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 RrC243_p5
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: 573aa    MW: 64158 Da    PI: 6.2566
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC243_p5genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B374.71.1e-23123223198
                EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE..E CS
         B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefelv 93 
                f+k+lt sd++++g +++ +k+a+e+       +   + +++l+ +d++g +W++k+i+r++++r++lt+GW+ Fv++++L +gD +vF   + +++el+
  RrC243_p5 123 FVKILTASDTSTHGGFSVLRKHATEClpaldmtQ--ATPTQELVTRDLHGFEWRFKHIFRGQPRRHLLTTGWSTFVSSKRLVAGDAFVFL--RGENGELR 218
                89****************************9543..445569************************************************..449999** PP

                EEEE- CS
         B3  94 vkvfr 98 
                v+v+r
  RrC243_p5 219 VGVRR 223
                ***98 PP
2Auxin_resp99.35.2e-33249328183
  Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                 a+ha++t+s+F v+Y+Pr   s+F+v v+k+++a+k+ +s+G+Rf+m+fe+e+s+er ++Gt+vgv dl++ +Wp S WrsL+
   RrC243_p5 249 ASHAVNTQSMFLVFYKPRI--SQFIVGVNKYMEAMKHGFSLGTRFRMRFEGEESPERIFTGTIVGVGDLSS-QWPASTWRSLQ 328
                 789***************8..9**********************************************777.*********97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019366.28E-40108252IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.103.3E-38116238IPR015300DNA-binding pseudobarrel domain
CDDcd100172.36E-20121223No hitNo description
PfamPF023621.2E-21123223IPR003340B3 DNA binding domain
PROSITE profilePS5086312.224123225IPR003340B3 DNA binding domain
SMARTSM010194.6E-21123225IPR003340B3 DNA binding domain
PfamPF065072.4E-30249328IPR010525Auxin response factor
PfamPF023093.9E-7462505IPR033389AUX/IAA domain
SuperFamilySSF542775.79E-12465545No hitNo description
PROSITE profilePS5174525.692469561IPR000270PB1 domain
PfamPF023095.5E-6509557IPR033389AUX/IAA 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: 573 aa     Download sequence    Send to blast
MENVDGDDSR STYQDQLYTE LWKACAGPLV DVPLTGERVF YFPQGHMEQL VASTNQGIES  60
EKIPDFKLPP KILCEVLNVT LKAEHETDEV YAQITLKPEE DQSEPTSLDQ PIVEPAKQMF  120
HSFVKILTAS DTSTHGGFSV LRKHATECLP ALDMTQATPT QELVTRDLHG FEWRFKHIFR  180
GQPRRHLLTT GWSTFVSSKR LVAGDAFVFL RGENGELRVG VRRLARHQNT MPASVISSQS  240
MHLGVLATAS HAVNTQSMFL VFYKPRISQF IVGVNKYMEA MKHGFSLGTR FRMRFEGEES  300
PERIFTGTIV GVGDLSSQWP ASTWRSLQVQ WDEPTTVQRP DKVSPWEIEP FLPSSPVSAP  360
AQQSQPKSKR SKPIESSVLS PGQASFFPLS QDPTNASLKQ FQAEALPPPP PPPPASCSYR  420
LFGFDLTSNP AAPIPPDKQP VDTCGGAAKC QDPITPTSAN EPKKQQTSRT RTKVQMQGIA  480
VGRAVDLTLL KSYDELIKEL EVMFEIQGQL LPRDKWIVVF TDDEGDMMLA GDDPWNEFCK  540
MAKKIFIYSS DEVKKMTRRI KSFSSLENEV SMD
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A1e-1651535117355Auxin response factor 1
4ldw_A1e-1651535117355Auxin response factor 1
4ldw_B1e-1651535117355Auxin response factor 1
4ldx_A1e-1651535117355Auxin response factor 1
4ldx_B1e-1651535117355Auxin 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
GenBankJN9794810.0JN979481.1 Brassica rapa subsp. pekinensis auxin response factor 18-1 (ARF18-1) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018492510.10.0PREDICTED: auxin response factor 18
SwissprotQ9C5W90.0ARFR_ARATH; Auxin response factor 18
TrEMBLA0A0D3DUY10.0A0A0D3DUY1_BRAOL; Auxin response factor
STRINGBo8g097320.10.0(Brassica oleracea)
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]