Asamizu E, Nakamura Y, Sato S, Tabata S
Generation of 7137 Non-redundant Expressed Sequence Tags from a Legume,Lotus japonicus.
DNA Research, 7, 127-130 (2000)
Figures and Tables
Table 1 Classification of 5'-end ESTs by similarity search against the non-redundant protein database.
Similarity Number of groups Number of clones Genes of known functiona) 3302 15613 Hypothetical genesb) 1143 3110 No similarityc) 2692 4260 Total 7137 22983 a) showed similarity to genes of known function,
b) showed similarity to hypothetical genes that have no definition of function,
c) showed no similarity
Table 2 Classification of the non-redundant EST groups with similarity to known protein genes by their functional categories.
Functional categories Number of non-
redundant groupsEnergy metabolism 379 Regulatory functions 370 Cellular structure, organization and biogenesis 263 Protein fate 246 Signal transduction 239 Protein synthesis 229 Transport and binding proteins 205 Cellular processes 161 Growth and development 116 Secondary metabolism 114 Environmental response 105 Amino-acid biosynthesis 97 Pathogen responses 91 Fatty acid and phospholipid metabolism 87 DNA metabolism 66 Purines, pyrimidines, nucleosides, and nucleotides 52 General transcription 52 Central intermediary metabolism 37 Biosynthesis of cofactors, prosthetic groups, and carriers 34 Other categories 16 Unclassified 343 Total 3302
Table 3 Codon usage of predicted translated sequences compiled from 87 randomly selected ESTs. Triplet, amino acid name, frequency per thousand and the number of appearances in the 9071 codons analyzed are listed.
UUU Phe 17.2 156 UCU Ser 24.3 220 UAU Tyr 10.1 92 UGU Cys 9.3 84 UUC Phe 29.7 269 UCC Ser 25.2 229 UAC Tyr 15.8 143 UGC Cys 10.6 96 UUA Leu 6.8 62 UCA Ser 19.2 174 UAA STOP 0 0 UGA STOP 0 0 UUG Leu 21.1 191 UCG Ser 5.3 48 UAG STOP 0 0 UGG Trp 10.9 99 CUU Leu 25.6 232 CCU Pro 20.7 188 CAU His 11.5 104 CGU Arg 8.4 76 CUC Leu 31 281 CCC Pro 14.9 135 CAC His 16.3 148 CGC Arg 10.8 98 CUA Leu 7.3 66 CCA Pro 15.2 138 CAA Gln 19.2 174 CGA Arg 6.8 62 CUG Leu 14 127 CCG Pro 9.4 85 CAG Gln 17.1 155 CGG Arg 3.9 35 AUU Ile 19.1 173 ACU Thr 14.6 132 AAU Asn 14.6 132 AGU Ser 8.9 81 AUC Ile 24.8 225 ACC Thr 23.3 211 AAC Asn 24 218 AGC Ser 12.8 116 AUA Ile 6.7 61 ACA Thr 15.7 142 AAA Lys 24.4 221 AGA Arg 13.3 121 AUG Met 23.5 213 ACG Thr 6 54 AAG Lys 30 272 AGG Arg 13.2 120 GUU Val 23.6 214 GCU Ala 30.8 279 GAU Asp 21.6 196 GGU Gly 17.1 155 GUC Val 15.2 138 GCC Ala 24 218 GAC Asp 19.8 180 GGC Gly 16.5 150 GUA Val 3.9 35 GCA Ala 17.6 160 GAA Glu 22.6 205 GGA Gly 17.1 155 GUG Val 16.9 153 GCG Ala 7.4 67 GAG Glu 25.6 232 GGG Gly 8.3 75
Lotus japonicus
Kazusa DNA Research Institute
Department of Plant Gene Research