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 RrC7820_p1
Organism
Raphanus raphanistrum
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: 584aa    MW: 65662.1 Da    PI: 6.7064
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC7820_p1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B373.13.5e-23142242198
                 EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE.. CS
          B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefel 92 
                 f+k+lt sd++++g +++ +k+a+e+       +   + +++l+ +d++g +W++k+i+r++++r++lt+GW+ Fv++++L +gD +vF   + +++ l
  RrC7820_p1 142 FVKILTASDTSTHGGFSVLRKHATEClpaldmtQ--ATPTQELVTRDLHGFEWRFKHIFRGQPRRHLLTTGWSTFVSSKRLVAGDAFVFL--RGENGDL 236
                 89****************************9543..445569************************************************..3488889 PP

                 EEEEE- CS
          B3  93 vvkvfr 98 
                 +v+v+r
  RrC7820_p1 237 RVGVRR 242
                 ***998 PP
2Auxin_resp981.4e-32268347183
  Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                 a+ha+ tk++F v+Y+Pr   s+F+v v+k+++a+k+ +s+G+Rf+m+fe+e+s+er ++Gt+vg+ dl++ +Wp SkWrsL+
  RrC7820_p1 268 ASHAVLTKTIFLVFYKPRI--SQFIVGVNKYMEAMKHGFSLGTRFRMRFEGEESPERMFTGTIVGIGDLSS-QWPASKWRSLQ 347
                 6899**************8..9**********************************************777.*********97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019365.23E-40127271IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.105.0E-38136257IPR015300DNA-binding pseudobarrel domain
CDDcd100171.96E-19140242No hitNo description
PfamPF023623.0E-21142242IPR003340B3 DNA binding domain
SMARTSM010191.3E-20142244IPR003340B3 DNA binding domain
PROSITE profilePS5086312.083142244IPR003340B3 DNA binding domain
PfamPF065071.0E-29268347IPR010525Auxin response factor
PfamPF023095.2E-14469564IPR033389AUX/IAA domain
SuperFamilySSF542771.5E-12476555No hitNo description
PROSITE profilePS5174525.765479571IPR000270PB1 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:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0005515Molecular Functionprotein binding
Sequence ? help Back to Top
Protein Sequence    Length: 584 aa     Download sequence    Send to blast
MEMISQPLSQ LLKKNPLQSL HFSVLIIIPG SYNDALYTEL WKACAGPLVD VPLAEERVFY  60
FPQGHMEQLV ASTNQGIESE EIPDFKLPPK ILCRVLSVML KAEHETDEVY AQITLKPEED  120
QSELTSLDPP IVEPTKQMFH SFVKILTASD TSTHGGFSVL RKHATECLPA LDMTQATPTQ  180
ELVTRDLHGF EWRFKHIFRG QPRRHLLTTG WSTFVSSKRL VAGDAFVFLR GENGDLRVGV  240
RRLARHQSTM PTSVISSQSM HLGVLATASH AVLTKTIFLV FYKPRISQFI VGVNKYMEAM  300
KHGFSLGTRF RMRFEGEESP ERMFTGTIVG IGDLSSQWPA SKWRSLQVQW DEPTTVQRPD  360
RVSPWEIEPF LSSSSVSTPS QQSQPKCKRS RPVESSVLTP TPAPTTFLYG FPQSQDPSST  420
ERNLGGLQAD PPPPPPASCY RLFGFDLTSN PPAPTPPDKC QEPITPSAAN EPKKQQKSRT  480
RTKVQMQGIA VGRAVDLTLL KSYDELIKEL EEMFEIKGQL LTRDKWVVVF TDDEGDMMLA  540
GDDPWNEFCK MAKKIFIYSS DEVKKMTTKL KSSSSLENDE SMVD
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A1e-1653037413359Auxin response factor 1
4ldw_A1e-1653037413359Auxin response factor 1
4ldw_B1e-1653037413359Auxin response factor 1
4ldx_A1e-1653037413359Auxin response factor 1
4ldx_B1e-1653037413359Auxin 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}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankJN9794820.0JN979482.1 Brassica rapa subsp. pekinensis auxin response factor 18-2 (ARF18-2) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_013741904.10.0auxin response factor 18-like
SwissprotQ9C5W90.0ARFR_ARATH; Auxin response factor 18
TrEMBLA0A397ZQF90.0A0A397ZQF9_BRACM; Auxin response factor
TrEMBLH9B4E30.0H9B4E3_BRARP; Auxin response factor
STRINGBra014419.1-P0.0(Brassica rapa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM74351841
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G61830.10.0auxin response factor 18
Publications ? help Back to Top
  1. Duarte JM, et al.
    Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis.
    Mol. Biol. Evol., 2006. 23(2): p. 469-78
    [PMID:16280546]
  2. Wójcikowska B,Gaj MD
    Expression profiling of AUXIN RESPONSE FACTOR genes during somatic embryogenesis induction in Arabidopsis.
    Plant Cell Rep., 2017. 36(6): p. 843-858
    [PMID:28255787]