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 LOC_Os03g05510.1
Common NameARL1, CRL1, LOC9271993, Os03g0149100, OSNPB_030149100
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; BOP clade; Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa
Family LBD
Protein Properties Length: 260aa    MW: 26736.6 Da    PI: 6.432
Description LBD family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os03g05510.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1DUF260126.71.1e-397106199
            DUF260   1 aCaaCkvlrrkCakdCvlapyfpaeq.pkkfanvhklFGasnvlkllkalpeeeredamsslvyeAearardPvyGavgvilklqqqleqlka 92 
                       +C aCk+lrrkC+++Cv+apyf++eq +++fa++hk+FGasnv+kll++lp  +r++a+ ++ yeA+ar+rdP+yG+v++i++lqqq+++l+a
  LOC_Os03g05510.1   7 PCGACKFLRRKCVRGCVFAPYFCHEQgAAHFAAIHKVFGASNVSKLLAHLPLADRPEAAVTISYEAQARLRDPIYGCVAHIFALQQQVMTLQA 99 
                       7*************************89***************************************************************** PP

            DUF260  93 elallke 99 
                       +la+lk+
  LOC_Os03g05510.1 100 QLASLKA 106
                       **99886 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5089122.3856108IPR004883Lateral organ boundaries, LOB
PfamPF031957.2E-387105IPR004883Lateral organ boundaries, LOB
Sequence ? help Back to Top
Protein Sequence    Length: 260 aa     Download sequence    Send to blast
MTGFGSPCGA CKFLRRKCVR GCVFAPYFCH EQGAAHFAAI HKVFGASNVS KLLAHLPLAD  60
RPEAAVTISY EAQARLRDPI YGCVAHIFAL QQQVMTLQAQ LASLKAAAAQ GIHHQDVGAT  120
TKGGYMSAAA TAADDQLGYG GYNQWCGSNG GGAPAASQPG AYSSNGGAGH GHDSITALLA  180
AGSDYMQHSL YHAFEHSEGA GAVDDGHAAA AAFEAAAESS SCGMAASFAA DESVWRSSSS  240
GYQDCEDLQS VAYAYLNRS*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5ly0_A4e-3531017104LOB family transfactor Ramosa2.1
5ly0_B4e-3531017104LOB family transfactor Ramosa2.1
Search in ModeBase
Expression -- Microarray ? help Back to Top
Source ID
Expression AtlasQ5UG13
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. ARL1 is an auxin-responsive factor involved in auxin-mediated cell dedifferentiation, and promotes the initial cell division in the pericycle cells adjacent to the peripheral vascular cylinder in the stem.
    [PMID: 15960615]
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os03g05510.1
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-
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs03g05510
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAB2002340.0AB200234.1 Oryza sativa Japonica Group CRL1 mRNA for LOB domain protein, complete cds.
GenBankAY7363750.0AY736375.1 Oryza sativa (japonica cultivar-group) adventitious rootless1 (ARL1) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015632119.10.0LOB domain-containing protein CRL1-like
SwissprotQ5UG130.0LBD_ORYSJ; LOB domain-containing protein CRL1
TrEMBLA0A0D3FDV00.0A0A0D3FDV0_9ORYZ; Uncharacterized protein
TrEMBLA0A0E0GGU90.0A0A0E0GGU9_ORYNI; Uncharacterized protein
TrEMBLA0A0E0NPQ80.0A0A0E0NPQ8_ORYRU; Uncharacterized protein
TrEMBLB8ANC20.0B8ANC2_ORYSI; Uncharacterized protein
TrEMBLI1P7L30.0I1P7L3_ORYGL; Uncharacterized protein
STRINGOS03T0149100-000.0(Oryza sativa)
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
AT2G42440.17e-57LBD family protein
Publications ? help Back to Top
  1. Inukai Y, et al.
    Crown rootless1, which is essential for crown root formation in rice, is a target of an AUXIN RESPONSE FACTOR in auxin signaling.
    Plant Cell, 2005. 17(5): p. 1387-96
    [PMID:15829602]
  2. Liu H, et al.
    ARL1, a LOB-domain protein required for adventitious root formation in rice.
    Plant J., 2005. 43(1): p. 47-56
    [PMID:15960615]
  3. 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]
  4. 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]
  5. 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]