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PlantRegMap/PlantTFDB v5.0
Plant Transcription
Factor Database
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| Home TFext BLAST Prediction Download Help About Links PlantRegMap |
- The flowchart for construction of PlantTFDB
- Data source
- Data source (TFext)
- Pipeline to construct comprehensive protein dataset
- Family assignment rules
- List of studies which use the Family assignment rules
- Thresholds for domain identification
- Summary of TFs in different taxonomic lineages of green plants and the origination stage of TF families
- Pipeline for parsing BLAST reciprocal best hits (RBHs) and inferring orthologous groups
- Pipeline for GO annotation
- Curation and projection of TF binding motifs
- Transcription factor information
- Multiple sequence alignment
- Phylogenetic trees
- Quick search
- TF prediction server
- Help for PlantRegMap
Data Source
| Species | Common name | Genome Anotation | UniGene | PlantGDB |
| - | IKGC | - | - | |
| Tausch's goatgrass | BGI | - | - | |
| - | VEGI(v2.5) | - | - | |
| grain amaranth | BYU | - | - | |
| - | TAGP | - | - | |
| pineapple | JGI(v3) | - | - | |
| columbine | JGI(v3.1) | - | - | |
| - | JGI(v1.1) | - | - | |
| lyrate rockcress | JGI(v1.0) | - | - | |
| thale cress | TAIR10 | - | - | |
| alpine rockcress | MPIPBR | - | - | |
| - | NCGR_PGC | - | - | |
| - | NCGR_PGC | - | - | |
| - | BGI | - | - | |
| - | NGD | - | - | |
| - | ORCAE | - | - | |
| beet | TBVR(v2) | - | - | |
| - | JGI(v1.2) | - | - | |
| purple false brome | JGI(v3.1) | - | - | |
| - | JGI(v1.1) | - | - | |
| rape | Genoscope(v5) | - | - | |
| - | NCBI 100 | - | - | |
| field mustard | NCBI 100 | - | - | |
| - | IIPG | - | - | |
| false flax | CSGP | - | - | |
| - | CCBR | - | - | |
| - | JGI(v1.1) | - | - | |
| - | JGI(v1.0) | - | - | |
| chilli pepper | PEP(v1.55) | - | - | |
| papaya | ASGPB | - | - | |
| Chinese chestnut | THGP(v1.1) | - | - | |
| Madagascar periwinkle | MPGR | - | - | |
| - | JGI(v5.5) | - | - | |
| - | JGI(v1.0) | - | - | |
| - | NCBI 101 | - | - | |
| - | ICuGI(v1) | - | - | |
| - | ICGC(v1.0) | - | - | |
| Valencia orange | ICGC(v1.1) | - | - | |
| - | JGI(v2) | - | - | |
| robusta coffee | CGSC | - | - | |
| - | MELONOMICS(v3.5) | - | - | |
| cucumber | JGI, V1.0 | - | - | |
| Queen Anne's lace | ARS-USDA(v2.0) | - | - | |
| carnation | DCA(v1.0) | - | - | |
| - | Dichan(v1) | - | - | |
| - | CNU(v1) | - | - | |
| - | JGI(v1.0) | - | - | |
| African oil palm | OG | - | - | |
| tef | Tef(v3) | - | - | |
| Murray red gum | ECGD | - | - | |
| - | JGI(v2.0) | - | - | |
| - | JGI(v1.0) | - | - | |
| strawberry | kazusa(v1.1) | - | - | |
| - | GDR(v1.1) | - | - | |
| - | LSMU | - | - | |
| soybean | Wm82.a2.v1 | - | - | |
| wild soybean | TCUHK | - | - | |
| - | GPGRP | - | - | |
| tree cotton | BGI-A2(v1.0) | - | - | |
| upland cotton | NAU-NBI(v1.1) | - | - | |
| - | JGI(v2.1) | - | - | |
| - | UBC | - | - | |
| barley | IBSC(v1.0) | - | - | |
| European hop | HOPBASE(v1.1) | - | - | |
| - | Kazusa(v1.0) | - | - | |
| - | Kazusa(v4.5) | - | - | |
| English walnut | JHU | - | - | |
| - | JGI(v1.1) | - | - | |
| - | JGI(v1.1) | - | - | |
| - | KFGP(v1.0) | - | - | |
| - | OGE | - | - | |
| - | BGI(v1.0) | - | - | |
| - | Kazusa(v3.0) | - | - | |
| apple | GDR(v1.0) | - | - | |
| cassava | JGI(v6.1) | - | - | |
| liverwort | JGI(v3.1) | - | - | |
| barrel medic | Mt4.0v1 | - | - | |
| - | JGI(v3.0) | - | - | |
| - | JGI(v3.0) | - | - | |
| spotted monkey flower | JGI(v2.0) | - | - | |
| - | BU | - | - | |
| - | BGI | - | - | |
| - | CIRAD | - | - | |
| - | CAS(v2.0) | - | - | |
| - | BTI | - | - | |
| wood tobacco | NCBI 100 | - | - | |
| tobacco | NCBI 100 | - | - | |
| - | NCBI 100 | - | - | |
| holy basil | OteDB | - | - | |
| - | JGI(v1.0) | - | - | |
| - | OGE | - | - | |
| - | OGE(v1.4) | - | - | |
| - | AGI1.1 | - | - | |
| - | OGE | - | - | |
| long-staminate rice | BGI | - | - | |
| - | OGE | - | - | |
| - | OGE | - | - | |
| - | OGE | - | - | |
| common wild rice | OGE | - | - | |
| Indian rice | RIS, Glean | - | - | |
| Japanese rice | MSU(v7) | - | - | |
| - | JGI(v2.0) | - | - | |
| - | JGI(v2.0) | - | - | |
| - | JGI(v2.0) | - | - | |
| - | JGI(v2.0) | - | - | |
| switchgrass | JGI(v3.1) | - | - | |
| large white petunia | SGN(v1.6.2) | - | - | |
| - | SGN(v1.0.1) | - | - | |
| - | BGI | - | - | |
| - | JGI(v1.0) | - | - | |
| - | PDK(v3) | - | - | |
| - | ICBR(v1.0) | - | - | |
| - | COSMOSS(v3.3) | - | - | |
| - | ConGenIE(v1.0) | - | - | |
| - | Rutgers | - | - | |
| Euphrates poplar | LZU | - | - | |
| black cottonwood | JGI(v3.0) | - | - | |
| Japanese apricot | BGI | - | - | |
| peach | JGI(v2.1) | - | - | |
| Douglas-fir | PRS(v1.0) | - | - | |
| - | CPETR(v1.0) | - | - | |
| jointed charlock | MSU | - | - | |
| radish | RGD | - | - | |
| castor bean | JCVI(v0.1) | - | - | |
| purple osier | JGI(v1.0) | - | - | |
| Chinese salvia | NDCTCM | - | - | |
| - | JGI(v1.0) | - | - | |
| beniseed | NCBI 100 | - | - | |
| - | JGI(v2.2) | - | - | |
| - | JGI(v1.1) | - | - | |
| - | VEGI(v1) | - | - | |
| tomato | ITAG(v2.3) | - | - | |
| aubergine | EGD | - | - | |
| - | spenn(v2.0) | - | - | |
| currant tomato | CSHL | - | - | |
| potato | PGSC | - | - | |
| sorghum | JGI(v3.1) | - | - | |
| - | JGI(v0.5) | - | - | |
| spinach | TBVR(v1) | - | - | |
| great duckweed | MIPS/IBIS(v2) | - | - | |
| - | NCBI 100 | - | - | |
| - | thellungiella(v2.0) | - | - | |
| cocoa | CGD(v1.1) | - | - | |
| peavine clover | JGI(v2) | - | - | |
| Wheat | IWGSC(v1.0)+popseq(v31) | - | - | |
| - | BGI | - | - | |
| - | UGSP | - | - | |
| adzuki bean | SNU(v3) | - | - | |
| mung bean | SNU(v6) | - | - | |
| wine grape | Genoscope | - | - | |
| - | JGI(v2.1) | - | - | |
| maize | MaizeSequence(AGPv3.31/5b+) | - | - | |
| Chinese jujube | NCBI 100 | - | - | |
| - | JGI(v2.2) | - | - | |
| Japanese lawn grass | ZGD(v1.1) | - | - | |
| Japanese carpet grass | ZGD(v1.0) | - | - | |
| - | ZGD(v1.0) | - | - | |
| peanut | - | Build #4 | 171a | |
| sweet wormwood | - | Build #6 | 183a | |
| sunflower | - | Build #12 | 169a | |
| garden lettuce | - | Build #17 | 187a | |
| white spruce | - | Build #15 | 175a | |
| Sitka spruce | - | Build #16 | 183a | |
| loblolly pine | - | Build #13 | 157a | |
| sugarcane | - | Build #15 | 157a | |
| cowpea | - | Build #4 | 167a |




