PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Home  TFext  BLAST  Prediction  Download  Help  About  Links  PlantRegMap
(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Rsa1.0_07665.1_g00001.1
Organism
Raphanus sativus
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus
Family ARF
Protein Properties Length: 782aa    MW: 86189.7 Da    PI: 6.4674
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Rsa1.0_07665.1_g00001.1genomeRGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B375.36.8e-24173274199
                              EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EE CS
                       B3   1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfv 80 
                              f+k+lt sd++++g +++p++ ae++      + +++ s++l+ +d++g +W++++iyr++++r++lt+GW+ Fv+++ L +gD v
  Rsa1.0_07665.1_g00001.1 173 FCKTLTASDTSTHGGFSVPRRAAEDCfapldyK-QQRPSQELIAKDLHGVEWKFRHIYRGQPRRHLLTTGWSIFVSQKSLVSGDAV 257
                              99****************************963.3445679********************************************* PP

                              EEEE-SSSEE..EEEEE-S CS
                       B3  81 vFkldgrsefelvvkvfrk 99 
                              +F   +++++el+++++r+
  Rsa1.0_07665.1_g00001.1 258 LFL--RDENGELRLGIRRS 274
                              ***..5689999****986 PP
2Auxin_resp1224.4e-40298379182
               Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsL 82 
                              +a+a+++ks+F+v+Y+Pra+++eFv+++ek+ +++++++++G+Rf+m+fe++ds+err++G+v+gv d+dp+rWpnSkWr+L
  Rsa1.0_07665.1_g00001.1 298 VANAVTNKSMFHVFYSPRATHAEFVIPYEKYITSIRNPICIGTRFRMRFEMDDSPERRCAGVVTGVCDSDPYRWPNSKWRCL 379
                              689******************************************************************************9 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.103.6E-40164285IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019366.41E-42167286IPR015300DNA-binding pseudobarrel domain
CDDcd100173.20E-21171273No hitNo description
PfamPF023629.0E-22173274IPR003340B3 DNA binding domain
SMARTSM010193.7E-23173275IPR003340B3 DNA binding domain
PROSITE profilePS5086313.422173275IPR003340B3 DNA binding domain
PfamPF065071.4E-33298379IPR010525Auxin response factor
SuperFamilySSF542774.32E-10656734No hitNo description
PROSITE profilePS5174521.899659741IPR000270PB1 domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009725Biological Processresponse to hormone
GO:0010050Biological Processvegetative phase change
GO:0010158Biological Processabaxial cell fate specification
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0005515Molecular Functionprotein binding
Sequence ? help Back to Top
Protein Sequence    Length: 782 aa     Download sequence    Send to blast
MEFDLNTEFA EVEEEENDEG GGARIEKGRL GVSPSSSSSC SSGSSSSSSS TTASASSIYS  60
ELWHACAGPL TCLPKKGNVV VYFPQGHLEQ VALVPYSTPL DIPKLDLSPQ IFCRVANVHL  120
LANKETDEVY TQVTLLPLQE LSMLNGEGKE VRESGGDEEK NGSSSVKRTP HMFCKTLTAS  180
DTSTHGGFSV PRRAAEDCFA PLDYKQQRPS QELIAKDLHG VEWKFRHIYR GQPRRHLLTT  240
GWSIFVSQKS LVSGDAVLFL RDENGELRLG IRRSARPRNG LPDSIIQKSS SSNILSLVAN  300
AVTNKSMFHV FYSPRATHAE FVIPYEKYIT SIRNPICIGT RFRMRFEMDD SPERRCAGVV  360
TGVCDSDPYR WPNSKWRCLL VRWDESFMSD HQERVSPWEI DPSGSLPPLS IQSSPRPKRP  420
WAGLLGTTTP QGNPITERGG FLDFEESVRP SKVLQGQENI GSVASSSPSL QGFDVMNRRI  480
LDFAEMQSHA NPVLLSSTRV KDRFGEFVDS TSLDLDRFPR VLQGQEICSL RSFPQIAGFT  540
PASASGSPSL GYTGGPFAYQ ANKSSFYPLA SQGIRSSHIP FQNPYNAGGD KSLSHPSGRK  600
FDAQSEGGLP KSVPFKIDVM GTEKGGDVNM NASTTGCKLF GFSLPVETPA SNPQSSSKRI  660
CTKVHKQGSL VGRAIDLSRL NGYNDLLTEL ERLFNMEGLL RDPEKGWRIL YTDSENDMMV  720
VGDDPWHDFC NVVLKIHLYT KEEVENGNDD NKSCLEQAAL MMEASKSSSV SQPDSSPTVT  780
RV
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldy_A1e-1125540516357Auxin response factor 1
4ldy_B1e-1125540516357Auxin 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). Could act as transcriptional activator or repressor. Formation of heterodimers with Aux/IAA proteins may alter their ability to modulate early auxin response genes expression. {ECO:0000269|PubMed:12036261}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapRsa1.0_07665.1_g00001.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankJN9794640.0JN979464.1 Brassica rapa subsp. pekinensis auxin response factor 4 (ARF4) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018446640.10.0PREDICTED: auxin response factor 4
RefseqXP_018446641.10.0PREDICTED: auxin response factor 4
RefseqXP_018446832.10.0PREDICTED: auxin response factor 4-like
SwissprotQ9ZTX90.0ARFD_ARATH; Auxin response factor 4
TrEMBLA0A0D3ED440.0A0A0D3ED44_BRAOL; Auxin response factor
STRINGBo9g143570.10.0(Brassica oleracea)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM95302636
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G60450.10.0auxin response factor 4
Publications ? help Back to Top
  1. Ozerova LV,Krasnikova MS,Troitsky AV,Solovyev AG,Morozov SY
    TAS3 Genes for small ta-siARF RNAs in plants belonging to subtribe Senecioninae: occurrence of prematurely terminated RNA precursors.
    Mol. Gen. Mikrobiol. Virusol., 2013.
    [PMID:24003511]
  2. Machida C,Nakagawa A,Kojima S,Takahashi H,Machida Y
    The complex of ASYMMETRIC LEAVES (AS) proteins plays a central role in antagonistic interactions of genes for leaf polarity specification in Arabidopsis.
    Wiley Interdiscip Rev Dev Biol, 2015 Nov-Dec. 4(6): p. 655-71
    [PMID:26108442]
  3. Pashkovskiy PP,Kartashov AV,Zlobin IE,Pogosyan SI,Kuznetsov VV
    Blue light alters miR167 expression and microRNA-targeted auxin response factor genes in Arabidopsis thaliana plants.
    Plant Physiol. Biochem., 2016. 104: p. 146-54
    [PMID:27031426]
  4. Matsumura Y, et al.
    A genetic link between epigenetic repressor AS1-AS2 and a putative small subunit processome in leaf polarity establishment of Arabidopsis.
    Biol Open, 2016. 5(7): p. 942-54
    [PMID:27334696]
  5. Guan C, et al.
    Spatial Auxin Signaling Controls Leaf Flattening in Arabidopsis.
    Curr. Biol., 2017. 27(19): p. 2940-2950.e4
    [PMID:28943086]
  6. Liu Z, et al.
    ARF2-ARF4 and ARF5 are Essential for Female and Male Gametophyte Development in Arabidopsis.
    Plant Cell Physiol., 2018. 59(1): p. 179-189
    [PMID:29145642]