PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Pavir.1NG554700.1.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
Family LBD
Protein Properties Length: 212aa    MW: 22000.2 Da    PI: 7.904
Description LBD family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.1NG554700.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1DUF260121.83.8e-38251261101
               DUF260   1 aCaaCkvlrrkCakdCvlapyfpaeq.pkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvilklqqqleq 89 
                          +C aCk+lrr+C+++Cv+apyf  +q +++fa++hk+FGasn +kll++lp  +r +a+ +++yeA+ar+rdPvyG+v+ i++lqqq++ 
  Pavir.1NG554700.1.p  25 PCGACKFLRRRCVPECVFAPYFSTDQgAARFAAIHKVFGASNASKLLSHLPVADRCEAVVTITYEAQARLRDPVYGCVAQIFALQQQVAI 114
                          7***********************9989************************************************************** PP

               DUF260  90 lkaelallkeel 101
                          l+a+l ++k++l
  Pavir.1NG554700.1.p 115 LQAQLMQAKAQL 126
                          *****9999875 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5089122.8124126IPR004883Lateral organ boundaries, LOB
PfamPF031952.5E-3725123IPR004883Lateral organ boundaries, LOB
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0010311Biological Processlateral root formation
GO:0005634Cellular Componentnucleus
Sequence ? help Back to Top
Protein Sequence    Length: 212 aa     Download sequence    Send to blast
MAGATSASGG AAAAAAAAPT GAGSPCGACK FLRRRCVPEC VFAPYFSTDQ GAARFAAIHK  60
VFGASNASKL LSHLPVADRC EAVVTITYEA QARLRDPVYG CVAQIFALQQ QVAILQAQLM  120
QAKAQLACSP PVSSHHWPAD HGSITALLRQ DTACSARTKP GGPLDDCFMP ELMASGFRDD  180
VVAAQHCAAK ADAGDLQYLA QAMMRSPNYS L*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5ly0_A1e-37171261111LOB family transfactor Ramosa2.1
5ly0_B1e-37171261111LOB 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 and faintly in shoots. {ECO:0000269|PubMed:12068116}.
Functional Description ? help Back to Top
Source Description
UniProtTranscriptional activator (PubMed:19717544, PubMed:22974309). Involved in lateral root formation. Regulated by the transcriptional activators ARF7 and ARF19 (PubMed:17259263). Functions in the initiation and emergence of lateral roots, in conjunction with LBD18, downstream of ARF7 and ARF19 (PubMed:19717544, PubMed:23749813). Acts downstream of the auxin influx carriers AUX1 and LAX1 in the regulation of lateral root initiation and development (PubMed:26059335). {ECO:0000269|PubMed:17259263, ECO:0000269|PubMed:19717544, ECO:0000269|PubMed:22974309, ECO:0000269|PubMed:23749813, ECO:0000269|PubMed:26059335}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00309DAPTransfer from AT2G42430Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapPavir.1NG554700.1.p
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By auxin. {ECO:0000269|PubMed:15659631, ECO:0000269|PubMed:17259263, ECO:0000269|PubMed:23749813}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC2432271e-175AC243227.1 Panicum virgatum clone PV_ABa011-D05, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_002454795.11e-111LOB domain-containing protein 16 isoform X2
SwissprotQ9SLB71e-58LBD16_ARATH; LOB domain-containing protein 16
TrEMBLA0A3L6RUC41e-117A0A3L6RUC4_PANMI; Uncharacterized protein
STRINGPavir.Aa00097.1.p1e-152(Panicum virgatum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP105993443
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G58190.11e-38lateral organ boundaries-domain 29
Publications ? help Back to Top
  1. Bargmann BO,Birnbaum KD,Brenner ED
    An undergraduate study of two transcription factors that promote lateral root formation.
    Biochem Mol Biol Educ, 2014 May-Jun. 42(3): p. 237-45
    [PMID:24615800]
  2. Cabrera J,Fenoll C,Escobar C
    Genes co-regulated with LBD16 in nematode feeding sites inferred from in silico analysis show similarities to regulatory circuits mediated by the auxin/cytokinin balance in Arabidopsis.
    Plant Signal Behav, 2015. 10(3): p. e990825
    [PMID:25664644]
  3. 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]
  4. Olmo R, et al.
    Molecular Transducers from Roots Are Triggered in Arabidopsis Leaves by Root-Knot Nematodes for Successful Feeding Site Formation: A Conserved Post-Embryogenic De novo Organogenesis Program?
    Front Plant Sci, 2017. 8: p. 875
    [PMID:28603536]
  5. Lee K,Seo PJ
    High-temperature promotion of callus formation requires the BIN2-ARF-LBD axis in Arabidopsis.
    Planta, 2017. 246(4): p. 797-802
    [PMID:28766014]
  6. Jeon E, et al.
    LBD14/ASL17 Positively Regulates Lateral Root Formation and is Involved in ABA Response for Root Architecture in Arabidopsis.
    Plant Cell Physiol., 2017. 58(12): p. 2190-2201
    [PMID:29040694]
  7. 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]
  8. Xu C, et al.
    Control of auxin-induced callus formation by bZIP59-LBD complex in Arabidopsis regeneration.
    Nat Plants, 2018. 4(2): p. 108-115
    [PMID:29358751]
  9. Liu J, et al.
    The WOX11-LBD16 Pathway Promotes Pluripotency Acquisition in Callus Cells During De Novo Shoot Regeneration in Tissue Culture.
    Plant Cell Physiol., 2018. 59(4): p. 734-743
    [PMID:29361138]
  10. 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]