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 Rsa1.0_02796.1_g00002.1
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: 568aa    MW: 63869.7 Da    PI: 6.39
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Rsa1.0_02796.1_g00002.1genomeRGDView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B373.13.3e-23127227198
                              EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-E CS
                       B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDf 79 
                              f+k+lt sd++++g +++ +k+a+e+       +   + +++l+ +d++g +W++k+i+r++++r++lt+GW+ Fv++++L +gD 
  Rsa1.0_02796.1_g00002.1 127 FVKILTASDTSTHGGFSVLRKHATEClpaldmtQ--ATPTQELVTRDLHGFEWRFKHIFRGQPRRHLLTTGWSTFVSSKRLVAGDA 210
                              89****************************9543..445569******************************************** PP

                              EEEEE-SSSEE..EEEEE- CS
                       B3  80 vvFkldgrsefelvvkvfr 98 
                              +vF   + +++ l+v+v+r
  Rsa1.0_02796.1_g00002.1 211 FVFL--RGENGDLRVGVRR 227
                              ****..3488889***998 PP
2Auxin_resp981.3e-32253332183
               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+
  Rsa1.0_02796.1_g00002.1 253 ASHAVLTKTIFLVFYKPRI--SQFIVGVNKYMEAMKHGFSLGTRFRMRFEGEESPERMFTGTIVGIGDLSS-QWPASKWRSLQ 332
                              6899**************8..9**********************************************777.*********97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019364.97E-40112256IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.104.7E-38121242IPR015300DNA-binding pseudobarrel domain
CDDcd100171.44E-19125227No hitNo description
PROSITE profilePS5086312.083127229IPR003340B3 DNA binding domain
SMARTSM010191.3E-20127229IPR003340B3 DNA binding domain
PfamPF023622.9E-21127227IPR003340B3 DNA binding domain
PfamPF065079.7E-30253332IPR010525Auxin response factor
PfamPF023094.3E-8453498IPR033389AUX/IAA domain
SuperFamilySSF542777.85E-12459539No hitNo description
PROSITE profilePS5174525.638462555IPR000270PB1 domain
PfamPF023091.1E-6502548IPR033389AUX/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: 568 aa     Download sequence    Send to blast
MANVDGNDLP TSFSRSYNDA LYTELWKACA GPLVDVPLAE ERVFYFPQGH MEQLVASTNQ  60
GIESEEIPDF KLPPKILCRV LSVMLKAEHE TDEVYAQITL KPEEDQSELT SLDPPIVEPT  120
KQMFHSFVKI LTASDTSTHG GFSVLRKHAT ECLPALDMTQ ATPTQELVTR DLHGFEWRFK  180
HIFRGQPRRH LLTTGWSTFV SSKRLVAGDA FVFLRGENGD LRVGVRRLAR HQSTMPTSVI  240
SSQSMHLGVL ATASHAVLTK TIFLVFYKPR ISQFIVGVNK YMEAMKHGFS LGTRFRMRFE  300
GEESPERMFT GTIVGIGDLS SQWPASKWRS LQVQWDEPTT VQRPDRVSPW EIEPFLSSSS  360
VSTPSQQSQP KCKRSRPVES SVLTPAPPTT FLYGFPQSQD PSTTERNLGG LQAETPPPPA  420
SCYRLFGFDL TSNPPAPIPP DKCQEPITPS AANEPKKQQK SRTRTKVQMQ GIAVGRAVDL  480
TLLKSYDELI KELEEMFEIN KGQLLTRDKW VVVFTDDEGD MMLAGDDPWN EFCKMAKKIF  540
IYSSDEVKKM TTKLKSSSSL ENDESMVD
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldx_A1e-1651835916359Auxin response factor 1
4ldx_B1e-1651835916359Auxin 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_02796.1_g00002.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
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]