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_Os01g13520.2
Common NameOsJ_01030
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: 548aa    MW: 60651.2 Da    PI: 6.4586
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os01g13520.2genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B351.91.4e-168703498
                      SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..EEEEE- CS
                B3 34 ktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelvvkvfr 98
                      ++l+ +d++g +W++k+iyr++++r++lt+GW+ Fv +++L +gD +v    +++++e +v+v+r
  LOC_Os01g13520.2  8 QELITKDLHGSEWRFKHIYRGQPRRHLLTTGWSTFVTSKKLISGDAFVYL--RSETGEQRVGVRR 70
                      47899******************************************999..4477778999997 PP
2Auxin_resp97.42.1e-3296177183
        Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                       a+ha++t+s+F v+Y+Pr s+s+++v+v+k+++a kv + vGmRfkm+fe+ed++ +++sGt+vg  d  +++W++S+W+sLk
  LOC_Os01g13520.2  96 ASHAIKTNSIFLVYYRPRLSQSQYIVSVNKYLAASKVGFNVGMRFKMSFEGEDVPVKKFSGTIVGEGD-LSLQWSGSEWKSLK 177
                       789*****************************************************************.566*********96 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS5086311.589172IPR003340B3 DNA binding domain
Gene3DG3DSA:2.40.330.103.9E-20285IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019366.8E-20299IPR015300DNA-binding pseudobarrel domain
PfamPF023628.5E-14770IPR003340B3 DNA binding domain
CDDcd100171.78E-9870No hitNo description
PfamPF065075.0E-2996177IPR010525Auxin response factor
PfamPF023093.0E-7429479IPR033389AUX/IAA domain
SuperFamilySSF542771.91E-9439516No hitNo description
PROSITE profilePS5174525.447443532IPR000270PB1 domain
Gene3DG3DSA:3.10.20.2401.1E-4445508No hitNo description
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
Sequence ? help Back to Top
Protein Sequence    Length: 548 aa     Download sequence    Send to blast
MSMATPTQEL ITKDLHGSEW RFKHIYRGQP RRHLLTTGWS TFVTSKKLIS GDAFVYLRSE  60
TGEQRVGVRR LVQKQSTMPA SVISSQSMHL GVLASASHAI KTNSIFLVYY RPRLSQSQYI  120
VSVNKYLAAS KVGFNVGMRF KMSFEGEDVP VKKFSGTIVG EGDLSLQWSG SEWKSLKVQW  180
DEVTNVNGPE RVSPWEIETC DGTAPAINVP LQSATKNKRP REPSETIDLQ SLEPAQEFWL  240
SGMPQQHEKT GIGSSEPNCI SGHQVVWPGE HPGYGAVSSS VCQNPLVLES WLKDFNSSNK  300
GVSPTLSEIS QKIFQVTSNE ARIATWPARS AYQAEEPTSK LSSNTAACGY RTEEVAPNAS  360
KVVEGKKEPA MFRLFGVDLM KCTSISTTTD DKSSVGAGEA SAKGTGSHED SGQLSAFSKV  420
TKEHIAADES PQEIQSHQNY TARTRIKVQM HGNAVGRAVD LANLDGYEQL MNELEEMFNI  480
KDLKQKWKVA FTDDEGDTME VGDDPWLEFC QMVRKIVLYP IEDEKKIEPH PKLLSSANPE  540
QDQKTGF*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A6e-861198155353Auxin response factor 1
4ldw_A6e-861198155353Auxin response factor 1
4ldw_B6e-861198155353Auxin response factor 1
4ldx_A7e-861198155353Auxin response factor 1
4ldx_B7e-861198155353Auxin response factor 1
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.222690.0callus| flower| leaf| panicle| root| seed
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO2139591530.0
Expression AtlasB9EUK4-
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_Os01g13520.2
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By auxin under light or dark conditions. {ECO:0000269|PubMed:17408882}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs01g13520
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAB0713000.0AB071300.1 Oryza sativa OsARF16 mRNA for auxin response factor 16, partial cds.
GenBankAK0640070.0AK064007.1 Oryza sativa Japonica Group cDNA clone:001-124-G08, full insert sequence.
GenBankAK1025210.0AK102521.1 Oryza sativa Japonica Group cDNA clone:J033095P08, full insert sequence.
GenBankEU8470080.0EU847008.1 Oryza sativa Japonica Group clone KCS385B05 auxin response factor mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015622434.10.0auxin response factor 1
SwissprotQ5NB850.0ARFA_ORYSJ; Auxin response factor 1
TrEMBLB9EUK40.0B9EUK4_ORYSJ; Auxin response factor
STRINGOS01T0236300-010.0(Oryza sativa)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G59750.31e-124auxin response factor 1
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]