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 OMERI01G28330.1
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: 655aa    MW: 71717 Da    PI: 8.0641
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
OMERI01G28330.1genomeOGEView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B378.76.1e-25115216199
                      EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SS CS
               B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgr 87 
                      f+k+lt sd++++g +++p++ ae++       ++    s++l+ +d++g +W++++iyr++++r++lt+GW++Fv+ ++L +gD v+F   + 
  OMERI01G28330.1 115 FCKTLTASDTSTHGGFSVPRRAAEDCfppldhkQLR--PSQELVAKDLHGAKWRFRHIYRGQPRRHLLTTGWSSFVNKKKLVSGDAVLFL--RG 204
                      99**************************99865444..4669************************************************..34 PP

                      SEE..EEEEE-S CS
               B3  88 sefelvvkvfrk 99 
                      +++el+++v+r+
  OMERI01G28330.1 205 DDGELRLGVRRA 216
                      89999****997 PP
2Auxin_resp114.21.2e-37241321182
       Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsL 82 
                      +a++++++svF+++YnPra++se+vv+++k++k+++++v++GmRfk++fe+ed+++rr sG+++gvs++dp+rWp+SkWrsL
  OMERI01G28330.1 241 VADSLKHGSVFHICYNPRATASEYVVPYWKFVKSFNHPVCIGMRFKFHFESEDVNQRR-SGMIAGVSEVDPIRWPGSKWRSL 321
                      578899****************************************************.9********************99 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019362.22E-4799254IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.105.1E-39110218IPR015300DNA-binding pseudobarrel domain
CDDcd100177.26E-23113215No hitNo description
PfamPF023626.0E-23115216IPR003340B3 DNA binding domain
PROSITE profilePS5086313.507115217IPR003340B3 DNA binding domain
SMARTSM010192.8E-24115217IPR003340B3 DNA binding domain
PfamPF065075.0E-31242321IPR010525Auxin 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
Sequence ? help Back to Top
Protein Sequence    Length: 655 aa     Download sequence    Send to blast
MGIDLNNTAS GGEEDAPAPA PVCRDLWHAC AGPVVSLPRR GSAVVYLPQG HLSAAGAGGG  60
IRGEVAVALP PHVACRVVDA ELCVFERNLH GGGIEREDDM EDGDEERKSR MLHMFCKTLT  120
ASDTSTHGGF SVPRRAAEDC FPPLDHKQLR PSQELVAKDL HGAKWRFRHI YRGQPRRHLL  180
TTGWSSFVNK KKLVSGDAVL FLRGDDGELR LGVRRATQLK NEAIFKAFSS ESSKMRTLSA  240
VADSLKHGSV FHICYNPRAT ASEYVVPYWK FVKSFNHPVC IGMRFKFHFE SEDVNQRRSG  300
MIAGVSEVDP IRWPGSKWRS LLVRWEDATD CNSQNRVSPW EIEIVGGSVS VAHSLSASSS  360
KRTKLCPQGN LDVPALYGNG RPDSVETEKF PRVLQGQELM GSRTHRVTCS PQSIDITKSK  420
SFDAWRFLTD ARSCMLGSST SRLPVQYSGY THQSVSFGES IGFPEVLQGQ EISQTVPPFQ  480
GMLPDACSAK SRYELKNYVC TPATMNGLSS ANEGYCLSLS TVPPSPPSSL MLYQTGVPQL  540
ELASKNNDKS GNDSQPALRQ HKLLSETSWD QFKIGKASTP GNATKPGNGG REVDRTSCRL  600
FGFSLTEKII PTDKDGEKEG SYETDCQNPR MLDLFGYNCS TPGALHALCA APLGI
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldy_A4e-932234319353Auxin response factor 1
4ldy_B4e-932234319353Auxin response factor 1
Search in ModeBase
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).
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK0723300.0AK072330.1 Oryza sativa Japonica Group cDNA clone:J023039P13, full insert sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015634503.10.0auxin response factor 3 isoform X2
SwissprotQ5JMM10.0ARFC_ORYSJ; Auxin response factor 3
TrEMBLA0A0E0C7V00.0A0A0E0C7V0_9ORYZ; Auxin response factor
STRINGOGLUM01G35360.10.0(Oryza glumipatula)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP51132756
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G33860.11e-140ARF family protein
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]