Skip to main content

Table 4 4-mer usage of exonic sequence at acceptor splice site of lost and corresponding retained introns

From: Intron gain and loss in segmentally duplicated genes in rice

Intron lost

Intron retained

Locus name*

4-mer†

Rank‡

Locus name§

Phase

4-mer

Rank

LOC_Os05g48520.1

ACCG

53

LOC_Os01g48540.1

0

ATCG

186

LOC_Os06g44300.1

TACA

136

LOC_Os02g08230.1

0

TACA

136

LOC_Os06g11920.1

GGCT

183

LOC_Os02g51600.1

0

GGTT

222

LOC_Os06g10850.1

GCCA

206

LOC_Os02g52830.1

0

GTGA

255

LOC_Os07g02440.1

GGCT

183

LOC_Os03g55420.1

0

GGAT

201

LOC_Os07g12340.1

CTGG

176

LOC_Os03g60080.1

0

TTGG

169

LOC_Os01g13130.1

GCCA

206

LOC_Os05g14240.1

0

GCGA

178

LOC_Os11g01820.1

GTCG

204

LOC_Os05g39600.1

0

GGCG

152

LOC_Os12g02840.1

GCCG

143

LOC_Os05g40650.1

0

GCTG

251

LOC_Os02g14430.1

GGCT

183

LOC_Os06g35480.1

0

GGGT

178

LOC_Os09g39720.1

ATAC

194

LOC_Os08g44590.1

0

ATAT

215

LOC_Os02g54640.1

GTGT

243

LOC_Os09g26160.1

0

GCAT

223

LOC_Os08g39370.1

GTGC

246

LOC_Os09g31130.1

0

ATCA

230

LOC_Os08g41880.1

ATGA

214

LOC_Os09g32840.1

0

ATGA

214

LOC_Os03g01820.1

GCGG

173

LOC_Os10g39810.1

0

ATGG

232

LOC_Os05g38420.1

GCGA

205

LOC_Os01g62490.1

1

GCGA

205

LOC_Os06g12960.1

AGGT

156

LOC_Os02g50810.1

1

AGGT

156

LOC_Os09g26160.1

GGCA

229

LOC_Os02g54640.1

1

AGGA

226

LOC_Os06g51050.1

GCGG

156

LOC_Os03g04060.1

1

GTGG

255

LOC_Os02g46780.1

GATT

244

LOC_Os04g50770.1

1

GTTT

251

LOC_Os01g50760.1

GAAA

246

LOC_Os05g46580.1

1

GGAA

247

LOC_Os11g09020.1

CCAA

156

LOC_Os12g08090.1

1

CCAA

156

LOC_Os05g04690.1

GAAC

235

LOC_Os01g18400.1

2

GAAC

235

LOC_Os05g48700.1

GGCG

189

LOC_Os01g55240.1

2

GGCC

158

LOC_Os05g39720.1

GAGG

218

LOC_Os01g61080.1

2

GAGG

218

LOC_Os07g49280.1

CTTC

163

LOC_Os03g18140.1

2

GTTC

251

LOC_Os07g49150.1

GTAC

255

LOC_Os03g18690.1

2

GTAT

256

LOC_Os07g49000.1

GTAC

255

LOC_Os03g19200.1

2

GTAC

255

LOC_Os09g26360.1

GTAC

255

LOC_Os08g34910.1

2

GTAC

255

LOC_Os08g41730.1

CACG

97

LOC_Os09g32800.1

2

GACG

158

LOC_Os12g08090.1

CGCC

18

LOC_Os11g09020.1

2

GGCG

189

LOC_Os01g09540.1

GTAC

255

LOC_Os05g10210.1

2

AACT

134

LOC_Os05g10210.1

GCCT

182

LOC_Os01g09540.1

2

GTCG

194

LOC_Os03g21820.1

CGTG

153

LOC_Os05g39990.1

2

GGTG

233

  1. *Locus name of the rice gene model with intron loss. †The exonic 4-mer at the acceptor splice site of the lost intron was inferred from the pair-wise alignment of the coding sequences as illustrated in Figure 5. ‡Each 4-mer is associated with an intron phase-dependent rank ranging from 1 to 256 as its based on the frequency of occurrence calculated from exonic 4-mers at the exon-intron boundary of all 33,011 FLS introns. §The corresponding rice duplicated gene with retained intron.