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 AC149818.2_FGP009
Common Namertcl1, ZEAMMB73_806980
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Andropogonodae; Andropogoneae; Tripsacinae; Zea
Family LBD
Protein Properties Length: 232aa    MW: 24697.2 Da    PI: 5.4883
Description LBD family protein
Gene Model
Gene Model ID Type Source Coding Sequence
AC149818.2_FGP009genomeMaizeSequenceView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
             DUF260   1 aCaaCkvlrrkCakdCvlapyfpaeq.pkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvilklqqqleqlk 91 
                        +C aCk+lrr+Ca++Cv+apyf++eq +++fa++hk+FGasn +kll++lp  +r++a++++ yeA+ar+rdP yG+v++i++lqqq++ l+
                        7*************************89**************************************************************** PP

             DUF260  92 aelall 97 
  AC149818.2_FGP009  99 TQLASL 104
                        **9876 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5089121.4316108IPR004883Lateral organ boundaries, LOB
PfamPF031953.6E-367104IPR004883Lateral organ boundaries, LOB
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000037anatomyshoot apex
PO:0004006anatomymesophyll cell
PO:0006310anatomytassel floret
PO:0006339anatomyjuvenile vascular leaf
PO:0006340anatomyadult vascular leaf
PO:0006341anatomyprimary shoot system
PO:0006354anatomyear floret
PO:0006505anatomycentral spike of ear inflorescence
PO:0008018anatomytransition vascular leaf
PO:0009009anatomyplant embryo
PO:0009025anatomyvascular leaf
PO:0009054anatomyinflorescence bract
PO:0020040anatomyleaf base
PO:0020104anatomyleaf sheath
PO:0020126anatomytassel inflorescence
PO:0020127anatomyprimary root
PO:0020136anatomyear inflorescence
PO:0020142anatomystem internode
PO:0020148anatomyshoot apical meristem
PO:0025142anatomyleaf tip
PO:0025287anatomyseedling coleoptile
PO:0025589anatomyleaf lamina tip
PO:0001007developmental stagepollen development stage
PO:0001009developmental stageD pollen mother cell meiosis stage
PO:0001052developmental stagevascular leaf expansion stage
PO:0001053developmental stagevascular leaf post-expansion stage
PO:0001094developmental stageplant embryo coleoptilar stage
PO:0001095developmental stageplant embryo true leaf formation stage
PO:0001180developmental stageplant proembryo stage
PO:0007001developmental stageearly whole plant fruit ripening stage
PO:0007003developmental stageIL.03 full inflorescence length reached stage
PO:0007006developmental stageIL.00 inflorescence just visible stage
PO:0007015developmental stageradicle emergence stage
PO:0007016developmental stagewhole plant flowering stage
PO:0007022developmental stageseed imbibition stage
PO:0007026developmental stageFL.00 first flower(s) open stage
PO:0007031developmental stagemid whole plant fruit ripening stage
PO:0007032developmental stagewhole plant fruit formation stage up to 10%
PO:0007045developmental stagecoleoptile emergence stage
PO:0007063developmental stageLP.07 seven leaves visible stage
PO:0007065developmental stageLP.05 five leaves visible stage
PO:0007072developmental stageLP.18 eighteen leaves visible stage
PO:0007094developmental stageLP.01 one leaf visible stage
PO:0007101developmental stageLP.09 nine leaves visible stage
PO:0007104developmental stageLP.15 fifteen leaves visible stage
PO:0007106developmental stageLP.03 three leaves visible stage
PO:0007112developmental stage1 main shoot growth stage
PO:0007116developmental stageLP.11 eleven leaves visible stage
PO:0007123developmental stageLP.06 six leaves visible stage
PO:0007633developmental stageendosperm development stage
PO:0021004developmental stageinflorescence initiation stage
Sequence ? help Back to Top
Protein Sequence    Length: 232 aa     Download sequence    Send to blast
3D Structure ? help Back to Top
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5ly0_A1e-3331017104LOB family transfactor Ramosa2.1
5ly0_B1e-3331017104LOB family transfactor Ramosa2.1
Search in ModeBase
Expression -- Microarray ? help Back to Top
Source ID
Expression AtlasAC149818.2_FG009
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}.
Function -- GeneRIF ? help Back to Top
  1. Cooperative action of RTCS and RTCL during shoot-borne root formation was demonstrated by rtcs-dependent repression of rtcl transcription in coleoptilar nodes.
    [PMID: 25902765]
Cis-element ? help Back to Top
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
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankEF0517330.0EF051733.1 Zea mays RTCS-like protein mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_001106034.11e-171RTCS-like 1
SwissprotQ5UG133e-93LBD_ORYSJ; LOB domain-containing protein CRL1
STRINGAC149818.2_FGP0091e-170(Zea mays)
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
AT2G42440.11e-59LBD family protein
Publications ? help Back to Top
  1. Taramino G, et al.
    The maize (Zea mays L.) RTCS gene encodes a LOB domain protein that is a key regulator of embryonic seminal and post-embryonic shoot-borne root initiation.
    Plant J., 2007. 50(4): p. 649-59
  2. 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
  3. 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
  4. 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
  5. Xu C, et al.
    Cooperative action of the paralogous maize lateral organ boundaries (LOB) domain proteins RTCS and RTCL in shoot-borne root formation.
    New Phytol., 2015. 207(4): p. 1123-33