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_Os04g59430.1
Common NameARF13, LOC9269399, Os04g0690600, OSJNBa0039K24.27
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: 530aa    MW: 57223.6 Da    PI: 5.5725
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os04g59430.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B3781e-24129233299
                       EEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SS CS
                B3   2 fkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgr 87 
                        k+lt+sd+++ g +++p+ +a+++       + ++ +s  lt+ d++g sWe+++iyr++++r++lt+GW++Fv+a++L +gD+vvF+  g 
  LOC_Os04g59430.1 129 AKQLTQSDANNGGGFSVPRLCADHIfpalnldDDPPVQS--LTMGDLQGDSWEFRHIYRGTPRRHLLTTGWSKFVNAKQLVAGDTVVFMWCGA 219
                       69*******************9777*****976676675..************************************************8865 PP

                       ..SEE..EEEEE-S CS
                B3  88 ..sefelvvkvfrk 99 
                          e++l+v+v+r+
  LOC_Os04g59430.1 220 paPERKLLVGVRRA 233
                       57999999999986 PP
2Auxin_resp45.53.2e-16256331174
        Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkma.fetedsserrl.sGtvvgvsdldpvrW 74 
                       a++ a+++ +F+v+Y+Pr ++ eFvv++ +v k l++++  Gm+++ + +e ed ++  +  Gt + +++ +  r 
  LOC_Os04g59430.1 256 AVRLAAEQAAFRVTYYPRHGAGEFVVPRVEVDKGLTTPWRCGMQVRAQvMEAEDTRRLAWlNGTLTNLRHQQIWRT 331
                       5778999***************************************9758***************99988666444 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019362.09E-26117237IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.101.9E-31120242IPR015300DNA-binding pseudobarrel domain
CDDcd100174.29E-18126232No hitNo description
PROSITE profilePS5086312.026128234IPR003340B3 DNA binding domain
SMARTSM010191.4E-15128234IPR003340B3 DNA binding domain
PfamPF023621.4E-21129233IPR003340B3 DNA binding domain
PfamPF065075.2E-12256336IPR010525Auxin response factor
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
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0009066anatomyanther
PO:0001004developmental stageanther development stage
PO:0007130developmental stagesporophyte reproductive stage
Sequence ? help Back to Top
Protein Sequence    Length: 530 aa     Download sequence    Send to blast
MARPPAATAP PPPPPPPPPP PPPIDRLVWL ACAAPLSRIP VVGTQVSYFP EGHAEQCPAP  60
LPDPLPSAHR FFLCTITAVD LSADTTTGEP YATISLLPLR HDAPAPAPAP APAAAELAEA  120
ESQEFRYYAK QLTQSDANNG GGFSVPRLCA DHIFPALNLD DDPPVQSLTM GDLQGDSWEF  180
RHIYRGTPRR HLLTTGWSKF VNAKQLVAGD TVVFMWCGAP APERKLLVGV RRAARYSGES  240
ACNARGRVQP QEVMEAVRLA AEQAAFRVTY YPRHGAGEFV VPRVEVDKGL TTPWRCGMQV  300
RAQVMEAEDT RRLAWLNGTL TNLRHQQIWR TLEVEWDASA ASSSMKNRFV NPWQVQPVDF  360
PPLPMGLKIS NNNISAPVCN GDSLLVPPIL MHPQPQPPAD IQGARHNNGH AYADIPSSST  420
PSMVRTQQLF PRDLQILVPH TDIVTPQNGS PPDNPVNTPL SASDGMKTIQ LFGVTITSPV  480
QGDTNGAFAS AQVNQVPEGV DDETATEEAS DTSLPDSLTN GHNQDGARL*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldy_A3e-532635921356Auxin response factor 1
4ldy_B3e-532635921356Auxin response factor 1
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.561500.0callus
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO329946580.0
Expression AtlasQ7XSS9-
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_Os04g59430.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs04g59430
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK1094490.0AK109449.1 Oryza sativa Japonica Group cDNA clone:001-113-A09, full insert sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015634416.10.0auxin response factor 13
SwissprotQ7XSS90.0ARFM_ORYSJ; Auxin response factor 13
TrEMBLA0A0D3G2270.0A0A0D3G227_9ORYZ; Auxin response factor
STRINGOS04T0690600-010.0(Oryza sativa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP113553137
Representative plantOGRP1320045
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G77850.14e-77auxin response factor 17
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. 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]