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 Gh_D12G1019
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Malvales; Malvaceae; Malvoideae; Gossypium
Family LBD
Protein Properties Length: 229aa    MW: 24034.4 Da    PI: 7.8012
Description LBD family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Gh_D12G1019genomeNAU-NBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1DUF260131.14.5e-41291291100
       DUF260   1 aCaaCkvlrrkCakdCvlapyfpaeq.pkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvilklqqqleqlkaelall 97 
                  +C aCk+lrrkC+++C++apyf +eq +++fa+vhk+FGasnv+kll ++p ++r da+ +++yeA+ar+rdPvyG+v++i++lqqq+ +l+ael++l
  Gh_D12G1019  29 PCGACKFLRRKCVPGCIFAPYFDSEQgAAHFAAVHKVFGASNVSKLLLHVPVHKRLDAVVTICYEAQARLRDPVYGCVAHIFALQQQVVNLQAELSYL 126
                  7***********************9989********************************************************************99 PP

       DUF260  98 kee 100
                  +++
  Gh_D12G1019 127 QAH 129
                  986 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5089123.04628130IPR004883Lateral organ boundaries, LOB
PfamPF031953.8E-4029127IPR004883Lateral organ boundaries, LOB
Sequence ? help Back to Top
Protein Sequence    Length: 229 aa     Download sequence    Send to blast
MSANTCSSGG AAGSSTGGAV GGGGGGGGPC GACKFLRRKC VPGCIFAPYF DSEQGAAHFA  60
AVHKVFGASN VSKLLLHVPV HKRLDAVVTI CYEAQARLRD PVYGCVAHIF ALQQQVVNLQ  120
AELSYLQAHL ATLELPSPPL PSPPPPPPQQ TLMEPPPLSI SDLPPATYDL STLFDPMVQP  180
SWAMQQRQIN QFDSSSLGSG DLQALARELL HRQGSPPRLP ASPSPSFSK
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5ly0_A2e-38251307111LOB family transfactor Ramosa2.1
5ly0_B2e-38251307111LOB family transfactor Ramosa2.1
Search in ModeBase
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}.
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By auxin. {ECO:0000269|PubMed:15659631, ECO:0000269|PubMed:19717544, ECO:0000269|PubMed:23749813}.
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankJX6157514e-63JX615751.1 Gossypium hirsutum clone NBRI_GE59919 microsatellite sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_016735183.11e-166PREDICTED: LOB domain-containing protein 18-like
SwissprotO221312e-80LBD18_ARATH; LOB domain-containing protein 18
TrEMBLA0A1U8NB541e-164A0A1U8NB54_GOSHI; LOB domain-containing protein 18-like
STRINGGorai.008G114400.11e-123(Gossypium raimondii)
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
AT2G45420.19e-76LOB 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]