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Table 1 Validation of predicted alternative splicing events in Arabidopsis circadian genes

From: Unproductive alternative splicing and nonsense mRNAs: A widespread phenomenon among plant circadian clock genes

Gene

AGI locus

Predicted AS event

Fragment size, bp

Confirmed by

LHY

AT1G01060.2

Retained intron 4 (AT1G01060.2)

224

RT-PCR, qRT-PCR, Sanger sequencing

AT1G01060.3

Retained intron 9 (AT1G01060.3)

188

RT-PCR

LCL1

AT5G02840.1

Retained intron 7

230

RT-PCR

AT5G02840.1

Retained intron 8

135

RT-PCR

AT5G02840.3

CCA1

AT2G46830.1

Retained intron 4

224

RT-PCR, qRT-PCR, Sanger sequencing

PRR7

AT5G02810

Retained intron 3

208

RT-PCR, Sanger sequencing

PRR9

AT2G46790

Retained intron 3

172

RT-PCR

CIR1, RVE2

AT5G37260

Alternative Poison Cassette Exon (PCE) in intron 1

218

RT-PCR, Sanger sequencing

CIR1, RVE2

AT5G37260

Retained intron 3

225

RT-PCR, Sanger sequencing

CKB3

AT3G60250

Retained intron 3

153

RT-PCR

Retained intron 4

272

RT-PCR

ASG4

AT1G01520

Retained intron 6

345

RT-PCR

RVE7, EPR1

AT1G18330

Retained intron 1

213

RT-PCR

RVE8, LCL5

AT3G09600

Retained intron 7

390

RT-PCR

Retained intron 8

589

RT-PCR

CCR2, GRP7

AT2G21660

Retained portion of the intron 1 (alternative donor splice site)

184

RT-PCR, qRT-PCR, Sanger sequencing

CCR1, GRP8

AT4G39260

Retained portion of the intron 1 (alternative donor splice site)

188

RT-PCR

  1. PCR conditions and primers used for validation of each AS event are compiled in Additional file 2.