From: Exploration of plant genomes in the FLAGdb++ environment
Data type | Feature number | Sources |
---|---|---|
Arabidopsis thaliana | ||
AGI coding genes | 28 094 | |
EuGène coding genes | 27 981 * | |
RNA genes | 1 288 | |
Transposable elements | 3 900 | TAIR [39] |
Curated repeat elements | 31 876 * | [36] |
Transcript sequences (EST, cDNA) | 1 281 393 | GenBank, aligned with SIM4 [41] |
Predicted smallRNA genes | 609 * | O. Voinnet et al. (unpublished data) |
2 D structures | 24 194 * | Predicted by SOPMA, PHD, DSC [15] |
3 D structures | 8 492 * | Predicted by Geno3 D [16] |
Curated annotations | 2 728 * | |
Paralogs in duplicated segments | 14 228 | TIGR-JCVI [43] |
FST | 407 192 | INRA, GABI, SAIL and SALK [44] |
CATMA probes (GST and GFT) | 35 283 * | |
Affymetrix micro-array probes | 266 372 | GeneChip® Arabidopsis ATH1 |
Chr. 4 tiling-array probes | 21 752 * | [26] |
Whole genome tiling-array probes | 1 434 492 * | TAG project (unpublished data) |
Promoter-array probes | 11 904 * | SAP project [27] |
MPSS from mRNA and smallRNA | 136 407 | |
Gene families | 3 500 | PFAM profiles [32] |
Protein motifs | 38 631 | PFAM profiles and HMMER [48] |
Oryza sativa | ||
Coding genes | 41 439 | |
RNA genes | 718 | TIGR-JCVI [49] |
Repeat elements | 16 185 | TIGR-JCVI [49] |
Transcript sequences (EST, cDNA) | 1 120 229 | GenBank, aligned with SIM4 [41] |
Curated annotations | 477 * | [35] |
FST | 79 612 | OryGenesDB [51] |
Gene families | 2 988 | PFAM profiles [32] |
Protein motifs | 60 789 | PFAM profiles and HMMER [48] |
Populus trichocarpa | ||
Coding genes | 45 555 | JGI [10] |
Repeat elements | 29 366 | JGI [10] |
Transcript sequences (EST, cDNA) | 322 996 | GenBank, aligned with SIM4 [41] |
Curated annotations | 3 176 * | J.-C. Leplé et al. (unpublished data) |
Gene families | 3 371 | PFAM profiles [32] |
Protein motifs | 49 723 | PFAM profiles and HMMER [48] |
Vitis vinifera | ||
IGGP coding genes | 26 347 | |
EuGène coding genes | 44 414 * | [19] |
Repeat elements | 336 729 | Genoscope [11] |
Transcript sequences (EST, cDNA) | 419 542 | GenBank, aligned with SIM4 [41] |
Curated annotations | 220 * | TPS [22] and other unpublished families |
Gene families | 2 970 | PFAM profiles [32] |
Protein motifs | 32 375 | PFAM profiles and HMMER [48] |