PlantTFDB
Plant Transcription Factor Database
v4.0
Previous version: v1.0, v2.0, v3.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT3G58190.1
Common NameASL16, F9D24.100, LBD29
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
Family LBD
Protein Properties Length: 218aa    MW: 24056.5 Da    PI: 6.4986
Description lateral organ boundaries-domain 29
Gene Model
Gene Model ID Type Source Coding Sequence
AT3G58190.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1DUF260124.26.7e-39111111100
       DUF260   1 aCaaCkvlrrkCakdCvlapyfpaeq.pkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvilklqqqleqlkaelall 97 
                  +C aCk+lrrkCak+Cv+apyf++eq +++fa++hk+FGasn +kll++lp ++r +a+ ++ yeA+ar++dP+yG+v++i++lqqq+ +l+ael+ l
  AT3G58190.1  11 PCGACKFLRRKCAKGCVFAPYFCHEQgASHFAAIHKVFGASNASKLLSHLPISDRCEAAITISYEAQARLQDPIYGCVSHIFALQQQVVNLQAELEIL 108
                  7*************************89*********************************************************************9 PP

       DUF260  98 kee 100
                  k++
  AT3G58190.1 109 KQQ 111
                  997 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5089122.26210112IPR004883Lateral organ boundaries, LOB
PfamPF031952.3E-3611109IPR004883Lateral organ boundaries, LOB
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0010311Biological Processlateral root formation
GO:0005634Cellular Componentnucleus
Sequence ? help Back to Top
Protein Sequence    Length: 218 aa     Download sequence    Send to blast
MTSSSSSSGS PCGACKFLRR KCAKGCVFAP YFCHEQGASH FAAIHKVFGA SNASKLLSHL  60
PISDRCEAAI TISYEAQARL QDPIYGCVSH IFALQQQVVN LQAELEILKQ QAAQSMIFAD  120
SPTSENPNSY YGDTTKAPYH HDHQNIYHHH DQTHLVYQTG SSGTVQHGDA TESSYHNETS  180
SGMGEFSIYS DLEQHLNTFN QDHLKELQSA NFGYISFS
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.272010.0root
Expression -- Microarray ? help Back to Top
Source ID E-value
Genevisible251565_at0.0
Expression AtlasAT3G58190-
AtGenExpressAT3G58190-
ATTED-IIAT3G58190-
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in roots. {ECO:0000269|PubMed:12068116}.
Functional Description ? help Back to Top
Source Description
TAIRThis gene contains two auxin-responsive element (AuxRE).
UniProtInvolved in lateral root formation. Regulated by the transcriptional activators ARF7 and ARF19. {ECO:0000269|PubMed:17259263}.
Function -- GeneRIF ? help Back to Top
  1. The ability of LBD29 to regulate lateral root initiation is associated with its maintenance of the cell division capacity of the pericycle in response to auxin and its involvement in the auxin signalling pathway.
    [PMID: 22334497]
  2. Data show that overexpression of each of the LBD genes promotes callus formation in the absence of exogenous phytohormones, while suppression of LBD function inhibits the callus induction process.
    [PMID: 22508267]
  3. LBD16, LBD29, and LBD18 are involved in cell cycle progression of the pericycle in response to auxin.
    [PMID: 22699776]
Cis-element ? help Back to Top
SourceLink
PlantRegMapAT3G58190.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By auxin. {ECO:0000269|PubMed:15659631, ECO:0000269|PubMed:17259263}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Regulation -- ATRM (Manually Curated Upstream Regulators) ? help Back to Top
Source Upstream Regulator (A: Activate/R: Repress)
ATRM AT1G19220 (A), AT5G20730 (A)
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT3G58190
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankBT0252820.0BT025282.1 Arabidopsis thaliana At3g58190 mRNA, complete cds.
GenBankAB4738490.0AB473849.1 Arabidopsis thaliana ASL16 mRNA for ASYMMETRIC LEAVES2-like 16 protein, complete cds.
GenBankAF4478930.0AF447893.1 Arabidopsis thaliana LOB DOMAIN 29 (LBD29) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_191378.11e-162protein ASYMMETRIC LEAVES 2-LIKE 16
SwissprotQ9M2J71e-164LBD29_ARATH; LOB domain-containing protein 29
TrEMBLD7LW121e-147D7LW12_ARALL; Lateral organ boundaries-domain 29, lob domain-containing protein 29
STRINGAT3G58190.11e-162(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
Representative plantOGRP40515100
MalvidsOGEM10828359
Publications ? help Back to Top
  1. Iwakawa H, et al.
    The ASYMMETRIC LEAVES2 gene of Arabidopsis thaliana, required for formation of a symmetric flat leaf lamina, encodes a member of a novel family of proteins characterized by cysteine repeats and a leucine zipper.
    Plant Cell Physiol., 2002. 43(5): p. 467-78
    [PMID:12040093]
  2. Shuai B,Reynaga-Peña CG,Springer PS
    The lateral organ boundaries gene defines a novel, plant-specific gene family.
    Plant Physiol., 2002. 129(2): p. 747-61
    [PMID:12068116]
  3. Zhao Y,Dai X,Blackwell HE,Schreiber SL,Chory J
    SIR1, an upstream component in auxin signaling identified by chemical genetics.
    Science, 2003. 301(5636): p. 1107-10
    [PMID:12893885]
  4. Dal Bosco C, et al.
    Inactivation of the chloroplast ATP synthase gamma subunit results in high non-photochemical fluorescence quenching and altered nuclear gene expression in Arabidopsis thaliana.
    J. Biol. Chem., 2004. 279(2): p. 1060-9
    [PMID:14576160]
  5. Pufky J,Qiu Y,Rao MV,Hurban P,Jones AM
    The auxin-induced transcriptome for etiolated Arabidopsis seedlings using a structure/function approach.
    Funct. Integr. Genomics, 2003. 3(4): p. 135-43
    [PMID:14648238]
  6. Redman JC,Haas BJ,Tanimoto G,Town CD
    Development and evaluation of an Arabidopsis whole genome Affymetrix probe array.
    Plant J., 2004. 38(3): p. 545-61
    [PMID:15086809]
  7. Okushima Y, et al.
    Functional genomic analysis of the AUXIN RESPONSE FACTOR gene family members in Arabidopsis thaliana: unique and overlapping functions of ARF7 and ARF19.
    Plant Cell, 2005. 17(2): p. 444-63
    [PMID:15659631]
  8. Okushima Y,Fukaki H,Onoda M,Theologis A,Tasaka M
    ARF7 and ARF19 regulate lateral root formation via direct activation of LBD/ASL genes in Arabidopsis.
    Plant Cell, 2007. 19(1): p. 118-30
    [PMID:17259263]
  9. Matsumura Y,Iwakawa H,Machida Y,Machida C
    Characterization of genes in the ASYMMETRIC LEAVES2/LATERAL ORGAN BOUNDARIES (AS2/LOB) family in Arabidopsis thaliana, and functional and molecular comparisons between AS2 and other family members.
    Plant J., 2009. 58(3): p. 525-37
    [PMID:19154202]
  10. Lee DJ,Park JW,Lee HW,Kim J
    Genome-wide analysis of the auxin-responsive transcriptome downstream of iaa1 and its expression analysis reveal the diversity and complexity of auxin-regulated gene expression.
    J. Exp. Bot., 2009. 60(13): p. 3935-57
    [PMID:19654206]
  11. Ikeyama Y,Tasaka M,Fukaki H
    RLF, a cytochrome b(5)-like heme/steroid binding domain protein, controls lateral root formation independently of ARF7/19-mediated auxin signaling in Arabidopsis thaliana.
    Plant J., 2010. 62(5): p. 865-75
    [PMID:20230485]
  12. Feng Z,Sun X,Wang G,Liu H,Zhu J
    LBD29 regulates the cell cycle progression in response to auxin during lateral root formation in Arabidopsis thaliana.
    Ann. Bot., 2012. 110(1): p. 1-10
    [PMID:22334497]
  13. Fan M,Xu C,Xu K,Hu Y
    LATERAL ORGAN BOUNDARIES DOMAIN transcription factors direct callus formation in Arabidopsis regeneration.
    Cell Res., 2012. 22(7): p. 1169-80
    [PMID:22508267]
  14. Feng Z,Zhu J,Du X,Cui X
    Effects of three auxin-inducible LBD members on lateral root formation in Arabidopsis thaliana.
    Planta, 2012. 236(4): p. 1227-37
    [PMID:22699776]
  15. Osakabe Y, et al.
    Osmotic stress responses and plant growth controlled by potassium transporters in Arabidopsis.
    Plant Cell, 2013. 25(2): p. 609-24
    [PMID:23396830]
  16. Efroni I, et al.
    Regulation of leaf maturation by chromatin-mediated modulation of cytokinin responses.
    Dev. Cell, 2013. 24(4): p. 438-45
    [PMID:23449474]
  17. Jin J, et al.
    An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors.
    Mol. Biol. Evol., 2015. 32(7): p. 1767-73
    [PMID:25750178]