PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Home  TFext  BLAST  Prediction  Download  Help  About  Links  PlantRegMap
(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID LOC_Os04g57610.3
Common NameARF12, ARF8, LOC4337363, Os04g0671900, OsJ_16583, OSJNBb0004A17.6
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: 819aa    MW: 90901 Da    PI: 6.317
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os04g57610.3genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B371.41.1e-22135236199
                       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+        ++++++  +l+ +d +  +W++++i+r++++r++lt+GW+ Fv+a++L +gD+v+F   +
  LOC_Os04g57610.3 135 FCKTLTASDTSTHGGFSVPRRAAERVfppldftQQPPAQ--ELIARDIHDIEWKFRHIFRGQPKRHLLTTGWSVFVSAKRLVAGDSVLFI--W 223
                       99***********************9*****86555544..8************************************************..8 PP

                       SSEE..EEEEE-S CS
                B3  87 rsefelvvkvfrk 99 
                       +++ +l+++++r+
  LOC_Os04g57610.3 224 NEKNQLLLGIRRA 236
                       899999****997 PP
2Auxin_resp112.63.7e-37261344183
        Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalk.vkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                       aahaa+t+s F+++YnPras+seFv++++k+ ka+  +++svGmRf+m fete+ss rr++Gt++ vsd+dpvrWp S Wrs+k
  LOC_Os04g57610.3 261 AAHAAATNSRFTIFYNPRASPSEFVIPLSKYIKAVFhTRISVGMRFRMLFETEESSVRRYMGTITEVSDADPVRWPSSYWRSVK 344
                       79*******************************986599******************************************985 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019367.72E-48120264IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.102.6E-41127250IPR015300DNA-binding pseudobarrel domain
CDDcd100175.35E-21134235No hitNo description
SMARTSM010191.4E-23135237IPR003340B3 DNA binding domain
PfamPF023627.6E-21135236IPR003340B3 DNA binding domain
PROSITE profilePS5086312.224135237IPR003340B3 DNA binding domain
PfamPF065071.5E-32261344IPR010525Auxin response factor
PfamPF023091.5E-7712803IPR033389AUX/IAA domain
SuperFamilySSF542771.9E-7715794No hitNo description
PROSITE profilePS5174524.037719803IPR000270PB1 domain
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:0009908Biological Processflower development
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0005515Molecular Functionprotein binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0009047anatomystem
PO:0007010developmental stagewhole plant fruit ripening stage
PO:0007130developmental stagesporophyte reproductive stage
Sequence ? help Back to Top
Protein Sequence    Length: 819 aa     Download sequence    Send to blast
MSSSSAASIG PPQPPPPPAP PEEEKKCLNS ELWHACAGPL VCLPTVGTRV VYFPQGHSEQ  60
VAASTNKEVE GHIPNYPNLP AQLICQLHDV TMHADVETDE VYAQMTLQPL NPQEQNDAYL  120
PAEMGIMSKQ PTNYFCKTLT ASDTSTHGGF SVPRRAAERV FPPLDFTQQP PAQELIARDI  180
HDIEWKFRHI FRGQPKRHLL TTGWSVFVSA KRLVAGDSVL FIWNEKNQLL LGIRRASRPQ  240
TVMPSSVLSS DSMHIGLLAA AAHAAATNSR FTIFYNPRAS PSEFVIPLSK YIKAVFHTRI  300
SVGMRFRMLF ETEESSVRRY MGTITEVSDA DPVRWPSSYW RSVKVGWDES TAGERPPRVS  360
LWEIEPLTTF PMYPSLFPLR VKHPWYSGVA SLHDDSNALM WLRGVAGEGG FQSLNFQSPG  420
IGSWGQQRLH PSLLSSDHDQ YQAVVAAAAA SQSGGYLKQQ FLHLQQPMQS PQEHCNLNPL  480
LQQQILQQAS QQQIINPDAQ NIQTMLSPSA IQQQLQQLQQ MQQVQNDQKQ KIQPDQSYQV  540
PTSAVLPSPT SLPSHLREKF GFSDPNANSS SFITSSSSDN MLDSSFLQGS SKAVDLSRFN  600
QPVASEQQQQ QQQAWKQKFM GSQSVSFGGS VLHNSPTSKD GSVENKIGRD VQNQSLFSPQ  660
VDSSSLLYNM VPNLTSNVSD GNLSTIPSGS TYLQNAMYGC LDDSSGLLQN TGENDPATRT  720
FVKVYKSGSV GRSLDITRFS NYAELREELG QMFGIKGQLD DPDRSGWQLV FVDRENDVLL  780
LGDDPWESFV NSVWYIKILS PEDVHKMGKQ GNDPRYLS*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldu_A1e-1622436547388Auxin response factor 5
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.801920.0callus| flower| leaf| panicle| seed| stem
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO329814780.0
Expression AtlasQ0J951-
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).
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00033PBMTransfer from AT5G37020Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os04g57610.3
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs04g57610
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK0714550.0AK071455.1 Oryza sativa Japonica Group cDNA clone:J023093B04, full insert sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015636874.10.0auxin response factor 12 isoform X3
SwissprotQ0J9510.0ARFL_ORYSJ; Auxin response factor 12
TrEMBLI1PQT00.0I1PQT0_ORYGL; Auxin response factor
STRINGOS04T0671900-010.0(Oryza sativa)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G30330.10.0auxin response factor 6
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. 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]
  3. 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]
  4. Qi Y, et al.
    OsARF12, a transcription activator on auxin response gene, regulates root elongation and affects iron accumulation in rice (Oryza sativa).
    New Phytol., 2012. 193(1): p. 109-20
    [PMID:21973088]
  5. Shen WJ,Ruan XL,Li XS,Zhao Q,Li HP
    RNA silencing suppressor Pns11 of rice gall dwarf virus induces virus-like symptoms in transgenic rice.
    Arch. Virol., 2012. 157(8): p. 1531-9
    [PMID:22592958]
  6. Wang S, et al.
    Auxin response factor (OsARF12), a novel regulator for phosphate homeostasis in rice (Oryza sativa).
    New Phytol., 2014. 201(1): p. 91-103
    [PMID:24111723]
  7. Fan J, et al.
    Infection of Ustilaginoidea virens intercepts rice seed formation but activates grain-filling-related genes.
    J Integr Plant Biol, 2015. 57(6): p. 577-90
    [PMID:25319482]