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_Os02g06910.1
Common NameARF6, ARF6A, LOC4328406, OJ1661_C12.26, Os02g0164900, OsJ_005343, OSJNBa0023I17.9
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: 909aa    MW: 100847 Da    PI: 6.2094
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os02g06910.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B3781e-24134235199
                       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++g++W++++i+r++++r++lt+GW+ Fv+a++L +gD+v+F   +
  LOC_Os02g06910.1 134 FCKTLTASDTSTHGGFSVPRRAAEKVfppldftQQPPAQ--ELMAKDLHGNEWKFRHIFRGQPKRHLLTTGWSVFVSAKRLVAGDSVLFI--W 222
                       99*****************************86555544..8************************************************..7 PP

                       SSEE..EEEEE-S CS
                B3  87 rsefelvvkvfrk 99 
                       +++ +l+++++r+
  LOC_Os02g06910.1 223 NDSNQLLLGIRRA 235
                       878889***9997 PP
2Auxin_resp119.62.4e-39260343183
        Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalk.vkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                       aahaast+s F+++YnPras+seFv++++k++ka++ +++svGmRf+m fete+ss rr++Gt++g+sdldpvrW nS+Wrs+k
  LOC_Os02g06910.1 260 AAHAASTNSRFTIFYNPRASPSEFVIPLAKYVKAVYhTRISVGMRFRMLFETEESSVRRYMGTITGISDLDPVRWMNSHWRSVK 343
                       79*********************************9789******************************************985 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019361.44E-48119263IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.102.7E-42126249IPR015300DNA-binding pseudobarrel domain
CDDcd100172.04E-21133234No hitNo description
SMARTSM010193.3E-25134236IPR003340B3 DNA binding domain
PfamPF023624.6E-23134235IPR003340B3 DNA binding domain
PROSITE profilePS5086313.098134236IPR003340B3 DNA binding domain
PfamPF065073.7E-34260343IPR010525Auxin response factor
PfamPF023099.4E-8771862IPR033389AUX/IAA domain
SuperFamilySSF542771.5E-7774853No hitNo description
PROSITE profilePS5174524.082777861IPR000270PB1 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:0009030anatomycarpel
PO:0007130developmental stagesporophyte reproductive stage
PO:0007606developmental stagegynoecium development stage
Sequence ? help Back to Top
Protein Sequence    Length: 909 aa     Download sequence    Send to blast
MKLSPSAGGV SDQPPSPPEV AEEQKCLNSE LWHACAGPLV SLPAVGSRVV YFPQGHSEQV  60
AASTNKEMES QIPNYPNLPP QLICQLHNVT MHADAETDEV YAQMTLQPLS PQELKDPFLP  120
AELGTASKQP TNYFCKTLTA SDTSTHGGFS VPRRAAEKVF PPLDFTQQPP AQELMAKDLH  180
GNEWKFRHIF RGQPKRHLLT TGWSVFVSAK RLVAGDSVLF IWNDSNQLLL GIRRANRPQT  240
VMPSSVLSSD SMHIGLLAAA AHAASTNSRF TIFYNPRASP SEFVIPLAKY VKAVYHTRIS  300
VGMRFRMLFE TEESSVRRYM GTITGISDLD PVRWMNSHWR SVKVGWDEST AGERQPRVSL  360
WEIEPLTTFP MYPSPFPLRL KRPWPTGLPS LYGGKEDDLA SSLMWLRDSQ NTGFQSLNFG  420
GLGMSPWMQP RLDSSLLGLQ PDMYQTIAAA AALQNTTKQV SPAMLQFQQP QNIVGRSSLL  480
SSQILQQAQP QFQQMYHQNI NGNSIQGHSQ PEYLQQPLQH CQSFNEQKPQ LQPQQQQQES  540
HQQQPQHQQM QQQKHLSNFQ TVPNALSVFS QLSSTPQSTP STLQTVSPFS QQHNFPDTNI  600
SCLSPSNVSS MHDTLRSFPS EAASDLPGVP RITPVPVSDP WSSKRVAVES TITSRPHDIS  660
SQIENFDLTP SSIPQNSTLA PLPGRECLVD QDGSSDPQNH FLFGVNIDSQ SLLMQDGIPS  720
LHNENSSSTI PYSTSNFLSP SQDDYPLSQT LTTPGCLDES GYVPCSDNAD QVKRPHATFV  780
KVYKSGTVGR LLDITRFSSY HELRSEVGRL FGLEGQLEDP LRSGWQLVFV DREDDVLLVG  840
DDPWQEFVNS VSCIKILSPQ EVQQMGKPGI ELFSTSARRL GNSCDNYMSR QESRSLSTGI  900
ASVGSVEF*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldu_A1e-1602736451388Auxin response factor 5
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.255970.0callus| flower| leaf| panicle| seed| stem
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO329805930.0
Expression AtlasQ6H6V4-
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).
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_Os02g06910.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs02g06910
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK0705690.0AK070569.1 Oryza sativa Japonica Group cDNA clone:J023056C15, full insert sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015625706.10.0auxin response factor 6
RefseqXP_025879024.10.0auxin response factor 6
SwissprotA2X1A10.0ARFF_ORYSI; Auxin response factor 6
SwissprotQ6H6V40.0ARFF_ORYSJ; Auxin response factor 6
TrEMBLA0A0E0NAA50.0A0A0E0NAA5_ORYRU; Auxin response factor
STRINGORUFI02G05060.10.0(Oryza rufipogon)
STRINGOS02T0164900-010.0(Oryza sativa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP20123685
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. Nozu Y,Tsugita A,Kamijo K
    Proteomic analysis of rice leaf, stem and root tissues during growth course.
    Proteomics, 2006. 6(12): p. 3665-70
    [PMID:16758443]
  4. 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]