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Table 4 Marker genes used in TRAC analysis.

From: Monitoring of transcriptional regulation in Pichia pastoris under protein production conditions

Probe name

Gene

Location of the probe in CDS

Probe length (nt)

Tm (°C)

GC%

Probe Sequence 5'-3'

Pool

ACS1

ERGO:RPPA07570

893–917

25

65.2

48.0

TACTTGGTGGTCAAAAGAGCTCCCA

1

SSE1/2

ERGO:RPPA10049

538–564

27

63.7

44.4

TTTGACGAGCTTCTCAACTGTCCTGTA

1

VPS17

ERGO:RPPA07986

1583–1611

29

64.2

44.8

ACCTGCAGACTGGGTGCTAACTTTTTTCT

1

LC

2F5Fab_light_chain

409–439

31

65.6

41.9

GTACTTTGGCCTCTCTGGGATAGAAGTTATT

1

RPL3

ERGO:RPPA07957

489–521

33

64.9

45.5

TTTTGGTTCAAAGGGGTCTTTCTGATCTGGGTG

1

SEC61

ERGO:RPPA04132

848–882

35

65.4

40.0

CATGATTGGCATGTTGGATGTGTAGAACAATCTGA

1

PDI1

ERGO:RPPA04694

768–804

37

64.3

40.5

GGCTAAAGGGATGTTAGCTTCAGCATATGATTTGAAG

1

TRR1

ERGO:RPPA06201

815–853

39

66.4

46.2

CGAAAACACCTGGAATAGATGTAAGGGAAGAACCTGGGA

1

RIB1

ERGO:RPPA08084

756–796

41

66

39.0

AAGAACGTTTGTCTGCTGGGTGTCTTAGTAAAAGATTTGCT

1

TKL1

ERGO:RPPA06932

1782–1824

43

67.5

39.5

TATTGGAACACCGTCTGGAAGGACTGATAATTGGTAAGATCTA

1

ARG1

ERGO:RPPA07954

813–857

45

70.1

44.4

GTCAAACCTGGAGTTTCATAACAACCTCTGGACTTGATTCCGATG

1

SNZ3/2

ERGO:RPPA10229

557–581

25

63.3

44.0

ATGGCAGCAGCTATCTTTTCAGGAT

2

PMT6

ERGO:RPPA04967

1054–1080

27

62.8

44.4

GTAATCTGTTGTTGGCTGGAACCTTGA

2

GCN4

ERGO:RPPA07905

359–387

29

67.1

48.3

AACGGCTGGAGTGGTAGCAAGAGTAGTTT

2

SSA4

ERGO:RPPA10651

1605–1635

31

65.9

45.2

CATATGATTCCAAGCCATTCTTGGCAGCAAC

2

HC

2F5Fab_heavy_chain

669–701

33

67.9

48.5

GATTTGGGCTCAACTTTCTTGTCCACCTTGGTG

2

KAR2

ERGO:RPPA06939

1325–1359

35

65

40.0

AGTTGGGATAGCAGTGTTTCTGTTGATTAAGGTAG

2

SEC53

ERGO:RPPA08162

349–385

37

63.8

40.5

CGTTTCTGAACTCAATGAATGTTCCTCTTCTGATTGG

2

IMH1

ERGO:RPPA04985

1949–1987

39

62.4

38.5

TGTCTTTTTCCAATTCATCTCGTTTGGAGAGGACTAAAG

2

BFR2

ERGO:RPPA04523

700–740

41

65.8

39.0

AACTCTTGGCTCACAATCTTGCTTTTGTTTAATAGCTTGCC

2

SEC31

ERGO:RPPA06211

1243–1285

43

70

44.2

TTTCGTCGACAAGAGTTTGGTAATCGTTTGTGCTGATGGTGCT

2

HSP90/82

ERGO:RPPA05876

891–915

25

63.9

48.0

CTTAACAGCCAATGGGTCTTCCCAA

3

ARO4

ERGO:RPPA09892

786–812

27

62.8

44.4

TTTCCGTGGGAACAGTCAATCATCAGA

3

ERO1

ERGO:RPPA06115

1531–1559

29

64.4

44.8

TCTCGGTGCCTTTGAGTGCCAATGAAAAT

3

TAL1

ERGO:RPPA08309

550–580

31

63.5

41.9

CCTTGTACCAGTCAAGAATACGTCCAACAAA

3

BMH2

ERGO:RPPA07190

546–578

33

66.1

48.5

AAATGACAGGCGCGGTCAGGAGAGTTTAGAATC

3

ROT2

ERGO:RPPA08267

1634–1668

35

63.3

40.0

ATACGACCTAGTAAGAACAAATGGCCTATGGTTTG

3

GLR1

ERGO:RPPA07699

965–1001

37

67.7

45.9

CTGTTAGATAGTTTTCTACCAGCAGCGATTGCGACAG

3

RAD16

ERGO:RPPA09210

1007–1045

39

63.6

38.5

TATTGTGGGCTTCGTCTAAAATGACCCTATAAAAATGCG

3

GSH2

ERGO:RPPA06484

949–989

41

61.8

39.0

AGAATTTGTTGAACTTTTTTACAACCGCTAAGCTGGGTCAG

3

RAD2

ERGO:RPPA08434

361–403

43

65.8

39.5

CTTGGGTAACCTCATCCGAATCTCTTTGGTCTTTTTTATGTTG

3

CNE1

ERGO:RPPA04260

749–793

45

69.9

42.2

GGATGTACAATTCAGCATCTTCGTTCCAGTTTTCTGGTTTCACAG

3

HOG1

ERGO:RPPA06104

581–605

25

67.8

56.0

TCATCTCGGCGAAAATGCACCCTGC

4

SEC18

ERGO:RPPA05138

1027–1053

27

63.5

40.7

TACCAATATCCAGCTTGTTGGTACCAA

4

CUP5

ERGO:RPPA08088

123–151

29

63.3

41.4

CACTGTATTCTTGATCAGTAAGTCTGGAC

4

SAR1

ERGO:RPPA08441

475–505

31

62.9

38.7

CCTGTCTTAAGTAGATAGAGCAGGTAAATAC

4

ARL3

ERGO:RPPA09566

336–368

33

62.5

42.4

AACGTCCTGTTTATTGGCAAGCATAAGAATCGG

4

DFM1

ERGO:RPPA10235

824–860

37

63.1

40.5

CATTTCTTATCGCAGTAGCTTGGTTTTTCCGTCTTTG

4

HEM12

ERGO:RPPA08255

816–852

37

63.1

40.5

TGGACGGAATAACCAATCCAACGAGACAACATCATAA

4

RAD54

ERGO:RPPA04321

2193–2231

39

63.9

38.5

ACACATGAACTCAATTGCAGTTTAGCTGATTGTCTTTGG

4

RPS23B

ERGO:RPPA09269

187–227

41

66.2

41.5

AACTGAACTCTGACACACTTTCTAATAGCGGAGTTAGGTTG

4

MSN2

ERGO:RPPA05326

985–1027

43

70.5

41.9

GCTCATTCGTGTCTATGGACTTTGCCCTCTTTCTTTGTTTTGT

4

SSO2

ERGO:RPPA06663

356–400

45

71.4

40.0

GCTGTTCTCTGTAGTTGCTTTCAATAATACGGTAGTCCTGAATAG

4

GLT1

ERGO:RPPA07339

1740–1764

25

63.4

48.0

CACAATCGATTCCCTGATGGGATCA

5

UBC1

ERGO:RPPA09581

273–299

27

64.4

44.4

AGAATAGGCGTCCAGGCATTCTTCAAT

5

HSP12

ERGO:RPPA05227

211–239

29

64.8

44.8

TGAACTTGCTCAACTAAGGTAGGTTGGGT

5

PFK1

ERGO:RPPA04164

2447–2479

33

63.4

39.4

TTTTACCCGATTTGTTCTTACCATCGTCTTCCT

5

CIT1

ERGO:RPPA10025

758–792

35

67.1

40.0

GATAGACAGGTATAATCTCATCAGCTCAACGAACT

5

HRD1

ERGO:RPPA05158

1188–1222

35

63.8

42.9

TGAAGGAATTATCGGAATTGGACTGCAGTGGGAAT

5

SNC1

ERGO:RPPA04520

275–313

39

63.9

41.0

AGGAACGATGATAACAATCAGCAAAATCACGATTCCCAG

5

KIN2

ERGO:RPPA04639

640–680

41

70.6

43.9

TTTACGGTTGCATCGTAGTCATCAAATTCTGTCCCGTCAAG

5

TSA1

ERGO:RPPA06990

540–582

43

66.5

44.2

GGACTTGGAAAAGAATTCCTTGGAAGCATCAACTTCTGGCTTG

5

CPR5

ERGO:RPPA09912

314–358

45

71.9

42.2

TGAAGTTCTCGTCCTTGAATCTGCTACCGTAGATAGATTTTCCTC

5

  1. The P. pastoris specific probes designed for TRAC, divided into five pools according to their migration in capillary electrophoresis. Location of the probe in the coding sequence (CDS) is indicated. All oligonucleotides are labelled with 6-FAM at 3' and 5' ends.