Supplementary Table 1. Oligonucleotide primer sequences and PCR conditions

Experiment / Primer sequence / Number of cycles/ annealing temp. / Product size
Quantitative RT-PCR,
long transcript specific (Fig 2e) / s: 5´- TGAAGCTCATTTTCTCCAACATCT -3´ / 40 cycles/ 60 °C / 71 bp
as: 5´- CTGCAGCTCGGGAAGGAA -3´
Probe: (5´- FAM, 3´- TAMRA-labeled)
5´- CTCCATCTATCGTTTCCACGCCCAGTT -3´
RT-PCR,
long transcript specific (Fig 2b) / s: 5´- GGCTGTGGTAGACCTGCTTC -3´ / 35 cycles/ 58 °C / 461 bp
as: 5´- AGACGGAGCAGGCCTAT -3´
RT-PCR, beta Actin control (Fig 2b) / s: 5´- TGGAATCCTGTGGCATCCATGAAA -3´ / 25 cycles/ 58 °C / 349 bp in
NM_007393
as: 5´- taaaacgcagctcagtaacagtccg -3´
PCR-amplification of template for in vitro transcription of probe for in situ hybridization (Fig 2c) / s: 5´- AGAATCCCGCGGTACGA -3´ / 35 cycles/ 58 °C / 395 bp
as: 5´- GTCAGCTCCCGCACCT -3´
PCR amplification of coding region of long Fgd2 transcript / s: 5´- GGCTAGCAGGATGGAGCGA -3´ / 38 cycles/ 66 °C / 2407 bp
as: 5´- GTGCTCTCAGGTTCTTGTGTAG -3´
PCR amplification of probe for northern hybridization (Fig 2d) / s: 5´- GGCTTGCGGCTATGTAG -3´ / 38 cycles/ 66 °C / 949 bp
as: 5´- GTGCTCTCAGGTTCTTGTGTAG -3´
PCR amplification of long transcript specific probe for northern hybridization (Fig 2b) / s: 5´- GGCTAGCAGGATGGAGCGA -3´ / 35 cycles/ 57°C / 361 bp
as: 5´- AGACGGAGCAGGCCTAT -3´
PCR amplification of left arm of targeting construct (SpeI site in forward primer) (Fig 3) * / f: 5´- CTGCTTCTGGGGTAACT -3´ / 35 cycles/ 65 °C / 3914 bp
r: 5´- ATAGGCCTGCTCCGTCT -3´
PCR amplification of right arm of targeting construct (EcoRV site in forward-, SalI site in reverse primer) (Fig 3) / f: 5´- AAGAATCCCGCGGTACGAACTG -3´ / 35 cycles/ 65 °C / 2589 bp
r: 5´- GACAACGCCCGACATCATAGAG -3´
PCR amplification of 5´-probe for detection of targeted allele (Fig 3) / f: 5´- ACAGGTCTCACGTAGCCGAATC -3´ / 35 cycles/ 56 °C / 642 bp
r: 5´- CGGGTGAAGCAGGTCTACCACA -3´
PCR amplification of 3´-probe for detection of targeted allele (Fig 3) / f: 5´- TGGATGCCGCTCAGTTGCTAAT -3´ / 35 cycles/ 56 °C / 652 bp
r: 5´- TGAAACTCAGTGTGTAGACCAG -3´

* A 180 bp deletion at the 3´-end of the left arm occurred during construction of the targeting vector

s, sense primer; as, antisense primer, f, forward primer, r, reverse primer