PlantTFDB
Plant Transcription Factor Database
v4.0
Previous version: v1.0, v2.0, v3.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID LOC_Os12g29520.1
Common NameARF24, LOC4352211, Os12g0479400
Organism
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: 842aa    MW: 92307.3 Da    PI: 6.7683
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
LOC_Os12g29520.1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B375.46.5e-24148249199
                       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_Os12g29520.1 148 FCKTLTASDTSTHGGFSVLRRHADEClppldmsQ--HPPTQELVAKDLHGVEWRFRHIFRGQPRRHLLQSGWSVFVSAKRLVAGDAFIFL--R 236
                       99*****************************544..455569************************************************..4 PP

                       SSEE..EEEEE-S CS
                B3  87 rsefelvvkvfrk 99 
                        +++el+v+v+r+
  LOC_Os12g29520.1 237 GENGELRVGVRRA 249
                       49999*****996 PP

2Auxin_resp111.86.9e-37274356183
        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_Os12g29520.1 274 AWHAVNTGTMFTVYYKPRTSPSEFVVPRDLYKESLKRNHSIGMRFKMTFEGEEAAEQRFTGTIVGVGDSDPSGWADSKWRSLK 356
                       89*******************************************************************************96 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019362.94E-41141277IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.102.8E-42141263IPR015300DNA-binding pseudobarrel domain
CDDcd100177.08E-22146248No hitNo description
SMARTSM010199.8E-24148250IPR003340B3 DNA binding domain
PfamPF023628.3E-22148249IPR003340B3 DNA binding domain
PROSITE profilePS5086311.899148250IPR003340B3 DNA binding domain
PfamPF065073.3E-34274356IPR010525Auxin response factor
PfamPF023091.2E-11701798IPR033389AUX/IAA domain
PROSITE profilePS5174523.837713797IPR000270PB1 domain
SuperFamilySSF542775.89E-12715789No 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: 842 aa     Download sequence    Send to blast
MAAAATAAAS PVEGLTGGGG GGGGGVDGLF VELWRACAGP LVTVPAVGER VFYLPQGHIE  60
QVEASTNQVA EQQGAPLYNL PWKIPCKVMN VELKAEPDTD EVYAQLTLLP EKQQDGNGSG  120
NGNVSKDKVE EEEVVPPAAT ERPRVHSFCK TLTASDTSTH GGFSVLRRHA DECLPPLDMS  180
QHPPTQELVA KDLHGVEWRF RHIFRGQPRR HLLQSGWSVF VSAKRLVAGD AFIFLRGENG  240
ELRVGVRRAM RQQANIPSSV ISSHSMHLGV LATAWHAVNT GTMFTVYYKP RTSPSEFVVP  300
RDLYKESLKR NHSIGMRFKM TFEGEEAAEQ RFTGTIVGVG DSDPSGWADS KWRSLKVRWD  360
EAASVPRPDR VSPWQIEPAN SPSPVNPLPA PRTKRARPNV LASSPDLSAV NKEVASKVMA  420
NSQQNGLPRA FHSQENMNLR SRFGDSNELN TSQKLTMWSS GSNQEKNNVS VQRELGSQSW  480
MQMRRPDGSS EILSGFQPLK DTRNPLSSFP SQISGNRSNT WNTINVHYPD QNANHNMYPG  540
TWSLMPPNTG FGVNQQNYLM TPDITLPQRS LNAKFGGNGA FTSLRAHGID QRSSGWLGHI  600
EPSSHIDDAS SSLIKPQPLV IDHNVQKAKG SSCMLFGISL DSPAKPELLI SPPSVAFDGK  660
LQQDALEEDE CSDPSKTVKP LDGAQHDSAR EKHQSCPDGT KNIQSKQQNG SSRSCKKVHK  720
QGIALGRSID LTKFTCYDEL IAELDQMFDF NGELNSSSKN WMVVYTDNEG DMMLVGDDPW  780
NEFCNMVHKI FIYTREEVQK MNPGALNSRS EDSRSTSVER GLVGEGLQGG LSTPSLNSEN  840
C*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldx_B1e-170193839359Auxin response factor 1
4ldx_A1e-170193839359Auxin response factor 1
4ldw_B1e-170193839359Auxin response factor 1
4ldw_A1e-170193839359Auxin response factor 1
4ldv_A1e-170193839359Auxin 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 binds specifically to the DNA sequence 5'-TGTCTC-3' found in the auxin-responsive promoter elements (AuxREs).
Cis-element ? help Back to Top
SourceLink
PlantRegMapLOC_Os12g29520.1
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_015620411.10.0PREDICTED: auxin response factor 24 isoform X1
RefseqXP_015620412.10.0PREDICTED: auxin response factor 24 isoform X1
SwissprotQ2QQX60.0ARFX_ORYSJ; Auxin response factor 24
TrEMBLI1R6D50.0I1R6D5_ORYGL; Auxin response factor
STRINGLOC_Os12g29520.10.0(Oryza sativa Japonica Group)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
Representative plantOGRP5501582
MonocotsOGMP117836111
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. 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]
  2. 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]