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 XP_009116845.1
Organism
Brassica rapa
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica
Family ARF
Protein Properties Length: 559aa    MW: 62715.3 Da    PI: 6.2565
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009116845.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B372.64.9e-23127227198
                     EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSS CS
              B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrs 88 
                     f+k+lt sd++++g +++ +k+a+e+       + ++++  +l+ +d++g +W++k+i+r++++r++lt+GW+ Fv++++L +gD +vF   + +
  XP_009116845.1 127 FVKILTASDTSTHGGFSVLRKHATEClpaldmtQAIPTQ--ELVTRDLHGFEWRFKHIFRGQPRRHLLTTGWSTFVSSKRLVAGDAFVFL--RGE 217
                     89****************************977555555..8************************************************..348 PP

                     EE..EEEEE- CS
              B3  89 efelvvkvfr 98 
                     ++ l+v+v+r
  XP_009116845.1 218 NGDLRVGVRR 227
                     8889***998 PP
2Auxin_resp99.93.5e-33253332183
      Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                     a+ha++t+++F v+Y+Pr   s+F+v+v+k+++a+k+ +s+G+Rf+m+fe+e+s+er ++Gt+vg+ dl++ +Wp S WrsL+
  XP_009116845.1 253 ASHAVNTQTMFLVFYKPRI--SQFIVSVNKYMEAMKHGFSLGTRFRMRFEGEESPERIFTGTIVGIGDLSS-QWPASTWRSLQ 332
                     789***************8..9**********************************************777.*********97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019362.35E-39112256IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.101.3E-37121242IPR015300DNA-binding pseudobarrel domain
CDDcd100176.61E-20125227No hitNo description
PROSITE profilePS5086311.998127229IPR003340B3 DNA binding domain
SMARTSM010192.2E-20127229IPR003340B3 DNA binding domain
PfamPF023624.2E-21127227IPR003340B3 DNA binding domain
PfamPF065071.3E-30253332IPR010525Auxin response factor
PfamPF023093.8E-13449543IPR033389AUX/IAA domain
SuperFamilySSF542773.14E-12452531No hitNo description
PROSITE profilePS5174525.792455547IPR000270PB1 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: 559 aa     Download sequence    Send to blast
MANVDGDDSR SSFPSSYQDQ LYTELWKACA GPLVEVPLVG ERVFYFPQGH MEQLVASTNQ  60
GIESEKIPDF KLPPKILCQV LSVMLKAEHD TDEVYAQITL KPEEDQSEPT SLDPPIVEPT  120
KQMFHSFVKI LTASDTSTHG GFSVLRKHAT ECLPALDMTQ AIPTQELVTR DLHGFEWRFK  180
HIFRGQPRRH LLTTGWSTFV SSKRLVAGDA FVFLRGENGD LRVGVRRLAR HQNTMPASVI  240
SSQSMHLGVL ATASHAVNTQ TMFLVFYKPR ISQFIVSVNK YMEAMKHGFS LGTRFRMRFE  300
GEESPERIFT GTIVGIGDLS SQWPASTWRS LQVQWDEPTT VQRPDKVSPW EIEPFLPSSP  360
ASTPSQQSQP KSKRSKPIES SSLSPGQASF LGVQAEPPPP PASSCYRLFG FDLTSNPPAP  420
IPPDKQPMDT SEAAKCQDPI TPSSVNEPKK QQTSRTRTKV QMQGIAVGRA VDLTLLKSYD  480
ELIKELEEMF EIQGQLLPRD KWIVVFTDDE GDMMLAGDDP WNEFCKMAKK IFIYSSDEVK  540
KMTRRMKSSS SLENEASMD
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A1e-1651935517355Auxin response factor 1
4ldw_A1e-1651935517355Auxin response factor 1
4ldw_B1e-1651935517355Auxin response factor 1
4ldx_A1e-1651935517355Auxin response factor 1
4ldx_B1e-1651935517355Auxin response factor 1
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Bra.309770.0leaf
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
PlantRegMapXP_009116845.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankKT0006080.0KT000608.1 Brassica napus note R1 line auxin response factor 18 (ARF18) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009116845.10.0PREDICTED: auxin response factor 18
SwissprotQ9C5W90.0ARFR_ARATH; Auxin response factor 18
TrEMBLA0A397Y4K60.0A0A397Y4K6_BRACM; Auxin response factor
STRINGBra007632.1-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]