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 Pavir.9KG589400.1.p
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Panicodae; Paniceae; Panicinae; Panicum
Family LBD
Protein Properties Length: 234aa    MW: 24648.3 Da    PI: 5.7609
Description LBD family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.9KG589400.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1DUF260127.84.9e-4071071100
               DUF260   1 aCaaCkvlrrkCakdCvlapyfpaeq.pkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvilklqqqleq 89 
                          +C aCk+lrrkC+++Cv+apyf++eq +++fa++hk+FGasnv+kll++lp  +r++a+ ++ yeA+ar+rdP+yG+v++i++lqqq+++
  Pavir.9KG589400.1.p   7 PCGACKFLRRKCVRGCVFAPYFCHEQgAAHFAAIHKVFGASNVSKLLAHLPLADRPEAAVTISYEAQARLRDPIYGCVAHIFALQQQVMT 96 
                          7*************************89************************************************************** PP

               DUF260  90 lkaelallkee 100
                          l+a+la+lk++
  Pavir.9KG589400.1.p  97 LQAQLASLKAQ 107
                          ******99987 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5089122.5746108IPR004883Lateral organ boundaries, LOB
PfamPF031955.6E-387105IPR004883Lateral organ boundaries, LOB
Sequence ? help Back to Top
Protein Sequence    Length: 234 aa     Download sequence    Send to blast
MTGFGSPCGA CKFLRRKCVR GCVFAPYFCH EQGAAHFAAI HKVFGASNVS KLLAHLPLAD  60
RPEAAVTISY EAQARLRDPI YGCVAHIFAL QQQVMTLQAQ LASLKAQAAQ GQGVHDDAKG  120
YMGSAAEQLG YGYPWCSSNG GAGAVGAPPS AYGNGGHESL TALLGSDYMQ QSLYHAFEQD  180
GAADDDGRQE AAFEAAADSS SFGAEESGWR SSSGYQDCED LQSVAYAYLN HRS*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5ly0_A7e-3531017104LOB family transfactor Ramosa2.1
5ly0_B7e-3531017104LOB family transfactor Ramosa2.1
Search in ModeBase
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in unelongating basal internodes, at the base of shoot in parenchyma cells adjacent to the peripheral vascular cylinder of the stem, and root pericycle cells (PubMed:15829602). Expressed in lateral and adventitious root primordia, tiller primordia, vascular tissues, scutellum, and young pedicels (PubMed:15960615). {ECO:0000269|PubMed:15829602, ECO:0000269|PubMed:15960615}.
Functional Description ? help Back to Top
Source Description
UniProtActs as positive regulator of adventitious (crown) root formation by promoting its initiation (PubMed:15829602, PubMed:15960615). Acts as positive regulator of lateral root formation. Regulated by the auxin response factor and transcriptional activator ARF23/ARF1 (PubMed:15829602). Involved in auxin-mediated cell dedifferentiation, and may promote the initial cell division in the pericycle cells adjacent to the peripheral vascular cylinder at the base of the stem (PubMed:15960615). May act upstream of the gene regulatory network controlling adventitious root (crown) development (PubMed:21806801). {ECO:0000269|PubMed:15829602, ECO:0000269|PubMed:15960615, ECO:0000269|PubMed:21806801}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapPavir.9KG589400.1.p
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Induced by auxin (PubMed:15829602, PubMed:15960615). Induced by ethylene (PubMed:15960615). {ECO:0000269|PubMed:15829602, ECO:0000269|PubMed:15960615}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankEF0517320.0EF051732.1 Zea mays rootless concerning crown and seminal lateral roots (rtcs) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_025797613.11e-148LOB domain-containing protein CRL1-like
SwissprotQ5UG131e-111LBD_ORYSJ; LOB domain-containing protein CRL1
TrEMBLA0A2S3IU951e-147A0A2S3IU95_9POAL; Uncharacterized protein
TrEMBLA0A2T7CHM31e-147A0A2T7CHM3_9POAL; Uncharacterized protein
STRINGPavir.Ib00283.1.p1e-169(Panicum virgatum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP25013893
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G42440.11e-56LBD family protein
Publications ? help Back to Top
  1. Coudert Y,PĂ©rin C,Courtois B,Khong NG,Gantet P
    Genetic control of root development in rice, the model cereal.
    Trends Plant Sci., 2010. 15(4): p. 219-26
    [PMID:20153971]
  2. Kitomi Y, et al.
    The auxin responsive AP2/ERF transcription factor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type-A response regulator of cytokinin signaling.
    Plant J., 2011. 67(3): p. 472-84
    [PMID:21481033]
  3. Coudert Y, et al.
    Transcript profiling of crown rootless1 mutant stem base reveals new elements associated with crown root development in rice.
    BMC Genomics, 2011. 12: p. 387
    [PMID:21806801]