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 ONIVA02G40360.1
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza
Family LBD
Protein Properties Length: 216aa    MW: 22457.6 Da    PI: 7.9346
Description LBD family protein
Gene Model
Gene Model ID Type Source Coding Sequence
ONIVA02G40360.1genomeOGEView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1DUF260121.93.5e-38211211100
           DUF260   1 aCaaCkvlrrkCakdCvlapyfpaeq.pkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvilklqqqleqlkae 93 
                      +C aCk+lrr+C+++Cv+apyf +eq +++fa++hk+FGasn +kll++lp  +r +a+ +++yeA+ar+rdPvyG+v+ i++lqqq++ l+a+
  ONIVA02G40360.1  21 PCGACKFLRRRCVPECVFAPYFSSEQgAARFAAIHKVFGASNASKLLSHLPVADRCEAVVTITYEAQARLRDPVYGCVAQIFALQQQVAILQAQ 114
                      7***********************9989****************************************************************** PP

           DUF260  94 lallkee 100
                      l +++++
  ONIVA02G40360.1 115 LMQARAQ 121
                      *999987 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5089122.95120122IPR004883Lateral organ boundaries, LOB
PfamPF031952.2E-3721119IPR004883Lateral 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: 216 aa     Download sequence    Send to blast
MAGATAAGAA AAAAGTGAGS PCGACKFLRR RCVPECVFAP YFSSEQGAAR FAAIHKVFGA  60
SNASKLLSHL PVADRCEAVV TITYEAQARL RDPVYGCVAQ IFALQQQVAI LQAQLMQARA  120
QLACGIQSSS HSPVSWPDSG SISALLRQDM ARRPPGGALD DCFGGGGALL PELMAAGFKD  180
DVAAVQMQQH CSKAVDAGEL QYLAQAMMRS TSNYSQ
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5ly0_A7e-39111251117LOB family transfactor Ramosa2.1
5ly0_B7e-39111251117LOB family transfactor Ramosa2.1
Search in ModeBase
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
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
GenBankAK0641870.0AK064187.1 Oryza sativa Japonica Group cDNA clone:002-104-C02, full insert sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015626197.11e-155LOB domain-containing protein 16
SwissprotQ9SLB72e-59LBD16_ARATH; LOB domain-containing protein 16
TrEMBLA0A0D9Z0981e-154A0A0D9Z098_9ORYZ; Uncharacterized protein
TrEMBLA0A0E0GEZ61e-154A0A0E0GEZ6_ORYNI; Uncharacterized protein
TrEMBLA0A0E0NMY51e-154A0A0E0NMY5_ORYRU; Uncharacterized protein
TrEMBLA2XB421e-154A2XB42_ORYSI; Uncharacterized protein
TrEMBLI1P5M21e-154I1P5M2_ORYGL; Uncharacterized protein
TrEMBLQ6K7131e-154Q6K713_ORYSJ; LOB domain protein-like
STRINGOGLUM02G38740.11e-155(Oryza glumipatula)
STRINGORUFI02G39110.11e-155(Oryza rufipogon)
STRINGOS02T0820500-011e-155(Oryza sativa)
STRINGONIVA02G40360.11e-155(Oryza nivara)
STRINGORGLA02G0327800.11e-155(Oryza glaberrima)
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
AT2G42430.16e-45lateral organ boundaries-domain 16
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]