Skip to main content

Table 3 4-mer usage of exonic sequence at donor 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 CAAG 256 LOC_Os01g48540.1 0 CAAG 256
LOC_Os06g44300.1 CGAG 245 LOC_Os02g08230.1 0 CGAG 245
LOC_Os06g11920.1 CAAG 256 LOC_Os02g51600.1 0 CAAG 256
LOC_Os06g10850.1 GAGG 219 LOC_Os02g52830.1 0 CCAT 211
LOC_Os07g02440.1 CGAC 130 LOC_Os03g55420.1 0 CGAG 245
LOC_Os07g12340.1 CAGG 234 LOC_Os03g60080.1 0 CAGG 234
LOC_Os01g13130.1 CGCC 154 LOC_Os05g14240.1 0 CATG 244
LOC_Os11g01820.1 GCTC 103 LOC_Os05g39600.1 0 CATG 244
LOC_Os12g02840.1 CCTC 172 LOC_Os05g40650.1 0 CCTC 172
LOC_Os02g14430.1 CCAG 251 LOC_Os06g35480.1 0 CAAC 193
LOC_Os09g39720.1 GGAG 246 LOC_Os08g44590.1 0 GGAG 246
LOC_Os02g54640.1 GTTC 28 LOC_Os09g26160.1 0 TTTT 133
LOC_Os08g39370.1 CAAC 193 LOC_Os09g31130.1 0 CAAC 193
LOC_Os08g41880.1 CGAG 245 LOC_Os09g32840.1 0 TGAG 253
LOC_Os03g01820.1 GAGG 219 LOC_Os10g39810.1 0 CAAG 256
LOC_Os05g38420.1 TTCG 225 LOC_Os01g62490.1 1 TTCG 225
LOC_Os06g12960.1 GACG 228 LOC_Os02g50810.1 1 CACG 222
LOC_Os09g26160.1 CATC 54 LOC_Os02g54640.1 1 CACA 171
LOC_Os06g51050.1 ACCG 223 LOC_Os03g04060.1 1 ACAG 250
LOC_Os02g46780.1 GCCG 227 LOC_Os04g50770.1 1 GCAG 251
LOC_Os01g50760.1 GGAG 247 LOC_Os05g46580.1 1 GGAG 247
LOC_Os11g09020.1 GTCG 216 LOC_Os12g08090.1 1 ATCT 194
LOC_Os05g04690.1 CGTG 88 LOC_Os01g18400.1 2 CATG 237
LOC_Os05g48700.1 TGAG 246 LOC_Os01g55240.1 2 TCCG 222
LOC_Os05g39720.1 GGTG 115 LOC_Os01g61080.1 2 GATG 217
LOC_Os07g49280.1 CAAG 254 LOC_Os03g18140.1 2 CCCG 142
LOC_Os07g49150.1 AGAG 251 LOC_Os03g18690.1 2 AGAG 251
LOC_Os07g49000.1 GGAG 245 LOC_Os03g19200.1 2 GGAG 245
LOC_Os09g26360.1 GAAG 249 LOC_Os08g34910.1 2 GAAG 249
LOC_Os08g41730.1 GCGG 208 LOC_Os09g32800.1 2 GCGG 208
LOC_Os12g08090.1 TGCG 115 LOC_Os11g09020.1 2 TGCT 163
LOC_Os01g09540.1 TCGG 225 LOC_Os05g10210.1 2 ATGG 238
LOC_Os05g10210.1 TCCA 175 LOC_Os01g09540.1 2 TAAG 248
LOC_Os03g21820.1 GCCG 195 LOC_Os05g39990.1 2 GCAG 252
  1. *Locus name of the rice gene model with intron loss. The exonic 4-mer at the donor 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 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.