PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Pavir.9KG525000.1.p
Organism
Panicum virgatum
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
Family LBD
Protein Properties Length: 260aa    MW: 27001.5 Da    PI: 8.1928
Description LBD family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.9KG525000.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1DUF260128.52.9e-40301301100
               DUF260   1 aCaaCkvlrrkCakdCvlapyfpaeq.pkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvilklqqqleq 89 
                          +C aCk+lrrkC+++C++apyf +eq +++fa+vhk+FGasnv+kll ++p ++r da+ +++yeA+ar+rdPvyG+v++i++lqqq+ +
  Pavir.9KG525000.1.p  30 PCGACKFLRRKCVSGCIFAPYFDSEQgAAHFAAVHKVFGASNVSKLLLQIPAHKRLDAVVTICYEAQARLRDPVYGCVAHIFALQQQVVN 119
                          7***********************9989************************************************************** PP

               DUF260  90 lkaelallkee 100
                          l+ael +l+++
  Pavir.9KG525000.1.p 120 LQAELTYLQAH 130
                          ******99876 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5089123.04629131IPR004883Lateral organ boundaries, LOB
PfamPF031951.7E-3930128IPR004883Lateral organ boundaries, LOB
Sequence ? help Back to Top
Protein Sequence    Length: 260 aa     Download sequence    Send to blast
MSAGGGTSTL GGGGGPSGSG SGGPSGGGGP CGACKFLRRK CVSGCIFAPY FDSEQGAAHF  60
AAVHKVFGAS NVSKLLLQIP AHKRLDAVVT ICYEAQARLR DPVYGCVAHI FALQQQVVNL  120
QAELTYLQAH LATLELPSPP PLPAPPQMQM PGPFSIADLP SSTSVPTTVD LSALFDPPPH  180
AQPPQWAVQQ QHHHHHQQHH HQLRQPTTPY GAPVRGGGSG MAETSGAGGG DLQALARELV  240
DRHRSGGVKL EHPPPPHSR*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5ly0_A2e-37261247104LOB family transfactor Ramosa2.1
5ly0_B2e-37261247104LOB family transfactor Ramosa2.1
Search in ModeBase
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: During lateral root formation, expressed in the lateral root primordia, and the developing, emerged, and mature lateral roots. {ECO:0000269|PubMed:19717544}.
UniprotTISSUE 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
Source Description
UniProtInvolved 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
SourceLink
PlantRegMapPavir.9KG525000.1.p
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By auxin. {ECO:0000269|PubMed:15659631, ECO:0000269|PubMed:19717544, ECO:0000269|PubMed:23749813}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankBT0614310.0BT061431.1 Zea mays full-length cDNA clone ZM_BFb0145J09 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_025797026.11e-122LOB domain-containing protein 18-like
SwissprotO221314e-70LBD18_ARATH; LOB domain-containing protein 18
TrEMBLA0A3L6TU891e-124A0A3L6TU89_PANMI; LOB domain-containing protein 30-like
STRINGPavir.J34872.1.p1e-176(Panicum virgatum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP33463782
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G45420.13e-67LOB domain-containing protein 18
Publications ? help Back to Top
  1. Heyndrickx KS,Vandepoele K
    Systematic identification of functional plant modules through the integration of complementary data sources.
    Plant Physiol., 2012. 159(3): p. 884-901
    [PMID:22589469]
  2. Lee HW, et al.
    Dimerization in LBD16 and LBD18 Transcription Factors Is Critical for Lateral Root Formation.
    Plant Physiol., 2017. 174(1): p. 301-311
    [PMID:28336771]
  3. Pandey SK,Kim J
    Coiled-coil motif in LBD16 and LBD18 transcription factors are critical for dimerization and biological function in arabidopsis.
    Plant Signal Behav, 2018. 13(1): p. e1411450
    [PMID:29227192]
  4. Pandey SK, et al.
    LBD18 uses a dual mode of a positive feedback loop to regulate ARF expression and transcriptional activity in Arabidopsis.
    Plant J., 2018. 95(2): p. 233-251
    [PMID:29681137]
  5. Lee HW, et al.
    LBD16 and LBD18 acting downstream of ARF7 and ARF19 are involved in adventitious root formation in Arabidopsis.
    BMC Plant Biol., 2019. 19(1): p. 46
    [PMID:30704405]