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_Os11g32110.1
Common NameARF1, ARF23, LOC4350610, Os11g0523800
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: 854aa    MW: 93983.6 Da    PI: 6.7931
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os11g32110.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B374.81e-23149250199
                       EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SS CS
                B3   1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgr 87 
                       f+k+lt sd++++g +++ +++a+e+      + + + +++l+ +d++g +W++++i+r++++r++l++GW+ Fv+a++L +gD ++F   + 
  LOC_Os11g32110.1 149 FCKTLTASDTSTHGGFSVLRRHADEClppldmSRQ-PPTQELVAKDLHGVEWRFRHIFRGQPRRHLLQSGWSVFVSAKRLVAGDAFIFL--RG 238
                       99*****************************7333.34459************************************************..44 PP

                       SEE..EEEEE-S CS
                B3  88 sefelvvkvfrk 99 
                       +++el+v+v+r+
  LOC_Os11g32110.1 239 ENGELRVGVRRA 250
                       9999*****996 PP
2Auxin_resp116.91.7e-38275357183
        Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                       a+ha++t+++F+v+Y+Pr+s++eFvv++++++++lk+++s+GmRfkm+fe+e+++e+r++Gt+vg+ d+dp  Wp+SkWrsLk
  LOC_Os11g32110.1 275 AWHAVNTGTMFTVYYKPRTSPAEFVVPYDRYMESLKQNYSIGMRFKMRFEGEEAPEQRFTGTIVGMGDSDPAGWPESKWRSLK 357
                       89*******************************************************************************96 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.103.2E-42142264IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019364.02E-41144278IPR015300DNA-binding pseudobarrel domain
CDDcd100177.27E-22147249No hitNo description
PROSITE profilePS5086311.899149251IPR003340B3 DNA binding domain
PfamPF023621.4E-21149250IPR003340B3 DNA binding domain
SMARTSM010199.9E-24149251IPR003340B3 DNA binding domain
PfamPF065078.4E-36275357IPR010525Auxin response factor
SuperFamilySSF542771.47E-11720801No hitNo description
PROSITE profilePS5174521.936725809IPR000270PB1 domain
PfamPF023092.2E-6771809IPR033389AUX/IAA 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:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0005515Molecular Functionprotein binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0009049anatomyinflorescence
PO:0001083developmental stageinflorescence development stage
PO:0007006developmental stageIL.00 inflorescence just visible stage
Sequence ? help Back to Top
Protein Sequence    Length: 854 aa     Download sequence    Send to blast
MATAEVGGGG GEGDAAAAAV ARAGGGGGGG GGGGEDALFT ELWSACAGPL VTVPRVGEKV  60
FYFPQGHIEQ VEASTNQVGE QRMQLYNLPW KILCEVMNVE LKAEPDTDEV YAQLTLLPES  120
KQQEDNGSTE EEVPSAPAAG HVRPRVHSFC KTLTASDTST HGGFSVLRRH ADECLPPLDM  180
SRQPPTQELV AKDLHGVEWR FRHIFRGQPR RHLLQSGWSV FVSAKRLVAG DAFIFLRGEN  240
GELRVGVRRA MRQQTNVPSS VISSHSMHLG VLATAWHAVN TGTMFTVYYK PRTSPAEFVV  300
PYDRYMESLK QNYSIGMRFK MRFEGEEAPE QRFTGTIVGM GDSDPAGWPE SKWRSLKVRW  360
DEASSIPRPE RVSPWQIEPA VSPPPVNPLP VPRTKRLRPN ATALPADSSA IAKEAATKVV  420
VESEPNGTQR TFQTQENATP KSGFGNSSEL ESAQKSIMRP SGFDREKNNT PIQWKLGSDG  480
RMQMSKPESY SEMLSGFQPP KDVQIPQGFC SLPEQITAGH SNFWHTVNAQ YQDQQSNHNM  540
FPSSWSFMPP NTRLGLNKQN YSMIQEAGVL SQRPGNTKFG NGVYAALPGR GTEQYSGGWF  600
GHMMPNSHMD DTQPRLIKPK PLVVAHGDVQ KAKGASCKLF GIHLDSPAKS EPLKSPSSVV  660
YDGTPQTPGA TEWRRPDVTE VEKCSDPSKA MKPLDTPQPD SVPEKPSSQQ ASRNMSCKSQ  720
GVSTRSCKKV HKQGIALGRS VDLTKFNGYE ELIAELDDMF DFNGELKGPK KEWMVVYTDN  780
EGDMMLVGDD PWIEFCDMVH KIFIYTREEV QRMNPGTLNS RSEDSHANSM ERGSVGREMR  840
GCLSTSSLNS ENC*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A1e-178203791354Auxin response factor 1
4ldw_A1e-178203791354Auxin response factor 1
4ldw_B1e-178203791354Auxin response factor 1
4ldx_A1e-178203791354Auxin response factor 1
4ldx_B1e-178203791354Auxin response factor 1
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.108170.0callus| flower| leaf| panicle| seed| stem
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO329820200.0
Expression AtlasQ2R3F5-
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_Os11g32110.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By auxin under light or dark conditions and gravitropic stimulation of coleptile. {ECO:0000269|PubMed:12369618, ECO:0000269|PubMed:17408882}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs11g32110
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAJ3063060.0AJ306306.1 Oryza sativa subsp. japonica mRNA for auxin response factor 1 (arf1 gene).
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015617186.10.0auxin response factor 23 isoform X1
RefseqXP_015617187.10.0auxin response factor 23 isoform X1
SwissprotQ2R3F50.0ARFW_ORYSJ; Auxin response factor 23
TrEMBLB9GAY80.0B9GAY8_ORYSJ; Auxin response factor
STRINGONIVA12G10760.10.0(Oryza nivara)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP117836111
Representative plantOGRP5501582
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G62000.30.0auxin response factor 2
Publications ? help Back to Top
  1. Contreras I,Ortiz-Zapater E,Castilho LM,Aniento F
    Characterization of Cop I coat proteins in plant cells.
    Biochem. Biophys. Res. Commun., 2000. 273(1): p. 176-82
    [PMID:10873582]
  2. Kobayashi-Uehara A,Shimosaka E,Handa H
    Cloning and expression analyses of cDNA encoding an ADP-ribosylation factor from wheat: tissue-specific expression of wheat ARF.
    Plant Sci., 2001. 160(3): p. 535-542
    [PMID:11166441]
  3. Waller F,Furuya M,Nick P
    OsARF1, an auxin response factor from rice, is auxin-regulated and classifies as a primary auxin responsive gene.
    Plant Mol. Biol., 2002. 50(3): p. 415-25
    [PMID:12369618]
  4. 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]
  5. Rice Chromosomes 11 and 12 Sequencing Consortia
    The sequence of rice chromosomes 11 and 12, rich in disease resistance genes and recent gene duplications.
    BMC Biol., 2005. 3: p. 20
    [PMID:16188032]
  6. Ren H, et al.
    Combinative effects of a bacterial type-III effector and a biocontrol bacterium on rice growth and disease resistance.
    J. Biosci., 2006. 31(5): p. 617-27
    [PMID:17301500]
  7. 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]
  8. Song Y,You J,Xiong L
    Characterization of OsIAA1 gene, a member of rice Aux/IAA family involved in auxin and brassinosteroid hormone responses and plant morphogenesis.
    Plant Mol. Biol., 2009. 70(3): p. 297-309
    [PMID:19266169]
  9. Kitajima A, et al.
    The rice alpha-amylase glycoprotein is targeted from the Golgi apparatus through the secretory pathway to the plastids.
    Plant Cell, 2009. 21(9): p. 2844-58
    [PMID:19767453]
  10. Kishimoto N, et al.
    Identification of the duplicated segments in rice chromosomes 1 and 5 by linkage analysis of cDNA markers of known functions.
    Theor. Appl. Genet., 1994. 88(6-7): p. 722-6
    [PMID:24186168]
  11. Sugano SS, et al.
    CRISPR/Cas9-mediated targeted mutagenesis in the liverwort Marchantia polymorpha L.
    Plant Cell Physiol., 2014. 55(3): p. 475-81
    [PMID:24443494]
  12. Kaneko K, et al.
    N-Glycomic and Microscopic Subcellular Localization Analyses of NPP1, 2 and 6 Strongly Indicate that trans-Golgi Compartments Participate in the Golgi to Plastid Traffic of Nucleotide Pyrophosphatase/Phosphodiesterases in Rice.
    Plant Cell Physiol., 2016. 57(8): p. 1610-28
    [PMID:27335351]