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 GRMZM2G092542_P01
Common Namertcs, rtcs1, Zm.102752
Organism
Zea mays
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: 244aa    MW: 25470.2 Da    PI: 6.0093
Description LBD family protein
Gene Model
Gene Model ID Type Source Coding Sequence
GRMZM2G092542_P01genomeMaizeSequenceView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1DUF260126.51.3e-3971071100
             DUF260   1 aCaaCkvlrrkCakdCvlapyfpaeq.pkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvilklqqqleqlk 91 
                        +C aCk+lrrkC+++Cv+apyf++eq +++fa++hk+FGasnv+kll++lp  +r +a+ ++ yeA+ar+rdP+yG+v++i++lqqq+++l+
  GRMZM2G092542_P01   7 PCGACKFLRRKCVRGCVFAPYFCHEQgAAHFAAIHKVFGASNVSKLLAHLPLADRAEAAVTISYEAQARLRDPIYGCVAHIFALQQQVMTLQ 98 
                        7*************************89**************************************************************** PP

             DUF260  92 aelallkee 100
                        a+la+lk++
  GRMZM2G092542_P01  99 AQLASLKAQ 107
                        ****99987 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5089122.3386108IPR004883Lateral organ boundaries, LOB
PfamPF031959.2E-387105IPR004883Lateral organ boundaries, LOB
Sequence ? help Back to Top
Protein Sequence    Length: 244 aa     Download sequence    Send to blast
MTGFGSPCGA CKFLRRKCVR GCVFAPYFCH EQGAAHFAAI HKVFGASNVS KLLAHLPLAD  60
RAEAAVTISY EAQARLRDPI YGCVAHIFAL QQQVMTLQAQ LASLKAQAAQ GQQGVHEDAK  120
GYVGSAAAEQ LGYGYPWCSG NGGAAAAAAG AVGAPAAQPG AYGNGAHESL TALLGSSDYM  180
QQSLYHAFEQ AGADDDDGRQ GYAFEAAAES SSLGAEESGW RSSSGYQDCE DLQSVAYAYL  240
NHRS
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5ly0_A3e-3531017104LOB family transfactor Ramosa2.1
5ly0_B3e-3531017104LOB family transfactor Ramosa2.1
Search in ModeBase
Expression -- Microarray ? help Back to Top
Source ID
Expression AtlasGRMZM2G092542
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. Arf34 (auxin response factor 34) expression is RTCS-dependent.
    [PMID: 22527397]
  2. 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]
  3. This study provides first insights into the molecular framework underlying seminal root initiation in maize and provides a starting point for further investigations of the molecular networks underlying RTCS-dependent seminal root initiation.
    [PMID: 28204533]
Cis-element ? help Back to Top
SourceLink
PlantRegMapGRMZM2G092542_P01
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
RefseqNP_001106033.11e-177rootless concerning crown and seminal roots 1
SwissprotQ5UG131e-108LBD_ORYSJ; LOB domain-containing protein CRL1
TrEMBLA5H4481e-175A5H448_MAIZE; Rootless concerning crown and seminal lateral roots
STRINGGRMZM2G092542_P011e-176(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
AT2G42440.18e-57LBD 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,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]
  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. Majer C,Xu C,Berendzen KW,Hochholdinger F
    Molecular interactions of ROOTLESS CONCERNING CROWN AND SEMINAL ROOTS, a LOB domain protein regulating shoot-borne root initiation in maize (Zea mays L.).
    Philos. Trans. R. Soc. Lond., B, Biol. Sci., 2012. 367(1595): p. 1542-51
    [PMID:22527397]
  6. 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]
  7. Tai H, et al.
    Non-syntenic genes drive RTCS-dependent regulation of the embryo transcriptome during formation of seminal root primordia in maize (Zea mays L.).
    J. Exp. Bot., 2017. 68(3): p. 403-414
    [PMID:28204533]