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_Os12g41950.1
Common NameARF25, ARF6B, LOC4352783, Os12g0613700, OsJ_035418
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: 900aa    MW: 99861.9 Da    PI: 6.2873
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os12g41950.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B375.36.9e-24132233199
                       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_Os12g41950.1 132 FCKTLTASDTSTHGGFSVPRRAAEKVfppldfsQQPPA--QELIARDLHDNEWKFRHIFRGQPKRHLLTTGWSVFVSAKRLVAGDSVIFI--W 220
                       99*****************************8544444..48************************************************..7 PP

                       SSEE..EEEEE-S CS
                B3  87 rsefelvvkvfrk 99 
                       +++ +l+++++r+
  LOC_Os12g41950.1 221 NDNNQLLLGIRRA 233
                       777778***9997 PP
2Auxin_resp118.74.6e-39258341183
        Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalk.vkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                       aahaa+t+s F+++YnPras+seFv++++k++ka++ ++vsvGmRf+m fete+ss rr++Gt++++sdld+vrWpnS+Wrs+k
  LOC_Os12g41950.1 258 AAHAAATNSRFTIFYNPRASPSEFVIPLAKYVKAVYhTRVSVGMRFRMLFETEESSVRRYMGTITSISDLDSVRWPNSHWRSVK 341
                       79*********************************9789******************************************985 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019367.06E-49117261IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.104.4E-43123247IPR015300DNA-binding pseudobarrel domain
CDDcd100174.85E-22131232No hitNo description
PROSITE profilePS5086312.703132234IPR003340B3 DNA binding domain
SMARTSM010197.9E-25132234IPR003340B3 DNA binding domain
PfamPF023624.7E-22132233IPR003340B3 DNA binding domain
PfamPF065073.0E-34258341IPR010525Auxin response factor
SuperFamilySSF542771.44E-6757840No hitNo description
PfamPF023092.8E-7763852IPR033389AUX/IAA domain
PROSITE profilePS5174522.727766850IPR000270PB1 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: 900 aa     Download sequence    Send to blast
MKLSPPASAD MPQALPENDG EQRCLNSELW HACAGPLVSL PVVRSRVVYF PQGHSEQVAA  60
STNKEVDAQI PNYPNLPPQL ICQLHNVTMH ADAETDEVYA QMTLQPLSPE EQKEPFLPME  120
LGAASKQPTN YFCKTLTASD TSTHGGFSVP RRAAEKVFPP LDFSQQPPAQ ELIARDLHDN  180
EWKFRHIFRG QPKRHLLTTG WSVFVSAKRL VAGDSVIFIW NDNNQLLLGI RRANRQQTVM  240
PSSVLSSDSM HIGLLAAAAH AAATNSRFTI FYNPRASPSE FVIPLAKYVK AVYHTRVSVG  300
MRFRMLFETE ESSVRRYMGT ITSISDLDSV RWPNSHWRSV KVGWDESTTG DKQPRVSLWE  360
IEPLTTFPMY PSAFPLRLKR PWASGLPMHG MFNGGGNDDF ARYSSLMWLR DGNRGTQSLN  420
FQGHGVSPWL QPRIDSPLLG LKPDTYQQMA AAALEEIRYG DPSKQHPATL QYQQTHNLNS  480
GLNSLFASHV LGQVQFQPQQ SPLQVVQQGH CQNTGDSGFL QGQLPRLQLH NTQQLLKEQE  540
LQQQQRQHVL QEQSSQEMQQ QLPSSDHHVA DVASESGSAP QAQSSLLSGS SFYNQNLLEG  600
NSDPPLHLHN NFHNFSNQEA SNLLILPRSS QLMASDGWPS KRLTLESAVH PEAPSMHPKI  660
EKVNHQGISH FPGAFPPQSA RGCSIVQDCR ADAENRLLSS SFELQDGMTS IITDANRETD  720
TMAIPLLRYS GADLTTENTL ATSNCLGESG TFNPLNNISV NPSQGATFVK VYKSGSLGRS  780
LDISRFSSYC ELRSELERLF GLEGQLEDPV RSGWQLVFVD RENDILLVGD DPWQEFANSV  840
WCIKILSPQE VQQLVRGGDG LLSSPGARMQ QSNACDDYSA SHNMQNIAGN IASVAPLDY*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldu_A1e-1631336238388Auxin response factor 5
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.222720.0callus| flower| leaf| panicle| root| seed| stem
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO379913260.0
Expression AtlasQ2QM84-
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_Os12g41950.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs12g41950
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK1217030.0AK121703.1 Oryza sativa Japonica Group cDNA clone:J033074F07, full insert sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015619766.10.0auxin response factor 25 isoform X1
SwissprotQ2QM840.0ARFY_ORYSJ; Auxin response factor 25
TrEMBLA0A0E0RJZ50.0A0A0E0RJZ5_ORYRU; Auxin response factor
STRINGORUFI12G20920.10.0(Oryza rufipogon)
STRINGOS12T0613700-010.0(Oryza sativa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP127122934
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. 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]
  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]
  5. Gao S, et al.
    CYTOKININ OXIDASE/DEHYDROGENASE4 Integrates Cytokinin and Auxin Signaling to Control Rice Crown Root Formation.
    Plant Physiol., 2014. 165(3): p. 1035-1046
    [PMID:24808099]