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 AC149818.2_FGP009
Common Namertcl1, ZEAMMB73_806980
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; 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
1DUF260121.25.8e-387104197
             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+
  AC149818.2_FGP009   7 PCGACKFLRRRCARGCVFAPYFCDEQgAAHFAAIHKVFGASNASKLLAHLPLADRPEAAATISYEAQARLRDPTYGCVAHIFALQQQVMALQ 98 
                        7*************************89**************************************************************** PP

             DUF260  92 aelall 97 
                        ++la+l
  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:0009001anatomyfruit
PO:0009009anatomyplant embryo
PO:0009025anatomyvascular leaf
PO:0009054anatomyinflorescence bract
PO:0009066anatomyanther
PO:0009074anatomystyle
PO:0009084anatomypericarp
PO:0009089anatomyendosperm
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
MTGFGSPCGA CKFLRRRCAR GCVFAPYFCD EQGAAHFAAI HKVFGASNAS KLLAHLPLAD  60
RPEAAATISY EAQARLRDPT YGCVAHIFAL QQQVMALQTQ LASLTVTAQG QQRVHDVDDA  120
KGYVGTAAAG QLGCSSNGSV APATYGNVGH ESLTALLRSE SDYLQQSPCH AFEHAGADDK  180
DDDGRQGNTF DFEAAADSSS FGAEESGWRS LSGYRDCEDL QSVAYAYLNH LS
3D Structure ? help Back to Top
Structure
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
SourceLink
PlantRegMapAC149818.2_FGP009
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
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
TrEMBLA0A1D6PJV61e-170A0A1D6PJV6_MAIZE; RTCS-like1
STRINGAC149818.2_FGP0091e-170(Zea mays)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP25013893
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
    [PMID:17425722]
  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
    [PMID:20153971]
  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
    [PMID:21481033]
  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
    [PMID:21806801]
  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
    [PMID:25902765]