PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID RrC7482_p1
Organism
Raphanus raphanistrum
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: 257aa    MW: 26561.8 Da    PI: 8.2887
Description LBD family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC7482_p1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1DUF260128.62.9e-40351351100
      DUF260   1 aCaaCkvlrrkCakdCvlapyfpaeq.pkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvilklqqqleqlkaelallk 98 
                 +C aCk+lrrkC+++C++apyf +eq ++ fa+vhk+FGasnv+kll ++p ++r+da+ +++yeA+ar+rdP+yG+v++i++lqqq+ +l+ae+++l+
  RrC7482_p1  35 PCGACKFLRRKCVPGCIFAPYFDSEQgSAYFAAVHKVFGASNVSKLLLHIPVHRRSDAVVTICYEAQARIRDPIYGCVAHIFALQQQVVNLQAEVSYLQ 133
                 7***********************998899******************************************************************999 PP

      DUF260  99 ee 100
                 ++
  RrC7482_p1 134 AH 135
                 86 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5089122.86634136IPR004883Lateral organ boundaries, LOB
PfamPF031952.8E-3935133IPR004883Lateral organ boundaries, LOB
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0010089Biological Processxylem development
GO:0010311Biological Processlateral root formation
GO:0005634Cellular Componentnucleus
Sequence ? help Back to Top
Protein Sequence    Length: 257 aa     Download sequence    Send to blast
MSGCGNTITA VGGGGSGGGS GGGGGGSISG GGGGPCGACK FLRRKCVPGC IFAPYFDSEQ  60
GSAYFAAVHK VFGASNVSKL LLHIPVHRRS DAVVTICYEA QARIRDPIYG CVAHIFALQQ  120
QVVNLQAEVS YLQAHLASLE LPQPQTRPPP LTQPQPLFFT QPPPLSLTDL PASASPLPST  180
YDLASIFDQS TPSWATQQRR FVDSRNQYGG SSSTSSPAVG LGGGNSDLQA LAHELLHRQG  240
SPPPAAADGS PSRSMSR
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5ly0_A6e-39311367111LOB family transfactor Ramosa2.1
5ly0_B6e-39311367111LOB 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}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00314DAPTransfer from AT2G45420Download
Motif logo
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
PlantRegMapRetrieveRetrieve
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018440274.10.0PREDICTED: LOB domain-containing protein 18
SwissprotO221311e-121LBD18_ARATH; LOB domain-containing protein 18
TrEMBLV4N2111e-136V4N211_EUTSA; Uncharacterized protein
STRINGXP_010508173.11e-141(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-110LOB 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]