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 OMERI01G39560.3
Organism
Oryza meridionalis
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
Family ARF
Protein Properties Length: 839aa    MW: 94301.8 Da    PI: 6.6109
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
OMERI01G39560.3genomeOGEView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B369.64.3e-22129230199
                      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+++  W++++i+r++++r++l++GW+ Fv++++L +gD ++F   + 
  OMERI01G39560.3 129 FCKTLTASDTSTHGGFSVLRRHADEClppldmtQSPPT--QELVAKDLHSMDWRFRHIFRGQPRRHLLQSGWSVFVSSKRLVAGDAFIFL--RG 218
                      99*****************************7555544..58************************************************..44 PP

                      SEE..EEEEE-S CS
               B3  88 sefelvvkvfrk 99 
                      +++el+v+v+r+
  OMERI01G39560.3 219 ENGELRVGVRRA 230
                      9999*****996 PP
2Auxin_resp113.52e-37255336183
       Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                      a+ha++tks+F+v+Y+Pr+s+seF+++++++++++k+++svGmRf+m+fe+e+++e+r++Gt++g ++ldp  Wp+S WrsLk
  OMERI01G39560.3 255 AWHAINTKSMFTVYYKPRTSPSEFIIPYDQYMESVKNNYSVGMRFRMRFEGEEAPEQRFTGTIIGSENLDP-VWPESSWRSLK 336
                      89*********************************************************************.9********96 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019369.16E-40121258IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.103.5E-39122244IPR015300DNA-binding pseudobarrel domain
CDDcd100175.73E-19127229No hitNo description
PROSITE profilePS5086311.265129231IPR003340B3 DNA binding domain
SMARTSM010191.5E-21129231IPR003340B3 DNA binding domain
PfamPF023628.6E-20129230IPR003340B3 DNA binding domain
PfamPF065076.2E-34255336IPR010525Auxin response factor
PfamPF023095.6E-14674778IPR033389AUX/IAA domain
SuperFamilySSF542774.76E-13689770No hitNo description
PROSITE profilePS5174526.238693786IPR000270PB1 domain
Gene3DG3DSA:3.10.20.2400.001711766No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0008285Biological Processnegative regulation of cell proliferation
GO:0009734Biological Processauxin-activated signaling pathway
GO:0009737Biological Processresponse to abscisic acid
GO:0009911Biological Processpositive regulation of flower development
GO:0010047Biological Processfruit dehiscence
GO:0010150Biological Processleaf senescence
GO:0010227Biological Processfloral organ abscission
GO:0045892Biological Processnegative regulation of transcription, DNA-templated
GO:0048481Biological Processplant ovule development
GO:0005634Cellular Componentnucleus
GO:0005515Molecular Functionprotein binding
GO:0043565Molecular Functionsequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 839 aa     Download sequence    Send to blast
MPPAAMAPPP PPQGSSTGDP LYDELWHACA GPLVTVPRVG DLVFYFPQGH IEQVEASMNQ  60
VADSQMRLYD LPSKLLCRVL NVELKAEQDT DEVYAQVMLM PEPEQNEMAV EKTTPTSGPV  120
QARPPVRSFC KTLTASDTST HGGFSVLRRH ADECLPPLDM TQSPPTQELV AKDLHSMDWR  180
FRHIFRGQPR RHLLQSGWSV FVSSKRLVAG DAFIFLRGEN GELRVGVRRA MRQLSNVPSS  240
VISSQSMHLG VLATAWHAIN TKSMFTVYYK PRTSPSEFII PYDQYMESVK NNYSVGMRFR  300
MRFEGEEAPE QRFTGTIIGS ENLDPVWPES SWRSLKVRWD EPSTIPRPDR VSPWKIEPAS  360
SPPVNPLPLS RVKRPRPNAP PASPESPILM KEAATKVDTD PAQAQRSQNG TVLQGQEQMT  420
LRSNLTESND SDVTAHKPMM WSPSPNAAKA HPLTFQQRPP MDNWMQLGRR ETDFKDVRSG  480
SQSFGDSPGF FMQNFDEAPN RLTSFKNQFQ DQGSARHYSD PYYFVSPQPS LTVESSTQMH  540
TDSKELHFWN GQSTTVYGNS RDQPQNFRFE QNSSSWLNQS FARPEQPRVI RPHASIAPVE  600
LEKTEGSGFK IFGFKVDTTN APNNHLSSPM AATHEPMLQT PSSLNQLQPV QTDCIPEVSV  660
STAGMATENE KSGQQAQQSS KDVQSKTQVA STRSCTKVHK QGVALGRSVD LSKFSNYDEL  720
KAELDKMFEF DGELVSSNKN WQIVYTDNEG DMMLVGDDPW EEFCSIVRKI YIYTKEEVQK  780
MNSKSNAPRK EDSSENEKGS VKRDDTRGSR FIIIAIAPLN SPQLSDVNIY LRSQPPSQK
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A1e-1691436112357Auxin response factor 1
4ldw_A1e-1691436112357Auxin response factor 1
4ldw_B1e-1691436112357Auxin response factor 1
4ldx_A1e-1691436112357Auxin response factor 1
4ldx_B1e-1691436112357Auxin response factor 1
Search in ModeBase
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1372376KRPRP
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
MP00574DAPTransfer from AT5G62000Download
Motif logo
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK0723090.0AK072309.1 Oryza sativa Japonica Group cDNA clone:J023022C23, full insert sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015650953.10.0auxin response factor 4
SwissprotQ5JK200.0ARFD_ORYSJ; Auxin response factor 4
TrEMBLA0A0E0CCH20.0A0A0E0CCH2_9ORYZ; Auxin response factor
STRINGOMERI01G39070.10.0(Oryza meridionalis)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP117836111
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. 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. 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]
  3. 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]