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_Os11g32110.4
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: 837aa    MW: 92644.2 Da    PI: 6.8803
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os11g32110.4genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B374.81e-23132233199
                       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_Os11g32110.4 132 FCKTLTASDTSTHGGFSVLRRHADEClppldmSRQ-PPTQELVAKDLHGVEWRFRHIFRGQPRRHLLQSGWSVFVSAKRLVAGDAFIFL--RG 221
                       99*****************************7333.34459************************************************..44 PP

                       SEE..EEEEE-S CS
                B3  88 sefelvvkvfrk 99 
                       +++el+v+v+r+
  LOC_Os11g32110.4 222 ENGELRVGVRRA 233
                       9999*****996 PP
2Auxin_resp116.91.7e-38258340183
        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_Os11g32110.4 258 AWHAVNTGTMFTVYYKPRTSPAEFVVPYDRYMESLKQNYSIGMRFKMRFEGEEAPEQRFTGTIVGMGDSDPAGWPESKWRSLK 340
                       89*******************************************************************************96 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.103.1E-42125247IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019363.92E-41127261IPR015300DNA-binding pseudobarrel domain
CDDcd100177.00E-22130232No hitNo description
SMARTSM010199.9E-24132234IPR003340B3 DNA binding domain
PfamPF023621.3E-21132233IPR003340B3 DNA binding domain
PROSITE profilePS5086311.899132234IPR003340B3 DNA binding domain
PfamPF065078.1E-36258340IPR010525Auxin response factor
SuperFamilySSF542771.47E-11703784No hitNo description
PROSITE profilePS5174521.936708792IPR000270PB1 domain
PfamPF023092.2E-6754792IPR033389AUX/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: 837 aa     Download sequence    Send to blast
MATAEVGGGG GGGGGGGEDA LFTELWSACA GPLVTVPRVG EKVFYFPQGH IEQVEASTNQ  60
VGEQRMQLYN LPWKILCEVM NVELKAEPDT DEVYAQLTLL PESKQQEDNG STEEEVPSAP  120
AAGHVRPRVH SFCKTLTASD TSTHGGFSVL RRHADECLPP LDMSRQPPTQ ELVAKDLHGV  180
EWRFRHIFRG QPRRHLLQSG WSVFVSAKRL VAGDAFIFLR GENGELRVGV RRAMRQQTNV  240
PSSVISSHSM HLGVLATAWH AVNTGTMFTV YYKPRTSPAE FVVPYDRYME SLKQNYSIGM  300
RFKMRFEGEE APEQRFTGTI VGMGDSDPAG WPESKWRSLK VRWDEASSIP RPERVSPWQI  360
EPAVSPPPVN PLPVPRTKRL RPNATALPAD SSAIAKEAAT KVVVESEPNG TQRTFQTQEN  420
ATPKSGFGNS SELESAQKSI MRPSGFDREK NNTPIQWKLG SDGRMQMSKP ESYSEMLSGF  480
QPPKDVQIPQ GFCSLPEQIT AGHSNFWHTV NAQYQDQQSN HNMFPSSWSF MPPNTRLGLN  540
KQNYSMIQEA GVLSQRPGNT KFGNGVYAAL PGRGTEQYSG GWFGHMMPNS HMDDTQPRLI  600
KPKPLVVAHG DVQKAKGASC KLFGIHLDSP AKSEPLKSPS SVVYDGTPQT PGATEWRRPD  660
VTEVEKCSDP SKAMKPLDTP QPDSVPEKPS SQQASRNMSC KSQGVSTRSC KKVHKQGIAL  720
GRSVDLTKFN GYEELIAELD DMFDFNGELK GPKKEWMVVY TDNEGDMMLV GDDPWIEFCD  780
MVHKIFIYTR EEVQRMNPGT LNSRSEDSHA NSMERGSVGR EMRGCLSTSS LNSENC*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A1e-177113629354Auxin response factor 1
4ldw_A1e-177113629354Auxin response factor 1
4ldw_B1e-177113629354Auxin 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_Os11g32110.4
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)
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]