| |
a. Genome : IRGSP sequenced and TIGR assembled pseudo-molecules/annotation version 5 (01/24/2007 RiceGE5), MSU assembled pseudo-molecules/annotation version 6.1 (RiceGE6) and the lastest version 7 (RiceGE7  ).
b. T-DNA / Ds FST / Mutants
- 1. Kitaake mutants UC Davis - the Fast-Neutron-Induced Kitaake Rice Mutant Population. It contains 1,504 mutants, 94,655 sites and total genes affected: 32,307.
- 2. Postech PFG T-DNA, S. Korea [Publication]
- 3. Rice Mutant Data, Huazhong Agricultural University, China [Publication]. We have uploaded RMD's newly comprehensive FSTs into our database. They have 85,315 sequences in total and 47,231 mapped onto the japanica genome and 46,481 onto the indica genome. Due to difference of their new names and the old ones, we will keep the old names a while. However, we will remove them later.
- 4. Taiwan Rice Insertion Mutant (TRIM), Academia Sinica src=/Images/new.gif>
- 5. NIAS Tos17 insertion mutants [RTIM], Japan [Publication]
- 6. CIRAD / Genoplante oryza tag lines, France [Publication]
- 7. Zhejiang Univ. rice T-DNA, China [Publication]
- 8. UCD dSpm/Ds, USA
- 9. CSIRO Ac/Ds, Australia [Publication]
- 10. PSNU Ds, Korea
- 11. EU-OSTID Ds, Netherlands
- 12. SHIP T-DNA, China.
c. cDNA and others
|
|
| Categery | Group | Sequences | v5 Mapped | v6 Mapped | v7 Mapped | Update |
|---|
| Gene | IRGSP/TIGR/MSU | | 57,142 | 57,840 | 66,153 | 01/18/2018 |
| Kitaake Mutants | Single Base Substitions | 1,504
mutants | | | 43,483 | 01/18/2018 |
| Deletions | | | 31,909 | 01/18/2018 |
| Insertions | | | 7,929 | 01/18/2018 |
| Invertions | | | 3,691 | 01/18/2018 |
| Translocations | | | 5,175 | 01/18/2018 |
| Tandem Duplications | | | 65 | 01/18/2018 |
| Insertions | RTIM | 77,740 | 17,937 | 77,701 | 78,848 | 01/18/2018 |
| Eu-CIRAD/Genoplante | 29,263 | 28,324 | 28,540 | 29,429 | 01/18/2018 |
| ZJU T-DNA | 741 | 714 | | 795 | 01/18/2018 |
| UCD FST | 17,730 | 17,683
dSpm: 12,856
Ds: 4,827 | 17,684
dSpm: 12,857
Ds: 4,827 | 18,777
dSpm: 12,984
Ds: 5,793 | 01/18/2018 |
| TRIM FST | 59,804 | 11,646 | 65,701 | 58,764 | 01/18/2018 |
| CSIRO FST | 611 | 589 | 592 | 596 | 01/18/2018 |
| RMD FST | 85,315 | 33,197 | 47,231 | 91792 | 01/18/2018 |
| PFG T-DNA | 107,171 | 106,095
67,282 lines | 106,100 | 99,559 | 01/18/2018 |
| GSNU Ds | 1,072 | 1,046 | 1,047 | 1,068 | 01/18/2018 |
| EU-OSTID Ds | 1,315 | 1,301 | 1,315 | 1,300 | 01/18/2018 |
| SHIP T-DNA | 10,381 | 10,281 (7,759 lines) | 10,281 | 10,934 | 01/18/2018 |
| Full-length cDNAs | KOME | 35,786 | 36,467 | 36,497 | 36,596 | 01/18/2018 |
| RiCD indica | 10,083 | 9,302 (9,155) | 9,325 | 9,396 | 01/18/2018 |
| Community | 3,371 | 3,079 | 3,459 | 8,171 | 01/18/2018 |
| Genomic DNA | Community Gene | 658 | 680 | | | 08/25/2007 |
| EST jap. contigs | | 1,040,140 | 1,007,456
ctg: 37,954 | | 1,255,251
226,050 | 08/25/2007 |
MPSS
(<=2 hits) | mRNA 17bp | 419,157 | 101,246 | | | 08/25/2007 |
| mRNA 20bp | 35,5700 | 76,059 | | | 08/25/2007 |
| Small RNA | 296,201 | 256,790 | 269,552 (<=3 hits) | | 06/08/2010 |
| miRNA | ASRP/Sanger | 68 | 391 | | | 04/22/2008 |
| miRBase | 15,632 | | 1,597 | | 06/08/2010 |
| small RNA | UC Davis CSRDB | 11809 | 16489 (10743) | | | 10/07/2008 |
| 113,196 | | 84,122 (<=3 hits) | | 06/08/2010 |
| SAGE | = 1 hit | | 32,804 | | | 08/25/2007 |
| Markers AFLP,RFLP,RAPD,STS | | | 7,845 | | | 08/25/2007 |
| Homology cDNA | Wheat | | 1,159 | 575 | | 07/06/2010 |
| Maize | | 32,226 (27K+ Arizona GI) | 45,843 | | 07/06/2010 |
| Barley | | 462 | 631 | | 07/06/2010 |
| Brassica | | 879 | 1,344 | | 07/06/2010 |
| Arabidopsis coding protein | 26,751 | 22,602 | 23,039 | | 07/06/2010 |
| Affymetrix rice genome array | sequence information (SIF) | 57,381 | 55,088 | | | 08/25/2007 |
| gene expression sample (GSM) | | 155 | | | 08/25/2007 |
| Yale Tiling Array | | | 12,896,594 | | | 08/25/2007 |
|
