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 RrC19905_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: 253aa    MW: 26524.8 Da    PI: 8.0852
Description LBD family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC19905_p1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1DUF260128.62.8e-40251251100
       DUF260   1 aCaaCkvlrrkCakdCvlapyfpaeq.pkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvilklqqqleqlkaelall 97 
                  +C aCk+lrrkC+++C++apyf +eq ++ fa+vhk+FGasnv+kll ++p ++r+da+ +++yeA+ar+rdP+yG+v++i++lqqq+ +l+ae+++l
  RrC19905_p1  25 PCGACKFLRRKCVPGCIFAPYFDSEQgSAYFAAVHKVFGASNVSKLLLHIPVHRRSDAVVTICYEAQARIRDPIYGCVAHIFALQQQVVNLQAEVSYL 122
                  7***********************998899******************************************************************99 PP

       DUF260  98 kee 100
                  +++
  RrC19905_p1 123 QAH 125
                  986 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5089122.86624126IPR004883Lateral organ boundaries, LOB
PfamPF031952.7E-3925123IPR004883Lateral organ boundaries, LOB
Sequence ? help Back to Top
Protein Sequence    Length: 253 aa     Download sequence    Send to blast
MSGGGNTVTA MGGGGCGGGS GGGGPCGACK FLRRKCVPGC IFAPYFDSEQ GSAYFAAVHK  60
VFGASNVSKL LLHIPVHRRS DAVVTICYEA QARIRDPIYG CVAHIFALQQ QVVNLQAEVS  120
YLQAHLASLE LPQPQTRPPP PPPQHHQSQP LFFSTPPPLS ITDLPASVSP LPSTYDLASA  180
FNQAASPSSW ATQQRRFGDP RHQYGGSLST SSATVGLGGG NSDLEALAHE LLHRQGSPPP  240
AATDDSPPRS MSR
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5ly0_A2e-38211267111LOB family transfactor Ramosa2.1
5ly0_B2e-38211267111LOB family transfactor Ramosa2.1
Search in ModeBase
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}.
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 -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018481520.10.0PREDICTED: LOB domain-containing protein 18-like
SwissprotO221311e-120LBD18_ARATH; LOB domain-containing protein 18
TrEMBLV4N2111e-137V4N211_EUTSA; Uncharacterized protein
STRINGXP_006397723.11e-138(Eutrema salsugineum)
STRINGXP_010508173.11e-138(Camelina sativa)
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
AT2G45420.11e-111LOB 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]