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_Os01g54990.1
Common NameARF3, LOC4327014, Os01g0753500, P0435B05.36, P0503C12.8
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: 732aa    MW: 79583.6 Da    PI: 7.9421
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os01g54990.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B378.57.2e-25191292199
                       EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-S CS
                B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldg 86 
                       f+k+lt sd++++g +++p++ ae++       ++    s++l+ +d++g +W++++iyr++++r++lt+GW++Fv+ ++L +gD v+F   +
  LOC_Os01g54990.1 191 FCKTLTASDTSTHGGFSVPRRAAEDCfppldhkQLR--PSQELVAKDLHGAKWRFRHIYRGQPRRHLLTTGWSSFVNKKKLVSGDAVLFL--R 279
                       99**************************99865444..4669************************************************..3 PP

                       SSEE..EEEEE-S CS
                B3  87 rsefelvvkvfrk 99 
                        +++el+++v+r+
  LOC_Os01g54990.1 280 GDDGELRLGVRRA 292
                       489999****997 PP
2Auxin_resp114.97.2e-38317397182
        Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsL 82 
                       +a++++++svF+++YnPra++se+vv+++k++k+++++v++GmRfk++fe+ed++err sG+++gvs++dp+rWp+SkWrsL
  LOC_Os01g54990.1 317 VADSLKHGSVFHICYNPRATASEYVVPYWKFVKSFNHPVCIGMRFKFHFESEDVNERR-SGMIAGVSEVDPIRWPGSKWRSL 397
                       578899****************************************************.9********************99 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019362.75E-47175330IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.106.1E-39186294IPR015300DNA-binding pseudobarrel domain
CDDcd100179.50E-23189291No hitNo description
PROSITE profilePS5086313.507191293IPR003340B3 DNA binding domain
PfamPF023627.0E-23191292IPR003340B3 DNA binding domain
SMARTSM010192.8E-24191293IPR003340B3 DNA binding domain
PfamPF065073.3E-31318397IPR010525Auxin 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:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA 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: 732 aa     Download sequence    Send to blast
MASSASSSSS PSSRPPLMAL PSFYRPPWPS ERGGEQRATD CWAGSPAAGG GRARATAMGI  60
DLNNTASGGE EDAPAPGPVC RDLWHACAGP VVSLPRRGSA VVYLPQGHLS AAGAGGGIRG  120
EVAVALPPHV ACRVVDVELC ADAATDEVYA RLALRAEGEV FERNLHGGGI EREDDMEDGD  180
EERKSRMLHM FCKTLTASDT STHGGFSVPR RAAEDCFPPL DHKQLRPSQE LVAKDLHGAK  240
WRFRHIYRGQ PRRHLLTTGW SSFVNKKKLV SGDAVLFLRG DDGELRLGVR RATQLKNEAI  300
FKAFSSESSK MRTLSAVADS LKHGSVFHIC YNPRATASEY VVPYWKFVKS FNHPVCIGMR  360
FKFHFESEDV NERRSGMIAG VSEVDPIRWP GSKWRSLLVR WEDATDCNSQ NRVSPWEIEI  420
VGGSISVAHS LSASSSKRTK LCPQGNLDVP ALYGNGRPDS VETEKFPRVL QGQELMGSRT  480
HRATCSPQSI DITKSKSFDA WRFLTDTRSC MLGSSTSRLP VQYSGYTHQS VSFGESIGFP  540
EVLQGQEISQ TVPPFQGMLP DACSAKSRYE LKNYVCTPAT MNGLSSANEG YCLSLSTVPP  600
SPPSSLMLYQ TGVPQLELAS KNNDKSGNDS QPALRQHKLL SETSWDQFKI GKASTPGNAT  660
KPGNGGREVD RTSCRLFGFS LTEKIIPTDK DGEKEVSYET DCQNPRMLDL FGYNCSTPGA  720
LHALCAAPLG I*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldy_A1e-1007941919353Auxin response factor 1
4ldy_B1e-1007941919353Auxin response factor 1
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.342490.0callus| flower| panicle| stem
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO329823530.0
Expression AtlasQ5JMM1-
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).
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os01g54990.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs01g54990
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK0723300.0AK072330.1 Oryza sativa Japonica Group cDNA clone:J023039P13, full insert sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015634503.10.0auxin response factor 3 isoform X2
SwissprotQ5JMM10.0ARFC_ORYSJ; Auxin response factor 3
TrEMBLA0A0D9YF290.0A0A0D9YF29_9ORYZ; Auxin response factor
STRINGOS01T0753500-010.0(Oryza sativa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP51132756
Representative plantOGRP1291845
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G33860.11e-152ARF family protein
Publications ? help Back to Top
  1. Kikuchi S, et al.
    Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice.
    Science, 2003. 301(5631): p. 376-9
    [PMID:12869764]
  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. Song X, et al.
    Rice RNA-dependent RNA polymerase 6 acts in small RNA biogenesis and spikelet development.
    Plant J., 2012. 71(3): p. 378-89
    [PMID:22443269]