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 LOC_Os01g48060.1
Common NameARF2, LOC4325895, Os01g0670800
Organism
Oryza sativa subsp. japonica
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 ARF
Protein Properties Length: 723aa    MW: 79112.9 Da    PI: 7.1733
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os01g48060.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B373.33e-23147248199
                       EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SS CS
                B3   1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgr 87 
                       f+k+lt sd++++g +++p++ ae++      +++ +  ++l+ +d++g +W++++iyr++++r++lt+GW++F + ++L +gD v+F   + 
  LOC_Os01g48060.1 147 FCKTLTASDTSTHGGFSVPRRAAEDCfppldySLQRPF-QELVAKDLHGTEWRFRHIYRGQPRRHLLTTGWSGFINKKKLVSGDAVLFL--RG 236
                       99****************************99777666.49************************************************..44 PP

                       SEE..EEEEE-S CS
                B3  88 sefelvvkvfrk 99 
                       +++el+++v+r+
  LOC_Os01g48060.1 237 EDGELRLGVRRA 248
                       9999*****996 PP
2Auxin_resp98.31.1e-32273357182
        Auxin_resp   1 aahaastksvFevvYnP....rastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsL 82 
                       +aha++ ks+F+++YnP    r s+seF+++++k+++++++++svGmRfk+++e+ed+serr +G+++g +++dp  W++SkW++L
  LOC_Os01g48060.1 273 VAHAVAVKSIFHIYYNPscthRLSQSEFIIPYWKFMRSFSQPFSVGMRFKLRYESEDASERRRTGIIIGSREADP-MWHGSKWKCL 357
                       799**************66666899**************************************************.9********9 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.102.0E-38139252IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019361.44E-42144284IPR015300DNA-binding pseudobarrel domain
CDDcd100173.95E-21145247No hitNo description
PROSITE profilePS5086312.901147249IPR003340B3 DNA binding domain
PfamPF023622.5E-21147248IPR003340B3 DNA binding domain
SMARTSM010192.5E-22147249IPR003340B3 DNA binding domain
PfamPF065072.3E-26273357IPR010525Auxin response factor
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009734Biological Processauxin-activated signaling pathway
GO:0010050Biological Processvegetative phase change
GO:0010158Biological Processabaxial cell fate specification
GO:0010582Biological Processfloral meristem determinacy
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0009009anatomyplant embryo
PO:0001081developmental stagemature plant embryo stage
PO:0007042developmental stagewhole plant fruit formation stage
Sequence ? help Back to Top
Protein Sequence    Length: 723 aa     Download sequence    Send to blast
MVGIDLNTVE EEEDEEEGGA TGTVTAPAEA RAGGAVCLEL WHACAGPVAP LPRKGSAVVY  60
LPQGHLEHLG AAPGSGPGAA VPPHVFCRVV DVSLHADAAT DEVYAQVSLV ADNEEVERRM  120
REGEDGAACD GEGEDAVKRP ARIPHMFCKT LTASDTSTHG GFSVPRRAAE DCFPPLDYSL  180
QRPFQELVAK DLHGTEWRFR HIYRGQPRRH LLTTGWSGFI NKKKLVSGDA VLFLRGEDGE  240
LRLGVRRAAQ LKNASPFPAL HNQISNTSSL SEVAHAVAVK SIFHIYYNPS CTHRLSQSEF  300
IIPYWKFMRS FSQPFSVGMR FKLRYESEDA SERRRTGIII GSREADPMWH GSKWKCLVVK  360
WDDDVECRRP NGVSPWEIEL SGSVSGSHLS TPHSKRLKSC FPQVNPDIVL PNGSVSSDFA  420
ESARFHKVLQ GQELLGLKTR DGTVNTASQA TEARNFQYTD ERSCSINMSN NILGVPRLGV  480
KTPSGNPGFS YHCSGFGESQ RFQEVLQGQE VFRPYRGGTL SDACIRGSGF RQPDGNHAPG  540
AAFKWLAPQG CDHHGITTSV LPQASSPSSV LMFPQTSSKM PGLEYIYGCL DRNENSRHFK  600
IGPTQDMTRT DQTLRLWPHL ISGKVLDECT RNEKLHSPVS GAEHESNNKC LNTNGCKIFG  660
ISLTEKAQAG DEVDCGNASY HSRLQSLKPQ MPKSLGSSCA TVHEQRPVVG RVVDISAVNT  720
MI*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldy_A1e-1113538718361Auxin response factor 1
4ldy_B1e-1113538718361Auxin response factor 1
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.63670.0callus| flower| leaf| panicle| seed| stem| vegetative meristem
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO193520340.0
Expression AtlasQ0JKI9-
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in roots, culms, leaves and young panicles. {ECO:0000269|PubMed:17408882}.
Functional Description ? help Back to Top
Source Description
UniProtAuxin response factors (ARFs) are transcriptional factors that bind specifically to the DNA sequence 5'-TGTCTC-3' found in the auxin-responsive promoter elements (AuxREs).
Function -- GeneRIF ? help Back to Top
  1. DL and OsETT2 act independently in awn formation, and that either gene alone is not sufficient for awn development.
    [PMID: 24330191]
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00021PBMTransfer from AT2G33860Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os01g48060.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By auxin under dark condition. {ECO:0000269|PubMed:17408882}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs01g48060
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAB0712910.0AB071291.1 Oryza sativa OsETTIN2 mRNA for Arabidopsis ETTIN-like protein 2, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015647434.10.0auxin response factor 2 isoform X1
SwissprotQ0JKI90.0ARFB_ORYSJ; Auxin response factor 2
TrEMBLI1NQJ00.0I1NQJ0_ORYGL; Auxin response factor
STRINGORGLA01G0213000.10.0(Oryza glaberrima)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP25373580
Representative plantOGRP66851018
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G33860.11e-162ARF family protein
Publications ? help Back to Top
  1. Sato Y, et al.
    Auxin response factor family in rice.
    Genes Genet. Syst., 2001. 76(6): p. 373-80
    [PMID:11922106]
  2. Wang D, et al.
    Genome-wide analysis of the auxin response factors (ARF) gene family in rice (Oryza sativa).
    Gene, 2007. 394(1-2): p. 13-24
    [PMID:17408882]
  3. Khanday I,Yadav SR,Vijayraghavan U
    Rice LHS1/OsMADS1 controls floret meristem specification by coordinated regulation of transcription factors and hormone signaling pathways.
    Plant Physiol., 2013. 161(4): p. 1970-83
    [PMID:23449645]
  4. Toriba T,Hirano HY
    The DROOPING LEAF and OsETTIN2 genes promote awn development in rice.
    Plant J., 2014. 77(4): p. 616-26
    [PMID:24330191]