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 RrC14353_p1
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus
Family LBD
Protein Properties Length: 238aa    MW: 25820.7 Da    PI: 7.6251
Description LBD family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC14353_p1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1DUF260118.63.5e-37151151100
       DUF260   1 aCaaCkvlrrkCakdCvlapyfpaeq.pkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvilklqqqleqlkaelall 97 
                  +C aCk+lrrkC +dC++a yf +eq +++fa++hk+FGasnv+kll ++p ++r +a+ +++yeA+ar++dPvyG+v++i++lqqq++ l+a++ ++
  RrC14353_p1  15 PCGACKFLRRKCLSDCIFATYFSSEQgAARFAAIHKVFGASNVSKLLLNVPIHDRFEAVVTIAYEAQARLHDPVYGCVSHIFSLQQQVAYLQAQVMQM 112
                  7***********************9989******************************************************************9988 PP

       DUF260  98 kee 100
                  k++
  RrC14353_p1 113 KAH 115
                  876 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5089121.99814116IPR004883Lateral organ boundaries, LOB
PfamPF031952.0E-3615113IPR004883Lateral organ boundaries, LOB
Sequence ? help Back to Top
Protein Sequence    Length: 238 aa     Download sequence    Send to blast
MATSGNSTTA GTGSPCGACK FLRRKCLSDC IFATYFSSEQ GAARFAAIHK VFGASNVSKL  60
LLNVPIHDRF EAVVTIAYEA QARLHDPVYG CVSHIFSLQQ QVAYLQAQVM QMKAHIAGHQ  120
TSAAEGTHQF ETWQQTSGSL IDGAYSIPYN HHNHTYYGHI SPNNPVSSQS SLEESFSNTS  180
SDVTTTANTR ETHQTGGGVY GKGDLGFQEG FPNKKRSVSY CNSDLGELQA LALRIMKN
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5ly0_A9e-3871093104LOB family transfactor Ramosa2.1
5ly0_B9e-3871093104LOB 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}.
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
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC2411041e-174AC241104.1 Brassica rapa subsp. pekinensis cultivar Inbred line 'Chiifu' clone KBrH017L09, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009133536.11e-163PREDICTED: LOB domain-containing protein 16-like
RefseqXP_013681149.11e-163LOB domain-containing protein 16-like
RefseqXP_013724346.11e-163LOB domain-containing protein 16-like
SwissprotQ9SLB71e-147LBD16_ARATH; LOB domain-containing protein 16
TrEMBLA0A291LR071e-162A0A291LR07_BRARR; Transcription factor LBD16b
TrEMBLA0A397ZY861e-162A0A397ZY86_BRACM; Uncharacterized protein
TrEMBLM4C7S91e-162M4C7S9_BRARP; Uncharacterized protein
STRINGBra000257.1-P1e-163(Brassica rapa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM10828359
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G42430.11e-116lateral 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]