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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.