Table 9. Coverage of genes with Pfam domains in the rice FL-cDNA libraries.
| Pfam ID (a) | InterPro ID (a) | Short name | All loci | CDS-AE | CDS-ANE | CDS-AE proportion (b) | Significance (c) | Ecoli (d) |
| PF00076 | IPR000504 | RNP1_RNA_bd | 233 | 204 | 29 | 87.6 | High | |
| PF00400 | IPR001680 | WD40 | 212 | 198 | 14 | 93.4 | High | |
| PF00036 | IPR002048 | EF_hand_Ca_bd | 164 | 137 | 27 | 83.5 | High | |
| PF00271 | IPR001650 | Helicase_C | 131 | 117 | 14 | 89.3 | High | 1 |
| PF00657 | IPR001087 | Lipase_GDSL | 113 | 92 | 21 | 81.4 | High | 1 |
| PF00515 | IPR001440 | TPR_1 | 108 | 99 | 9 | 91.7 | High | 1 |
| PF00226 | IPR001623 | DnaJ_N | 108 | 92 | 16 | 85.2 | High | 1 |
| PF00004 | IPR003959 | AAA_ATPase_core | 106 | 94 | 12 | 88.7 | High | 1 |
| PF00106 | IPR002198 | SDR | 97 | 80 | 17 | 82.5 | High | 1 |
| PF00561 | IPR000073 | AB_hydrolase_1 | 91 | 81 | 10 | 89.0 | High | 1 |
| PF00069 | IPR000719 | Prot_kinase | 1289 | 892 | 397 | 69.2 | Low | 1 |
| PF00560 | IPR001611 | LRR | 890 | 533 | 357 | 59.9 | Low | 1 |
| PF00646 | IPR001810 | F-box | 716 | 413 | 303 | 57.7 | Low | |
| PF00931 | IPR002182 | NB-ARC | 427 | 212 | 215 | 49.6 | Low | |
| PF07197 | IPR010811 | DUF1409 | 253 | 6 | 247 | 2.4 | Low | |
| PF06654 | IPR009546 | DUF1165 | 231 | 4 | 227 | 1.7 | Low | |
| PF00098 | IPR001878 | Znf_CCHC | 226 | 46 | 180 | 20.4 | Low | |
| PF03578 | IPR005213 | HGWP | 215 | 3 | 212 | 1.4 | Low | |
| PF05699 | IPR008906 | HATC | 215 | 32 | 183 | 14.9 | Low | |
| PF00023 | IPR002110 | ANK | 176 | 113 | 63 | 64.2 | Low | 1 |
| Domain-coded CDS | 24247 | 17459 | 6788 | 72.0 | ||||
a
: The domain information was taken from TIGR OSA1 (http://www.tigr.org/tdb/e2k1/osa1/index.shtml).
b
: The ratio was calculated as the number of CDS-AE loci/total number of loci.
c
: Significances of difference were examined between the CDS-AE proportion for genes encoding the respective domain and that for genes encoding the entire domains examined by the chi-squared test. High (Low) represents the cloning efficiency of genes encoding the respective domain was higher (lower) than the collection efficiency of genes encoding the entire domains examined.
d
: Pfam domain data for E. coli K12 published at http://www.sanger.ac.uk/Software/Pfam/. A value of 1 indicates that genes encoding the corresponding domain are found in the E. coli K12 genome.