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_Os12g29520.4
Common NameARF24, LOC4352211, Os12g0479400
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: 841aa    MW: 92250.2 Da    PI: 6.7683
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os12g29520.4genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B375.46.5e-24147248199
                       EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-S CS
                B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldg 86 
                       f+k+lt sd++++g +++ +++a+e+       +  ++ +++l+ +d++g +W++++i+r++++r++l++GW+ Fv+a++L +gD ++F   +
  LOC_Os12g29520.4 147 FCKTLTASDTSTHGGFSVLRRHADEClppldmsQ--HPPTQELVAKDLHGVEWRFRHIFRGQPRRHLLQSGWSVFVSAKRLVAGDAFIFL--R 235
                       99*****************************544..455569************************************************..4 PP

                       SSEE..EEEEE-S CS
                B3  87 rsefelvvkvfrk 99 
                        +++el+v+v+r+
  LOC_Os12g29520.4 236 GENGELRVGVRRA 248
                       49999*****996 PP
2Auxin_resp111.86.9e-37273355183
        Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                       a+ha++t+++F+v+Y+Pr+s+seFvv+++ ++++lk++ s+GmRfkm fe+e+++e+r++Gt+vgv d+dp+ W +SkWrsLk
  LOC_Os12g29520.4 273 AWHAVNTGTMFTVYYKPRTSPSEFVVPRDLYKESLKRNHSIGMRFKMTFEGEEAAEQRFTGTIVGVGDSDPSGWADSKWRSLK 355
                       89*******************************************************************************96 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.102.8E-42140262IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019362.94E-41140276IPR015300DNA-binding pseudobarrel domain
CDDcd100177.06E-22145247No hitNo description
SMARTSM010199.8E-24147249IPR003340B3 DNA binding domain
PROSITE profilePS5086311.899147249IPR003340B3 DNA binding domain
PfamPF023628.2E-22147248IPR003340B3 DNA binding domain
PfamPF065073.3E-34273355IPR010525Auxin response factor
PfamPF023091.2E-11700797IPR033389AUX/IAA domain
PROSITE profilePS5174523.837712796IPR000270PB1 domain
SuperFamilySSF542775.89E-12714788No 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
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0009009anatomyplant embryo
PO:0001081developmental stagemature plant embryo stage
PO:0007042developmental stagewhole plant fruit formation stage
Sequence ? help Back to Top
Protein Sequence    Length: 841 aa     Download sequence    Send to blast
MAAAATAAAS PVEGLTGGGG GGGGVDGLFV ELWRACAGPL VTVPAVGERV FYLPQGHIEQ  60
VEASTNQVAE QQGAPLYNLP WKIPCKVMNV ELKAEPDTDE VYAQLTLLPE KQQDGNGSGN  120
GNVSKDKVEE EEVVPPAATE RPRVHSFCKT LTASDTSTHG GFSVLRRHAD ECLPPLDMSQ  180
HPPTQELVAK DLHGVEWRFR HIFRGQPRRH LLQSGWSVFV SAKRLVAGDA FIFLRGENGE  240
LRVGVRRAMR QQANIPSSVI SSHSMHLGVL ATAWHAVNTG TMFTVYYKPR TSPSEFVVPR  300
DLYKESLKRN HSIGMRFKMT FEGEEAAEQR FTGTIVGVGD SDPSGWADSK WRSLKVRWDE  360
AASVPRPDRV SPWQIEPANS PSPVNPLPAP RTKRARPNVL ASSPDLSAVN KEVASKVMAN  420
SQQNGLPRAF HSQENMNLRS RFGDSNELNT SQKLTMWSSG SNQEKNNVSV QRELGSQSWM  480
QMRRPDGSSE ILSGFQPLKD TRNPLSSFPS QISGNRSNTW NTINVHYPDQ NANHNMYPGT  540
WSLMPPNTGF GVNQQNYLMT PDITLPQRSL NAKFGGNGAF TSLRAHGIDQ RSSGWLGHIE  600
PSSHIDDASS SLIKPQPLVI DHNVQKAKGS SCMLFGISLD SPAKPELLIS PPSVAFDGKL  660
QQDALEEDEC SDPSKTVKPL DGAQHDSARE KHQSCPDGTK NIQSKQQNGS SRSCKKVHKQ  720
GIALGRSIDL TKFTCYDELI AELDQMFDFN GELNSSSKNW MVVYTDNEGD MMLVGDDPWN  780
EFCNMVHKIF IYTREEVQKM NPGALNSRSE DSRSTSVERG LVGEGLQGGL STPSLNSENC  840
*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A1e-170163827359Auxin response factor 1
4ldw_A1e-170163827359Auxin response factor 1
4ldw_B1e-170163827359Auxin response factor 1
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Os.183080.0callus| flower| leaf| panicle| root| seed| stem
Expression -- Microarray ? help Back to Top
Source ID E-value
GEO329770790.0
Expression AtlasQ2QQX6-
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_Os12g29520.4
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Phenotype -- Mutation ? help Back to Top
Source ID
RiceGEOs12g29520
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK0652540.0AK065254.1 Oryza sativa Japonica Group cDNA clone:J013002J11, full insert sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015620411.10.0auxin response factor 24 isoform X1
RefseqXP_015620412.10.0auxin response factor 24 isoform X1
SwissprotQ2QQX60.0ARFX_ORYSJ; Auxin response factor 24
TrEMBLI1R6D50.0I1R6D5_ORYGL; Auxin response factor
STRINGOS12T0479400-020.0(Oryza sativa)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G62000.30.0auxin response factor 2
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. Rice Chromosomes 11 and 12 Sequencing Consortia
    The sequence of rice chromosomes 11 and 12, rich in disease resistance genes and recent gene duplications.
    BMC Biol., 2005. 3: p. 20
    [PMID:16188032]
  3. 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]
  4. Li G, et al.
    Rice actin-binding protein RMD is a key link in the auxin-actin regulatory loop that controls cell growth.
    Proc. Natl. Acad. Sci. U.S.A., 2014. 111(28): p. 10377-82
    [PMID:24982173]