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 OMERI04G24630.2
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: 1665aa    MW: 185095 Da    PI: 5.9772
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
OMERI04G24630.2genomeOGEView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B370.12.8e-22183284199
                      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+        ++++++  +l+ +d +  +W++++i+r++++r++lt+GW+ Fv+a++L +gD+v+F   ++
  OMERI04G24630.2 183 FCKTLTASDTSTHGGFSVPRRAAERVfppldftQQPPAQ--ELIARDIHDIEWKFRHIFRGQPKRHLLTTGWSVFVSAKRLVAGDSVLFI--WN 272
                      99***********************9*****86555544..8************************************************..88 PP

                      SEE..EEEEE-S CS
               B3  88 sefelvvkvfrk 99 
                      ++ +l+++++r+
  OMERI04G24630.2 273 EKNQLLLGIRRA 284
                      99999****997 PP
2B370.12.8e-229831084199
                       EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE- CS
               B3    1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkld 85  
                       f+k+lt sd++++g +++p++ ae+        ++++++  +l+ +d +  +W++++i+r++++r++lt+GW+ Fv+a++L +gD+v+F   
  OMERI04G24630.2  983 FCKTLTASDTSTHGGFSVPRRAAERVfppldftQQPPAQ--ELIARDIHDIEWKFRHIFRGQPKRHLLTTGWSVFVSAKRLVAGDSVLFI-- 1070
                       99***********************9*****86555544..8************************************************.. PP

                       SSSEE..EEEEE-S CS
               B3   86 grsefelvvkvfrk 99  
                       ++++ +l+++++r+
  OMERI04G24630.2 1071 WNEKNQLLLGIRRA 1084
                       8899999****997 PP
3Auxin_resp111.49.1e-37309392183
       Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalk.vkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                      aahaa+t+s F+++YnPras+seFv++++k+ ka+  +++svGmRf+m fete+ss rr++Gt++ vsd+dpvrWp S Wrs+k
  OMERI04G24630.2 309 AAHAAATNSRFTIFYNPRASPSEFVIPLSKYIKAVFhTRISVGMRFRMLFETEESSVRRYMGTITEVSDADPVRWPSSYWRSVK 392
                      79*******************************986599******************************************985 PP
4Auxin_resp111.49.1e-3711091192183
       Auxin_resp    1 aahaastksvFevvYnPrastseFvvkvekvekalk.vkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83  
                       aahaa+t+s F+++YnPras+seFv++++k+ ka+  +++svGmRf+m fete+ss rr++Gt++ vsd+dpvrWp S Wrs+k
  OMERI04G24630.2 1109 AAHAAATNSRFTIFYNPRASPSEFVIPLSKYIKAVFhTRISVGMRFRMLFETEESSVRRYMGTITEVSDADPVRWPSSYWRSVK 1192
                       79*******************************986599******************************************985 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019362.09E-47168312IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.107.0E-41175298IPR015300DNA-binding pseudobarrel domain
CDDcd100171.59E-20182283No hitNo description
PfamPF023621.9E-20183284IPR003340B3 DNA binding domain
PROSITE profilePS5086312.224183285IPR003340B3 DNA binding domain
SMARTSM010191.4E-23183285IPR003340B3 DNA binding domain
PfamPF065073.8E-32309392IPR010525Auxin response factor
SuperFamilySSF542775.4E-6762837No hitNo description
PROSITE profilePS5174521.572766854IPR000270PB1 domain
SuperFamilySSF1019362.09E-479681112IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.107.0E-419751098IPR015300DNA-binding pseudobarrel domain
CDDcd100171.59E-209821083No hitNo description
PfamPF023621.9E-209831084IPR003340B3 DNA binding domain
PROSITE profilePS5086312.2249831085IPR003340B3 DNA binding domain
SMARTSM010191.4E-239831085IPR003340B3 DNA binding domain
PfamPF065073.8E-3211091192IPR010525Auxin response factor
PfamPF023093.9E-715591650IPR033389AUX/IAA domain
SuperFamilySSF542773.53E-715621641No hitNo description
PROSITE profilePS5174524.03715661650IPR000270PB1 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:0009908Biological Processflower development
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0005515Molecular Functionprotein binding
Sequence ? help Back to Top
Protein Sequence    Length: 1665 aa     Download sequence    Send to blast
MVAISELGLR VCASLVWSEE EEMSSSSAAS IGPPQPPPPP APPEEEKKCL NSELWHACAG  60
PLVCLPTVGT RVVYFPQGHS EQVAASTNKE VEGHIPNYPN LPAQLICQLH DVTMHADVET  120
DEVYAQMTLQ PLNPVRRLGF LHDVCSAELL MVWRSEIFYA QEQNDAYLPA EMGIMSKQPT  180
NYFCKTLTAS DTSTHGGFSV PRRAAERVFP PLDFTQQPPA QELIARDIHD IEWKFRHIFR  240
GQPKRHLLTT GWSVFVSAKR LVAGDSVLFI WNEKNQLLLG IRRASRPQTV MPSSVLSSDS  300
MHIGLLAAAA HAAATNSRFT IFYNPRASPS EFVIPLSKYI KAVFHTRISV GMRFRMLFET  360
EESSVRRYMG TITEVSDADP VRWPSSYWRS VKVGWDESTA GERPPRVSLW EIEPLTTFPM  420
YPSLFPLRVK HPWYSGVASL HDDSNALMWL RGVAGEGGFQ SLNFQSPGIG SWGQQRLHPS  480
LLSSDHDQYQ AVVAAAAASQ SGGYLKQQFL HLQQPMQSPQ EHCNLNPLLQ QQILQQASQQ  540
QIINPDAQNI QTMLSPSAIQ QQLQQLQQMQ QVQNDQKQKI QPDQSYQVPT SAVLPSPTSL  600
PSHLREKFGF SDPNANSSSF ITSSSSDNML DSSFLQGSSK AVDLSRFNQP VASEQQQQQQ  660
AWKQKFMGSQ SVSFGGSVLH NSPTSKDGSV ENKIGRDVQN QSLFSPQVDS SSLLYNMVPN  720
LTSNVSDGNL STIPSGSTYL QNAMYGCLDD SSGLLQNTGE NDPATRTFVK VYKSGSVGRS  780
LDITRFSNYA ELREELGQMF GIKGQLDDPD RSGWQLVFVD RENDVLLLGD DPWELRVCAS  840
LVWSEEEEMS SSSAASIGPP QPPPPPAPPE EEKKCLNSEL WHACAGPLVC LPTVGTRVVY  900
FPQGHSEQVA ASTNKEVEGH IPNYPNLPAQ LICQLHDVTM HADVETDEVY AQMTLQPLNP  960
QEQNDAYLPA EMGIMSKQPT NYFCKTLTAS DTSTHGGFSV PRRAAERVFP PLDFTQQPPA  1020
QELIARDIHD IEWKFRHIFR GQPKRHLLTT GWSVFVSAKR LVAGDSVLFI WNEKNQLLLG  1080
IRRASRPQTV MPSSVLSSDS MHIGLLAAAA HAAATNSRFT IFYNPRASPS EFVIPLSKYI  1140
KAVFHTRISV GMRFRMLFET EESSVRRYMG TITEVSDADP VRWPSSYWRS VKVGWDESTA  1200
GERPPRVSLW EIEPLTTFPM YPSLFPLRVK HPWYSGVASL HDDSNALMWL RGVAGEGGFQ  1260
SLNFQSPGIG SWGQQRLHPS LLSSDHDQYQ AVVAAAAASQ SGGYLKQQFL HLQQPMQSPQ  1320
EHCNLNPLLQ QQILQQASQQ QIINPDAQNI QTMLSPSAIQ QQLQQLQQMQ QVQNDQKQKI  1380
QPDQSYQVPT SAVLPSPTSL PSHLREKFGF SDPNANSSSF ITSSSSDNML DSSFLQGSSK  1440
AVDLSRFNQP VASEQQQQQQ AWKQKFMGSQ SVSFGGSVLH NSPTSKDGSV ENKIGRDVQN  1500
QSLFSPQVDS SSLLYNMVPN LTSNVSDGNL STIPSGSTYL QNAMYGCLDD SSGLLQNTGE  1560
NDPATRTFVK VYKSGSVGRS LDITRFSNYA ELREELGQMF GIKGQLDDPD RSGWQLVFVD  1620
RENDVLLLGD DPWESFVNSV WYIKILSPED VHKMGKQGND PRYLS
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldu_A1e-15446121347388Auxin response factor 5
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).
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
GenBankAK0714550.0AK071455.1 Oryza sativa Japonica Group cDNA clone:J023093B04, full insert sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015636874.10.0auxin response factor 12 isoform X3
SwissprotQ0J9510.0ARFL_ORYSJ; Auxin response factor 12
SwissprotQ258Y50.0ARFL_ORYSI; Auxin response factor 12
TrEMBLA0A0E0DJY40.0A0A0E0DJY4_9ORYZ; Auxin response factor
STRINGOMERI04G24270.50.0(Oryza meridionalis)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G30330.10.0auxin response factor 6
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. Qi Y, et al.
    OsARF12, a transcription activator on auxin response gene, regulates root elongation and affects iron accumulation in rice (Oryza sativa).
    New Phytol., 2012. 193(1): p. 109-20
    [PMID:21973088]
  3. Shen WJ,Ruan XL,Li XS,Zhao Q,Li HP
    RNA silencing suppressor Pns11 of rice gall dwarf virus induces virus-like symptoms in transgenic rice.
    Arch. Virol., 2012. 157(8): p. 1531-9
    [PMID:22592958]
  4. Wang S, et al.
    Auxin response factor (OsARF12), a novel regulator for phosphate homeostasis in rice (Oryza sativa).
    New Phytol., 2014. 201(1): p. 91-103
    [PMID:24111723]
  5. Fan J, et al.
    Infection of Ustilaginoidea virens intercepts rice seed formation but activates grain-filling-related genes.
    J Integr Plant Biol, 2015. 57(6): p. 577-90
    [PMID:25319482]