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 Ciclev10021992m
Common NameCICLE_v10021992mg
Organism
Citrus clementina
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Sapindales; Rutaceae; Aurantioideae; Citrus
Family LBD
Protein Properties Length: 238aa    MW: 24526.9 Da    PI: 8.0101
Description LBD family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Ciclev10021992mgenomeICGCView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1DUF260130.76.2e-41341341100
           DUF260   1 aCaaCkvlrrkCakdCvlapyfpaeq.pkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvilklqqqleqlkae 93 
                      +C aCk+lrrkC+++C++apyf +eq +++fa+vhk+FGasnv+kll ++p ++r da+ +++yeA+ar+rdPvyG+v++i++lqqq+ +l+ae
  Ciclev10021992m  34 PCGACKFLRRKCVPGCIFAPYFDSEQgAAHFAAVHKVFGASNVSKLLLHIPVHKRLDAVVTICYEAQARLRDPVYGCVAHIFALQQQVVNLQAE 127
                      7***********************9989****************************************************************** PP

           DUF260  94 lallkee 100
                      l++l+++
  Ciclev10021992m 128 LSYLQAH 134
                      **99986 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5089123.04633135IPR004883Lateral organ boundaries, LOB
PfamPF031955.9E-4034132IPR004883Lateral 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: 238 aa     Download sequence    Send to blast
MSANPSISGS VGGGGGGGGS SSGCGGGSGG SSGPCGACKF LRRKCVPGCI FAPYFDSEQG  60
AAHFAAVHKV FGASNVSKLL LHIPVHKRLD AVVTICYEAQ ARLRDPVYGC VAHIFALQQQ  120
VVNLQAELSY LQAHLATLEL PSPPPPPPSQ NQMTAPPLSI SGLPSASSMP ATYDLSTLFD  180
PMVQPAPWAM QQRQMDPRQF GGGDLQAMAR ELLHRQGSPP PGSMPCTDAS SSPSLSK*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5ly0_A6e-38301357111LOB family transfactor Ramosa2.1
5ly0_B6e-38301357111LOB family transfactor Ramosa2.1
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1719SGSVGGGGGGGGS
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Ccl.200230.0fruit
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: During lateral root formation, expressed in the lateral root primordia, and the developing, emerged, and mature lateral roots. {ECO:0000269|PubMed:19717544}.
UniprotTISSUE SPECIFICITY: Expressed in roots, stems, leaves and flowers (PubMed:12068116, PubMed:24484953). Expressed in vascular tissues of hypocotyls, leaves, roots, developing floral organs and siliques (PubMed:19088331). {ECO:0000269|PubMed:12068116, ECO:0000269|PubMed:19088331, ECO:0000269|PubMed:24484953}.
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_006445237.11e-171LOB domain-containing protein 18
RefseqXP_006491458.11e-171LOB domain-containing protein 18
SwissprotO221315e-87LBD18_ARATH; LOB domain-containing protein 18
TrEMBLA0A067HD701e-170A0A067HD70_CITSI; Uncharacterized protein
TrEMBLV4TY071e-170V4TY07_9ROSI; Uncharacterized protein
STRINGXP_006491458.11e-171(Citrus sinensis)
STRINGXP_006445237.11e-171(Citrus clementina)
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
AT2G45420.15e-89LOB 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]