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_Os04g57610.1
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: 823aa    MW: 91314.4 Da    PI: 6.317
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os04g57610.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B371.41.1e-22139240199
                       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_Os04g57610.1 139 FCKTLTASDTSTHGGFSVPRRAAERVfppldftQQPPAQ--ELIARDIHDIEWKFRHIFRGQPKRHLLTTGWSVFVSAKRLVAGDSVLFI--W 227
                       99***********************9*****86555544..8************************************************..8 PP

                       SSEE..EEEEE-S CS
                B3  87 rsefelvvkvfrk 99 
                       +++ +l+++++r+
  LOC_Os04g57610.1 228 NEKNQLLLGIRRA 240
                       899999****997 PP
2Auxin_resp112.63.7e-37265348183
        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_Os04g57610.1 265 AAHAAATNSRFTIFYNPRASPSEFVIPLSKYIKAVFhTRISVGMRFRMLFETEESSVRRYMGTITEVSDADPVRWPSSYWRSVK 348
                       79*******************************986599******************************************985 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019367.85E-48124268IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.102.7E-41131254IPR015300DNA-binding pseudobarrel domain
CDDcd100175.40E-21138239No hitNo description
PfamPF023627.7E-21139240IPR003340B3 DNA binding domain
PROSITE profilePS5086312.224139241IPR003340B3 DNA binding domain
SMARTSM010191.4E-23139241IPR003340B3 DNA binding domain
PfamPF065071.6E-32265348IPR010525Auxin response factor
PfamPF023091.5E-7716807IPR033389AUX/IAA domain
SuperFamilySSF542771.9E-7719798No hitNo description
PROSITE profilePS5174524.037723807IPR000270PB1 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: 823 aa     Download sequence    Send to blast
MSSSSAASIG PPQPPPPPAP PEEGGWLEKK CLNSELWHAC AGPLVCLPTV GTRVVYFPQG  60
HSEQVAASTN KEVEGHIPNY PNLPAQLICQ LHDVTMHADV ETDEVYAQMT LQPLNPQEQN  120
DAYLPAEMGI MSKQPTNYFC KTLTASDTST HGGFSVPRRA AERVFPPLDF TQQPPAQELI  180
ARDIHDIEWK FRHIFRGQPK RHLLTTGWSV FVSAKRLVAG DSVLFIWNEK NQLLLGIRRA  240
SRPQTVMPSS VLSSDSMHIG LLAAAAHAAA TNSRFTIFYN PRASPSEFVI PLSKYIKAVF  300
HTRISVGMRF RMLFETEESS VRRYMGTITE VSDADPVRWP SSYWRSVKVG WDESTAGERP  360
PRVSLWEIEP LTTFPMYPSL FPLRVKHPWY SGVASLHDDS NALMWLRGVA GEGGFQSLNF  420
QSPGIGSWGQ QRLHPSLLSS DHDQYQAVVA AAAASQSGGY LKQQFLHLQQ PMQSPQEHCN  480
LNPLLQQQIL QQASQQQIIN PDAQNIQTML SPSAIQQQLQ QLQQMQQVQN DQKQKIQPDQ  540
SYQVPTSAVL PSPTSLPSHL REKFGFSDPN ANSSSFITSS SSDNMLDSSF LQGSSKAVDL  600
SRFNQPVASE QQQQQQQAWK QKFMGSQSVS FGGSVLHNSP TSKDGSVENK IGRDVQNQSL  660
FSPQVDSSSL LYNMVPNLTS NVSDGNLSTI PSGSTYLQNA MYGCLDDSSG LLQNTGENDP  720
ATRTFVKVYK SGSVGRSLDI TRFSNYAELR EELGQMFGIK GQLDDPDRSG WQLVFVDREN  780
DVLLLGDDPW ESFVNSVWYI KILSPEDVHK MGKQGNDPRY LS*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldu_A1e-1612836947388Auxin 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_Os04g57610.1
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_015636872.10.0auxin response factor 12 isoform X1
SwissprotQ0J9510.0ARFL_ORYSJ; Auxin response factor 12
TrEMBLI1PQT00.0I1PQT0_ORYGL; Auxin response factor
STRINGORGLA04G0254900.10.0(Oryza glaberrima)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP58503039
Representative plantOGRP8561456
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G30330.20.0auxin 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]