

variable (detects all family members/alleles)

variable


Jacob R

TTATTTGGTGTAGGAGTTGGTAATGGG


Oligo pairs were designed to amplify short sections of Igl or URE3-BP. For Igl, four pairs of oligos were used: one amplifying the 5' end (Igl 5' oligo pair) and one the 3' end (Igl 3' oligo pair) of Igl1 and Igl2 simultaneously; and a pair each to amplify a short section unique to Igl1 or Igl2 (Igl1 oligo pair and Igl2 oligo pair, which have the same reverse primer in common) near the 5' end of the mRNA. Three oligo pairs were used to amplify short sections of URE3-BP: one pair the 5' end, one pair the middle, and one pair the 3' end. The actin and Jacob primers were designed to amplify all family members or alleles [35].

Linford et al. BMC Microbiology 2009 9:38   doi:10.1186/1471-2180-9-38

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