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 (TFext)
The deadline for species collection was Jun. 20th, 2019. 52 newly sequenced species were collected. For these species, gene sets annotated by corresponding genome projects are used.
Species | Common name | Genome assembly | Gene Anotation | PubMed ID |
Indian licorice | Abrus_2018 (GCA_003935025.1) | NCBI(v100) | - | |
- | ASM278626v1 (GCA_002786265.1) | NCBI | 28902843 | |
Garden asparagus | Aspof.V1 | Phytozome(v1.1) | 29093472 | |
- | v2.0 | Phytozome(v2.1) | 28428306 | |
- | AHAU_CSS_1 (GCA_004153795.1) | NCBI(v100) | 30642496 | |
- | ASM227188v2 (GCA_002271885.2) | NCBI | 30336638 | |
Scotch bonnet | ASM227189v2 (GCA_002271895.2) | NCBI | 29089032 | |
- | Cbr_1.0 (GCA_003427395.1) | NCBI | 30007417 | |
Quinoa | v1.0 | Phytozome(v1.0) | 28178233 | |
- | v5 | Phytozome(v5.2.3.2) | 28484037 | |
- | v1.0 | Kazusa(v1.1) | 30689773 | |
- | ASBRC_Ckan_1.0 (GCA_003546025.1) | NCBI | 30626928 | |
Satsuma orange | CUMW_v1.0 (GCA_002897195.1) | NCBI | 29259619 | |
Arabica coffee | Cara_1.0 (GCA_003713225.1) | NCBI(v100) | - | |
- | Ceug_1.0 (GCA_003713205.1) | NCBI(v100) | - | |
Jute | CCACVL1_1.0 (GCA_001974805.1) | EnsemblPlants(v43) | 28134914 | |
Boston marrow | Cmax_1.0 (GCA_002738345.1) | NCBI(v100) | 28917590 | |
Canada pumpkin | Cmos_1.0 (GCA_002738365.1) | NCBI(v100) | 28917590 | |
Field pumpkin | ASM280686v2 (GCA_002806865.2) | NCBI | 29112324 | |
Artichoke | CcrdV1 (GCA_001531365.1) | NCBI | 26786968 | |
- | ASM160598v2 (GCA_001605985.2) | NCBI(v101) | 28258650 | |
Guinea yam | TDr96_F1_Pseudo_Chromosome_v1.0 (GCA_002240015.2) | EnsemblPlants(v43) | 28927400 | |
Durian | Duzib1.0 (GCA_002303985.1) | NCBI(v100) | 28991254 | |
- | Bedadeti_annotated (GCA_001884845.1) | NCBI | 29896517 | |
- | Himp0.1 (GCA_002762385.1) | NCBI | - | |
- | ASM216827v2 (GCA_002168275.2) | NCBI(v100) | - | |
Para rubber tree | ASM165405v1 (GCA_002003025.1) | NCBI(v100) | 27108962 | |
Japanese morning glory | Asagao_1.1 (GCA_001879475.1) | NCBI(v100) | 27824041 | |
South American air plant | v1.0 | Phytozome(v1.1) | 29196618 | |
Narrow-leaved blue lupine | LupAngTanjil_v1.0 (GCA_001865875.1) | EnsemblPlants(v43) | 27557478 | |
- | MC_HNAU_1.0 (GCA_002174775.1) | NCBI | 28552780 | |
Balsam pear | ASM199503v1 (GCA_900491585.1) | NCBI(v100) | 28028039 | |
- | ASM337056v1 (GCA_003370565.1) | NCBI | - | |
- | NIATTr2 (GCA_001879085.1) | EnsemblPlants(v43) | 28536194 | |
Wild olive | v1.0 | Phytozome(v1.0) | 29078332 | |
- | Oryza_glumaepatula_v1.5 (GCA_000576495.1) | EnsemblPlants(v43) | 29358651 | |
- | Oryza_nivara_v1.0 (GCA_000576065.1) | EnsemblPlants(v43) | 29358651 | |
Opium poppy | ASM357369v1 (GCA_003573695.1) | NCBI(v100) | 30166436 | |
- | PanWU01x14_asm01 (GCA_002914805.1) | NCBI | - | |
Gean | v1.0 | GDR(v1.0.a1) | 28541388 | |
Plum | v1.0 | GDR(v1.0.a1) | 30603097 | |
Granado | ASM220158v1 (GCA_002864125.1) | NCBI | 29271050 | |
Pear | v1.0 | GDR(v1.0) | 24699266 | |
Cork oak | CorkOak1.0 (GCA_002906115.1) | NCBI(v100) | 29786699 | |
China rose | v2.0 | GDR(v2.0) | 29713014 | |
Japanese rose | v1.0 | GDR(v1.0) | 29045613 | |
Black raspberry | v3.0 | GDR(v3.0) | 30107523 | |
Bonfire salvia | SspV1 (GCA_004379255.1) | NCBI | - | |
- | TetSoc1 (GCA_002891735.1) | NCBI | 29294063 | |
- | TorRG33x02_asm01 (GCA_002914845.1) | NCBI | 30175293 | |
- | ASM349008v1 (GCA_003490085.1) | NCBI | 29922311 | |
Wild emmer wheat | WEWSeq_v.1.0 (GCA_002162155.1) | EnsemblPlants(v43) | 28684525 |