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 OMERI04G12260.4
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: 547aa    MW: 60615.7 Da    PI: 6.5666
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
OMERI04G12260.4genomeOGEView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B375.37.2e-24126226198
                      EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSS CS
               B3   1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrs 88 
                      f+k+lt sd++++g +++ +++aee+      ++++++ ++l+ +d++g +W +++i+r++++r++lt+GW+ Fv++++L +gD ++F   + +
  OMERI04G12260.4 126 FCKTLTASDTSTHGGFSVLRRHAEEClpqldmSQNPPC-QELVAKDLHGTEWHFRHIFRGQPRRHLLTTGWSVFVSSKRLVAGDAFIFL--RGE 216
                      99*****************************7556666.59************************************************..449 PP

                      EE..EEEEE- CS
               B3  89 efelvvkvfr 98 
                      ++el+v+v+r
  OMERI04G12260.4 217 SGELRVGVRR 226
                      999*****97 PP
2Auxin_resp101.11.4e-33252337183
       Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsd...ldpvrWpnSkWrsLk 83 
                      a+ha+st++ F+v+Y+Pr+s+seFvv+v+k+++a k+++svGmRfkm+fe+++++err+sGt++g+     +  + W +S W+sLk
  OMERI04G12260.4 252 ASHAISTGTLFSVFYKPRTSRSEFVVSVNKYLEAKKQNLSVGMRFKMRFEGDEAPERRFSGTIIGIGSvpaMLKSPWADSDWKSLK 337
                      789*************************************************************987611156679********96 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019361.03E-44112255IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.103.7E-41123241IPR015300DNA-binding pseudobarrel domain
CDDcd100176.18E-22124226No hitNo description
PROSITE profilePS5086311.533126228IPR003340B3 DNA binding domain
PfamPF023621.3E-21126226IPR003340B3 DNA binding domain
SMARTSM010191.1E-20126228IPR003340B3 DNA binding domain
PfamPF065079.2E-32252337IPR010525Auxin response factor
PfamPF023094.4E-7341433IPR033389AUX/IAA domain
PROSITE profilePS5174523.136397485IPR000270PB1 domain
SuperFamilySSF542777.85E-10399470No 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: 547 aa     Download sequence    Send to blast
MAAAMEMAAN PGGSGTCSDA LFRELWHACA GPLVTVPKRG ERVYYFPQGH MEQLEASTNQ  60
QLDQYLPMFN LPSKILCSVV NVELRAEADS DEVYAQIMLQ PEADQSELTS LDPEPQDLEK  120
CTAHSFCKTL TASDTSTHGG FSVLRRHAEE CLPQLDMSQN PPCQELVAKD LHGTEWHFRH  180
IFRGQPRRHL LTTGWSVFVS SKRLVAGDAF IFLRGESGEL RVGVRRLMRQ VNNMPSSVIS  240
SHSMHLGVLA TASHAISTGT LFSVFYKPRT SRSEFVVSVN KYLEAKKQNL SVGMRFKMRF  300
EGDEAPERRF SGTIIGIGSV PAMLKSPWAD SDWKSLKPPL RNKRARPPAS PSVVAELPPS  360
FDVDSDQISQ PSNGNKSDAP GTSSERSPLE SQSRQVRSCT KVIMQGMAVG RAVDLTKLNS  420
YGDLRRKLEE MFDIQGDLCP TLKRWQVVYT DDEDDMMLVG DDPWDMVKRI YIYSYEEAKL  480
LAPKSKLPVI GDTIKLSGMN SSHESVDLDN HASEVEWVEG AVMGFGRQWV EAAASRHLRS  540
GGSAGAG
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A0.013371332Auxin response factor 1
4ldw_A0.013371332Auxin response factor 1
4ldw_B0.013371332Auxin 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
GenBankAK0649250.0AK064925.1 Oryza sativa Japonica Group cDNA clone:J013000N16, full insert sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015636800.10.0auxin response factor 9 isoform X3
SwissprotQ0JCZ40.0ARFI_ORYSJ; Auxin response factor 9
TrEMBLA0A0E0DEN50.0A0A0E0DEN5_9ORYZ; Auxin response factor
STRINGORUFI04G14900.10.0(Oryza rufipogon)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G59750.40.0auxin 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]