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 Bradi3g55680.1.p
Common NameBRADI_3g55680, LOC100823689
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Pooideae; Brachypodieae; Brachypodium
Family LBD
Protein Properties Length: 210aa    MW: 21861.9 Da    PI: 8.0256
Description LBD family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Bradi3g55680.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1DUF260115.43.6e-36161171101
            DUF260   1 aCaaCkvlrrkCakdCvlapyfpaeq.pkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvilklqqqleqlka 92 
                       +C aCk+lrr+C+++Cv+apyf +e+ +++fa++hk+FGasn  kll++lp  er +a+ ++++eA+ r+rdPvyG+v+ i++lqqq++ l+a
  Bradi3g55680.1.p  16 PCGACKFLRRRCVAECVFAPYFSSEHgASRFAAIHKVFGASNAAKLLAHLPAAERCEAVVTITFEAQSRLRDPVYGCVAQIFALQQQVAILQA 108
                       7*********************999979***************************************************************** PP

            DUF260  93 elallkeel 101
                       +l ++k++l
  Bradi3g55680.1.p 109 QLMQAKAQL 117
                       **9999875 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5089122.4615117IPR004883Lateral organ boundaries, LOB
PfamPF031952.5E-3516114IPR004883Lateral 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: 210 aa     Download sequence    Send to blast
MAAGAGGVGA AGAGSPCGAC KFLRRRCVAE CVFAPYFSSE HGASRFAAIH KVFGASNAAK  60
LLAHLPAAER CEAVVTITFE AQSRLRDPVY GCVAQIFALQ QQVAILQAQL MQAKAQLACG  120
IQSTSPAASL ISQQHHHHHQ WPDSASSISA LLRQQEGSGF GGAATLPELM GGDGVTPMSS  180
MQQHCSKVDG GELQYLAQAM MRSPNYSGF*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5ly0_A1e-35121207117LOB family transfactor Ramosa2.1
5ly0_B1e-35121207117LOB 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
Cis-element ? help Back to Top
SourceLink
PlantRegMapBradi3g55680.1.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
GenBankAK3685151e-133AK368515.1 Hordeum vulgare subsp. vulgare mRNA for predicted protein, complete cds, clone: NIASHv2075A19.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_003572959.11e-151LOB domain-containing protein 16
SwissprotQ9SLB74e-57LBD16_ARATH; LOB domain-containing protein 16
TrEMBLI1IE141e-150I1IE14_BRADI; Uncharacterized protein
STRINGBRADI3G55680.11e-150(Brachypodium distachyon)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP105993443
Representative plantOGRP40515100
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G42430.12e-41lateral 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]