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 GSVIVT01027621001
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; rosids incertae sedis; Vitales; Vitaceae; Vitis
Family LBD
Protein Properties Length: 265aa    MW: 28194.3 Da    PI: 8.0307
Description LBD family protein
Gene Model
Gene Model ID Type Source Coding Sequence
GSVIVT01027621001genomeGenoscopeView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1DUF260127.65.8e-40421421100
             DUF260   1 aCaaCkvlrrkCakdCvlapyfpaeq.pkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvilklqqqleqlk 91 
                        +C aCk+lrrkC+ +C++apyf  eq +++fa+vhk+FGasnv+kll ++p ++r da+ +++yeA+ar+rdPvyG+v++i++lqqq+ +l+
  GSVIVT01027621001  42 PCGACKFLRRKCVVGCIFAPYFDPEQgAAHFAAVHKVFGASNVSKLLGHIPVHKRLDAVVTICYEAQARLRDPVYGCVAHIFALQQQVVNLQ 133
                        7*********************666659**************************************************************** PP

             DUF260  92 aelallkee 100
                        ael++l+++
  GSVIVT01027621001 134 AELSYLQAH 142
                        ****99986 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5089122.73441143IPR004883Lateral organ boundaries, LOB
PfamPF031952.0E-3942140IPR004883Lateral 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: 265 aa     Download sequence    Send to blast
MDFATFVINY IKDKCDFSYL FTKRDATPHS KLTSGGGGGG GPCGACKFLR RKCVVGCIFA  60
PYFDPEQGAA HFAAVHKVFG ASNVSKLLGH IPVHKRLDAV VTICYEAQAR LRDPVYGCVA  120
HIFALQQQVV NLQAELSYLQ AHLATLELPS PPPPPPPPPP VMVTPPSLSI SDLPSASSMP  180
PTYDLSSLFD PMVQPSSWPM QQHRQIDPRQ FGGSRGPTDL PSTAGGSGGG DLQALARELL  240
HRHSSALGGH VPCTESSMPP SISK*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5ly0_A2e-38381437111LOB family transfactor Ramosa2.1
5ly0_B2e-38381437111LOB family transfactor Ramosa2.1
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Vvi.119290.0fruit
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 -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAM4632580.0AM463258.1 Vitis vinifera, whole genome shotgun sequence, contig VV78X156046.15, clone ENTAV 115.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_002279521.11e-168PREDICTED: LOB domain-containing protein 18
SwissprotO221313e-82LBD18_ARATH; LOB domain-containing protein 18
TrEMBLA0A438IWZ61e-166A0A438IWZ6_VITVI; LOB domain-containing protein 18
TrEMBLF6I3731e-166F6I373_VITVI; Uncharacterized protein
STRINGVIT_15s0048g00830.t011e-167(Vitis vinifera)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
Representative plantOGRP40515100
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G45420.15e-78LOB 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]