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Table 1 Primers and conditions for PCR

From: Molecular breakpoint cloning and gene expression studies of a novel translocation t(4;15)(q27;q11.2) associated with Prader-Willi syndrome

RT-PCR

   Gene/Exon

fwd (5'-3')

rev (5'-3'); complement strand

size

T ann.

   ZNF127

GGG TTG CGG TTT TGC TAT TA

TTT CTC GTG TGC TTC AAT GC

168 bp

59C

   MAGEL2

CTG AAG CCT GGG ACT TTC TG

GGA CCT TGG CCA CAA ACT TA

225 bp

59C

   Necdin

GAA GAA GCA CTC CAC CTT CG

CCA TGA TTT GCA TCT TGG TG

164 bp

59C

   SNRPN Ex 1–3

ATG GAG CGG GCA AGG GAT CGC

GGT ACA ACT GAC ACT CTT GG

124 bp

53C

   SNRPN Ex 14/16

CTG CAA ACA TAG GAG ATG ATA GTT CC

CTT ATG AAA GCA CTG AGA TGA AGC C

459 bp

53C

   SNRPN Ex 16/17

GAA AGT GAC CTA AAG AGT GTC ATT G

CTT GCA GTT GGA CAG CCG ACT C

515 bp

53C

   SNRPN Ex 17/18

AGA TAT CTT TAA AAT TGA GTC TTC TGT CCA

TGA AGA TGC AGC ACT TTT GAA GAA

218 bp

53C

   SNRPN Ex 19/20a

CAT TGT GCT TAT TTA CTA TTT TTG TAG ACG

CTG CAG GTG GTG ACC ATG TG

150 bp

53C

   AK094315

TCT TCT CTA CCC TCA TTC CCA GC

TCG CTA CAC CCC TTT GCT TAT G

222 bp

53C

   AB061718

AGG AGG GGT TCA AAG ATG C

CTG GTA AAC AAA CTG GTA AAG GTG

204 bp

50C

   HBII-85/PWCR1

CGA TGA TGA GTC CCC CAT AAA AAC

CAG TTC CGA TGA GAA CGA CG

79 bp

53C

   HBII-13

GGA TTT GTG ATG AGC TGT GTT TAC

GGA CTT CAG AGT AAT CAC GTT G

67 bp

54C

   HBII-438A/B

GGA TCG ATG ATG AGA ATA ATT ATT G

GGA CCT CAG ATT GAC ATC TG

67 bp

53C

   GABRB3

TCA GGC GGC ATT GGC GAT ACC

ATA AAA ACT TGA CAG GCA GAG

352 bp

52C

   GABRA5

AAT ATT GCC TTA ATG TTT CTA

GCC TAT TCT ATT TCT TCG TGT

425 bp

48C

   GABRG3

GCG TAT TCA CAT AGA CAT CTT G

GAT TGG TCA CTA CTG GTC TGG

188 bp

52C

   GAPDH

TGG GCT ACA CTG AGC ACC AG

GGG TGT CGC TGT TGA AGT CA

50 bp

53C

Quantitative RT-PCR

   Gene/Exon

fwd (5'-3')

rev (5'-3');complement strand

size

T ann.

   SNURF Ex2

ACG AAC TAC AGA ACA GCA CGT ACC

CTG CGT TTG ACT TGG ACT TCC

50 bp

60C

   SNURF Ex3

TTC TCA GCA GCA GCA AGT ACC T

TGC CTC AGT TCA GCC TGG A

50 bp

60C

   HBII-437

ATC ATT ATT TCT TGA ATT GG

CCC TCA CGC TCC CTT TGC

50 bp

60C

   SNRPN Ex 14/15

CTG CAA ACA TAG GAG ATG ATA GTT CC

CAA AGA CGA TAA AAT GTT CCT TCT TG

50 bp

60C

   SNRPN Ex 19/20a

GGA ACC ACC ATT TGT CTA TGA TCC

CTG CAG GTG GTG ACC ATG TG

50 bp

60C

   HBII-438

ATA ATT GTC TGA GGA TGC T

GAT TGA CAT CTG GAA TGA GTC

50 bp

60C

   HBII-85/PWCR1

TCG ATG ATG AGT CCC CCA TAA

CAT TTT GTT CAG CTT TTC CAA GG

50 bp

60C

PCR to generate Southern probes in intron 17

   Gene/Exon

fwd (5'-3')

rev (5'-3');complement strand

size

T ann.

   SB 1

ACC ATC AGT GAA TGA CCT GTT GC

CCC AGC CTC TTT CCT ATG TCT TG

565 bp

53C

   SB 3

TGG TAA ACT GAT GAG AGC ACA GCC

GCC TGG GAG ACA GAA TGA GAA AC

416 bp

53C