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_009138752.1
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: 555aa    MW: 62438.2 Da    PI: 6.3892
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009138752.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B374.31.5e-23127227198
                     EEEE-..-HHHHTT-EE--HHH.HTT.....---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE CS
              B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.....ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsef 90 
                     f+k+lt sd++++g +++ +k+a+e+     +g+ + +++l+ +d++g +W++k+i+r++++r++lt+GW+ Fv++++L +gD +vF   + +++
  XP_009138752.1 127 FVKILTASDTSTHGGFSVLRKHATEClpaldMGQATPTQELVTRDLHGFEWRFKHIFRGQPRRHLLTTGWSTFVSSKRLVAGDAFVFL--RGENG 219
                     89*****************************666666779************************************************..34888 PP

                     ..EEEEE- CS
              B3  91 elvvkvfr 98 
                      l+v+v+r
  XP_009138752.1 220 DLRVGVRR 227
                     89***998 PP
2Auxin_resp96.83.2e-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 S WrsL+
  XP_009138752.1 253 ASHAVVTKTIFLVFYKPRI--SQFIVGVNKYMEAMKHGFSLGTRFRMRFEGEESPERMFTGTIVGIGDLSS-QWPASTWRSLQ 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
SuperFamilySSF1019367.46E-40112256IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.101.1E-37121242IPR015300DNA-binding pseudobarrel domain
CDDcd100171.84E-19125227No hitNo description
SMARTSM010191.1E-20127229IPR003340B3 DNA binding domain
PfamPF023621.5E-21127227IPR003340B3 DNA binding domain
PROSITE profilePS5086312.069127229IPR003340B3 DNA binding domain
PfamPF065071.5E-29253332IPR010525Auxin response factor
PfamPF023091.0E-7443487IPR033389AUX/IAA domain
SuperFamilySSF542771.05E-11449527No hitNo description
PROSITE profilePS5174524.228451543IPR000270PB1 domain
PfamPF023091.2E-6491535IPR033389AUX/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: 555 aa     Download sequence    Send to blast
MANVDGDDLR TSLSRSYNDE LYTELWKACA GPLVEVPLAG EKVFYFPQGH MEQLVASTNQ  60
GIESEEIPDF KLPPKILCRV LSVMLKAEHD TDEVYAQITL KPEEDQSELT SLDPPLVEPT  120
KQMFHSFVKI LTASDTSTHG GFSVLRKHAT ECLPALDMGQ ATPTQELVTR DLHGFEWRFK  180
HIFRGQPRRH LLTTGWSTFV SSKRLVAGDA FVFLRGENGD LRVGVRRLAR HQSTMPTSVI  240
SSQSMHLGVL ATASHAVVTK TIFLVFYKPR ISQFIVGVNK YMEAMKHGFS LGTRFRMRFE  300
GEESPERMFT GTIVGIGDLS SQWPASTWRS LQVQWDEPTT FQRPDRVSPW EIEPFLSSPP  360
VSTPAQQSQP KCKRSRPVES SVLTPAPPSF LYGFPQSQET PSPPPPSASS CYRLFGFDLT  420
SNPPAPIPPD KCQEPITPSA ANEPKKQQKQ RTRTKVIMQG VAVGRAVDLT LLKSYNELIK  480
ELEEMFEIKG QLLTREKWVV VFTDDEGDMM LAGDDPWNEF CKMAKKIFIY SSDEVKKMTT  540
MLKSSSSLEN DESMD
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A1e-1631835716357Auxin response factor 1
4ldw_A1e-1631835716357Auxin response factor 1
4ldw_B1e-1631835716357Auxin response factor 1
4ldx_A1e-1631835716357Auxin response factor 1
4ldx_B1e-1631835716357Auxin 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_009138752.1
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_009138752.10.0PREDICTED: auxin response factor 18
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]