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 Dca8999.1
Organism
Dianthus caryophyllus
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; Caryophyllales; Caryophyllaceae; Caryophylleae; Dianthus
Family LBD
Protein Properties Length: 232aa    MW: 24302.5 Da    PI: 7.2336
Description LBD family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Dca8999.1genomeDCAView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1DUF2601315.2e-41301301100
     DUF260   1 aCaaCkvlrrkCakdCvlapyfpaeq.pkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvilklqqqleqlkaelallke 99 
                +C aCk+lrrkC+ dC++apyf ++q + +fa+vhk+FGasnv+kll+++p ++r da+ +++yeA+ar+rdPvyG+v++i++lqqq+ +l+ael++l++
  Dca8999.1  30 PCGACKFLRRKCVMDCIFAPYFDSDQgSGHFAAVHKVFGASNVSKLLQHMPVHKRLDAVVTICYEAQARLRDPVYGCVAHIFALQQQVVNLQAELSYLQA 129
                7***********************99889*******************************************************************9998 PP

     DUF260 100 e 100
                +
  Dca8999.1 130 H 130
                6 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5089123.12129131IPR004883Lateral organ boundaries, LOB
PfamPF031958.5E-4030128IPR004883Lateral 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: 232 aa     Download sequence    Send to blast
MSCANPSSSG GGGGGSGGSS SGGGGGGGGP CGACKFLRRK CVMDCIFAPY FDSDQGSGHF  60
AAVHKVFGAS NVSKLLQHMP VHKRLDAVVT ICYEAQARLR DPVYGCVAHI FALQQQVVNL  120
QAELSYLQAH LSSLEVPTPP PPPPQPLMPP PALSISDLPS ASTVPATYDL SSLYDPMVQP  180
SWIMQQQQQQ QRGPMDLPQF GSMVNTGPTH GSTSSGDFQA LARELLHKHG SS
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5ly0_A6e-37261317111LOB family transfactor Ramosa2.1
5ly0_B6e-37261317111LOB 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_010692269.11e-102PREDICTED: LOB domain-containing protein 18
SwissprotO221312e-71LBD18_ARATH; LOB domain-containing protein 18
TrEMBLA0A0K9QPJ98e-99A0A0K9QPJ9_SPIOL; Uncharacterized protein
STRINGXP_010692269.11e-101(Beta vulgaris)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G00220.14e-72LBD family protein
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]