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 Itr_sc000088.1_g00016.1
Organism
Ipomoea trifida
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Convolvulaceae; Ipomoeeae; Ipomoea
Family LBD
Protein Properties Length: 236aa    MW: 26031.9 Da    PI: 6.6337
Description LBD family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Itr_sc000088.1_g00016.1genomeKazusaView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1DUF260122.91.7e-3891091100
                   DUF260   1 aCaaCkvlrrkCakdCvlapyfpaeq.pkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvilklqq 85 
                              +C aCk+lrrkC+k+Cv+apyf++eq +++fa++hk+FGasn +kll++lp  +r +a+ ++ yeA+ar++dP+yG+v++i++lqq
  Itr_sc000088.1_g00016.1   9 PCGACKFLRRKCVKGCVFAPYFCHEQgASHFAAIHKVFGASNASKLLSHLPVGDRAEAAITISYEAQARLQDPIYGCVSHIFALQQ 94 
                              7*************************89********************************************************** PP

                   DUF260  86 qleqlkaelallkee 100
                              q+ +l+a+la+lke+
  Itr_sc000088.1_g00016.1  95 QVINLRAQLASLKEQ 109
                              **********99987 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5089121.7998110IPR004883Lateral organ boundaries, LOB
PfamPF031951.7E-369107IPR004883Lateral 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: 236 aa     Download sequence    Send to blast
MSGSTSGSPC GACKFLRRKC VKGCVFAPYF CHEQGASHFA AIHKVFGASN ASKLLSHLPV  60
GDRAEAAITI SYEAQARLQD PIYGCVSHIF ALQQQVINLR AQLASLKEQA AQTFCNSSAN  120
PNHDRSWGRQ ACYSQENVQG WFGSGTLESV PQFPSNNVGE MGFYSNGNLN HHHLNPICNQ  180
TSILPEENMS YATSFEEGSS SMDSLDIQTD NKPWPPAYHD DRDDLQSVAF RYLQHH
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5ly0_A2e-3361038104LOB family transfactor Ramosa2.1
5ly0_B2e-3361038104LOB family transfactor Ramosa2.1
Search in ModeBase
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}.
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}.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_019165055.11e-150PREDICTED: LOB domain-containing protein 29-like
SwissprotQ5UG133e-65LBD_ORYSJ; LOB domain-containing protein CRL1
TrEMBLA0A438F0I77e-93A0A438F0I7_VITVI; LOB domain-containing protein 29
TrEMBLA5AIW97e-93A5AIW9_VITVI; Uncharacterized protein
STRINGVIT_07s0005g03020.t014e-93(Vitis vinifera)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA84462230
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G58190.13e-68lateral organ boundaries-domain 29
Publications ? help Back to Top
  1. Coudert Y,Périn 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]