PlantRegMap/PlantTFDB v5.0
Plant Transcription
Factor Database
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Transcription Factor Information
Basic Information? help Back to Top | |||||||||
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TF ID | Pavir.9KG249000.1.p | ||||||||
Organism | |||||||||
Taxonomic ID | |||||||||
Taxonomic Lineage |
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Panicodae; Paniceae; Panicinae; Panicum
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Family | LBD | ||||||||
Protein Properties | Length: 268aa MW: 27928.5 Da PI: 7.4229 | ||||||||
Description | LBD family protein | ||||||||
Gene Model |
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Signature Domain? help Back to Top | |||||||
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No. | Domain | Score | E-value | Start | End | HMM Start | HMM End |
1 | DUF260 | 127 | 8.7e-40 | 36 | 136 | 1 | 100 |
DUF260 1 aCaaCkvlrrkCakdCvlapyfpaeq.pkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvilklqqqleq 89 +C aCk+lrrkC+++C++apyf +eq +++fa vhk+FGasnv+kll ++p+++r da+ +++yeA+ar+rdP+yG+v++i++lqqq+ + Pavir.9KG249000.1.p 36 PCGACKFLRRKCVSGCIFAPYFDSEQgAAHFASVHKVFGASNVSKLLLQIPPHKRLDAVVTVCYEAQARLRDPIYGCVSHIFALQQQVVK 125 7***********************9989************************************************************** PP DUF260 90 lkaelallkee 100 l++el +l+ + Pavir.9KG249000.1.p 126 LQTELTYLQGH 136 *****998865 PP |
Protein Features ? help Back to Top | ||||||
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Database | Entry ID | E-value | Start | End | InterPro ID | Description |
PROSITE profile | PS50891 | 23.348 | 35 | 137 | IPR004883 | Lateral organ boundaries, LOB |
Pfam | PF03195 | 3.5E-39 | 36 | 134 | IPR004883 | Lateral organ boundaries, LOB |
Sequence ? help Back to Top |
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Protein Sequence Length: 268 aa Download sequence Send to blast |
MSSSMAGASA GGSGAGGSSG AGAGAGVGGG SGGGGPCGAC KFLRRKCVSG CIFAPYFDSE 60 QGAAHFASVH KVFGASNVSK LLLQIPPHKR LDAVVTVCYE AQARLRDPIY GCVSHIFALQ 120 QQVVKLQTEL TYLQGHLSTM EIPTPPPFAG QPQMPMTATF SSVSNLPSSS NVPASVDLST 180 LLDSQTQSQQ WAFQFQQQQI LQQQQEQQLL LQQQQYLQMG EGSNRGASGS GTLDDGGDLQ 240 ALAMELLDRR QRMAVGSPPK PPTPATQ* |
3D Structure ? help Back to Top | ||||||
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PDB ID | Evalue | Query Start | Query End | Hit Start | Hit End | Description |
5ly0_A | 2e-40 | 32 | 130 | 7 | 104 | LOB family transfactor Ramosa2.1 |
5ly0_B | 2e-40 | 32 | 130 | 7 | 104 | LOB family transfactor Ramosa2.1 |
Search in ModeBase |
Expression -- Description ? help Back to Top | ||||||
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Source | Description | |||||
Uniprot | DEVELOPMENTAL STAGE: During lateral root formation, expressed in the lateral root primordia, and the developing, emerged, and mature lateral roots. {ECO:0000269|PubMed:19717544}. | |||||
Uniprot | TISSUE SPECIFICITY: Expressed in roots, stems, leaves and flowers (PubMed:12068116, PubMed:24484953). Expressed in vascular tissues of hypocotyls, leaves, roots, developing floral organs and siliques (PubMed:19088331). {ECO:0000269|PubMed:12068116, ECO:0000269|PubMed:19088331, ECO:0000269|PubMed:24484953}. |
Functional Description ? help Back to Top | ||||||
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Source | Description | |||||
UniProt | Involved in the positive regulation of tracheary element (TE) differentiation. Involved in a positive feedback loop that maintains or promotes NAC030/VND7 expression that regulates TE differentiation-related genes (PubMed:19088331). Functions in the initiation and emergence of lateral roots, in conjunction with LBD16, downstream of ARF7 and ARF19 (PubMed:19717544, PubMed:23749813). Transcriptional activator that directly regulates EXPA14, a gene encoding a cell wall-loosening factor that promotes lateral root emergence. Activates EXPA14 by directly binding to a specific region of its promoter (PubMed:22974309). Transcriptional activator that directly regulates EXPA17, a gene encoding a cell wall-loosening factor that promotes lateral root emergence (PubMed:23872272). Acts downstream of the auxin influx carriers AUX1 and LAX1 in the regulation of lateral root initiation and development (PubMed:26059335). {ECO:0000269|PubMed:19088331, ECO:0000269|PubMed:19717544, ECO:0000269|PubMed:22974309, ECO:0000269|PubMed:23749813, ECO:0000269|PubMed:23872272, ECO:0000269|PubMed:26059335}. |
Cis-element ? help Back to Top | |
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Source | Link |
PlantRegMap | Pavir.9KG249000.1.p |
Regulation -- Description ? help Back to Top | ||||||
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Source | Description | |||||
UniProt | INDUCTION: By auxin. {ECO:0000269|PubMed:15659631, ECO:0000269|PubMed:19717544, ECO:0000269|PubMed:23749813}. |
Regulation -- PlantRegMap ? help Back to Top | ||||||
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Source | Upstream Regulator | Target Gene | ||||
PlantRegMap | Retrieve | - |
Annotation -- Nucleotide ? help Back to Top | ||||||
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Source | Hit ID | E-value | Description | |||
GenBank | BT061431 | 1e-129 | BT061431.1 Zea mays full-length cDNA clone ZM_BFb0145J09 mRNA, complete cds. |
Annotation -- Protein ? help Back to Top | |||||||
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Source | Hit ID | E-value | Description | ||||
Refseq | XP_025791842.1 | 1e-109 | LOB domain-containing protein 30-like | ||||
Swissprot | O22131 | 2e-67 | LBD18_ARATH; LOB domain-containing protein 18 | ||||
TrEMBL | A0A1E5UT08 | 1e-114 | A0A1E5UT08_9POAL; LOB domain-containing protein 18 | ||||
STRING | Pavir.Ib02517.1.p | 0.0 | (Panicum virgatum) |
Orthologous Group ? help Back to Top | |||
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Lineage | Orthologous Group ID | Taxa Number | Gene Number |
Monocots | OGMP3346 | 37 | 82 |
Best hit in Arabidopsis thaliana ? help Back to Top | ||||||
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Hit ID | E-value | Description | ||||
AT4G00220.1 | 1e-60 | LBD family protein |
Link Out ? help Back to Top | |
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Phytozome | Pavir.9KG249000.1.p |
Publications ? help Back to Top | |||
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