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_009103678.1
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: 705aa    MW: 77897.9 Da    PI: 7.57
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009103678.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B375.94.6e-24112213199
                     EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSS CS
              B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrs 88 
                     f k+lt+sd+++ g +++p+ +ae++        +++ +  t++ +d +g++W++++iyr++++r++lt+GW+ Fv++++L +gD++vF   +++
  XP_009103678.1 112 FAKTLTQSDANNGGGFSVPRYCAETIfprldytAEPPVQ--TVIAKDIHGETWKFRHIYRGTPRRHLLTTGWSTFVNQKKLIAGDSIVFL--RSE 202
                     89****************************987555555..8************************************************..458 PP

                     EE..EEEEE-S CS
              B3  89 efelvvkvfrk 99 
                     ++ l+v+++r+
  XP_009103678.1 203 TGDLCVGIRRA 213
                     8999****996 PP
2Auxin_resp114.41e-37281364183
      Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrl.sGtvvgvsdldpvrWpnSkWrsLk 83 
                     a+ +a+ +++FevvY+Prast+eF+vk+++v++a++++++ GmRfkmafetedss++++ +Gtv++v+ +dp+rWpnS+Wr+L+
  XP_009103678.1 281 AVARAACGQAFEVVYYPRASTPEFCVKASDVRSAMRIRWCSGMRFKMAFETEDSSRISWfMGTVSAVQVADPIRWPNSPWRLLQ 364
                     56778899**************************************************************************97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.105.7E-37104216IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019362.35E-29105215IPR015300DNA-binding pseudobarrel domain
CDDcd100172.18E-21111212No hitNo description
SMARTSM010191.9E-21112214IPR003340B3 DNA binding domain
PROSITE profilePS5086313.098112214IPR003340B3 DNA binding domain
PfamPF023627.5E-22112213IPR003340B3 DNA binding domain
PfamPF065072.9E-32282364IPR010525Auxin response factor
PROSITE profilePS5174518.934592671IPR000270PB1 domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0007389Biological Processpattern specification process
GO:0009734Biological Processauxin-activated signaling pathway
GO:0009738Biological Processabscisic acid-activated signaling pathway
GO:0009743Biological Processresponse to carbohydrate
GO:0010154Biological Processfruit development
GO:0031540Biological Processregulation of anthocyanin biosynthetic process
GO:0048366Biological Processleaf development
GO:0048441Biological Processpetal development
GO:0048442Biological Processsepal development
GO:0048589Biological Processdevelopmental growth
GO:0048829Biological Processroot cap development
GO:0051301Biological Processcell division
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0005515Molecular Functionprotein binding
Sequence ? help Back to Top
Protein Sequence    Length: 705 aa     Download sequence    Send to blast
MEQERSLDPQ LWHACAGSMV QIPSLNSTVF YFPQGHAEHA HAPPDFHAPR VPPLILCRVA  60
SVKFLADSET DEVYSKITLL PLPGNDLDLE NDAVLGLTPS PDVNGNEKPA SFAKTLTQSD  120
ANNGGGFSVP RYCAETIFPR LDYTAEPPVQ TVIAKDIHGE TWKFRHIYRG TPRRHLLTTG  180
WSTFVNQKKL IAGDSIVFLR SETGDLCVGI RRAKRGGLGS NGDNNSNSNN PYPGFSGFLR  240
DDEITTSKLM MMKRNATGGG GNANDANAPG GRVRVEAVAE AVARAACGQA FEVVYYPRAS  300
TPEFCVKASD VRSAMRIRWC SGMRFKMAFE TEDSSRISWF MGTVSAVQVA DPIRWPNSPW  360
RLLQVAWDEP DLLQNVKRVS PWLVELVSNM PAIHLSPFSP RKKLRIPQPF DFPFDGTKFP  420
MFSPGFAAGN NGGGESMCYL STNDNNNNAP AGIQGARQAQ QLFGSPSPSL LSDLNLNTFH  480
SGNKLQQSSS SPAMFLSGFN PRHHYDNIVV PRQTRDAEFN NNISCSLTIG NPGLVQDKKK  540
SGSVKTHQFL LFGQPILTEQ QVMNRKRALE EEAEKEEKGG LTWNYGLQGI ETGHCKVFME  600
SEDVGRTLDL SVIGSYQELY RKLAEMFGIE ERSDLLTHVV YRDANGVTKR IGDEPFSDFM  660
RATKRLTIKM DISGDNVRKT WITGIRNGEN GIDSSTKTGQ LSIFA
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldu_A7e-74738551388Auxin response factor 5
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Bra.69540.0bud| root
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in the whole plant. {ECO:0000269|PubMed:10476078}.
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_009103678.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankJN9794750.0JN979475.1 Brassica rapa subsp. pekinensis auxin response factor 10 (ARF10) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009103678.10.0PREDICTED: auxin response factor 10
RefseqXP_009103679.10.0PREDICTED: auxin response factor 10
SwissprotQ9SKN50.0ARFJ_ARATH; Auxin response factor 10
TrEMBLH9B4D60.0H9B4D6_BRARP; Auxin response factor
STRINGBra011955.1-P0.0(Brassica rapa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM58027130
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G28350.10.0auxin response factor 10
Publications ? help Back to Top
  1. Yang ZB, et al.
    TAA1-regulated local auxin biosynthesis in the root-apex transition zone mediates the aluminum-induced inhibition of root growth in Arabidopsis.
    Plant Cell, 2014. 26(7): p. 2889-904
    [PMID:25052716]
  2. Bennett T,van den Toorn A,Willemsen V,Scheres B
    Precise control of plant stem cell activity through parallel regulatory inputs.
    Development, 2014. 141(21): p. 4055-64
    [PMID:25256342]
  3. Ye Y, et al.
    Germostatin resistance locus 1 encodes a PHD finger protein involved in auxin-mediated seed dormancy and germination.
    Plant J., 2016. 85(1): p. 3-15
    [PMID:26611158]
  4. Nguyen TC,Obermeier C,Friedt W,Abrams SR,Snowdon RJ
    Disruption of Germination and Seedling Development in Brassica napus by Mutations Causing Severe Seed Hormonal Imbalance.
    Front Plant Sci, 2016. 7: p. 322
    [PMID:27014334]
  5. Liu Z, et al.
    Repression of callus initiation by the miRNA-directed interaction of auxin-cytokinin in Arabidopsis thaliana.
    Plant J., 2016. 87(4): p. 391-402
    [PMID:27189514]
  6. 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]
  7. Wójcik AM,Nodine MD,Gaj MD
    miR160 and miR166/165 Contribute to the LEC2-Mediated Auxin Response Involved in the Somatic Embryogenesis Induction in Arabidopsis.
    Front Plant Sci, 2017. 8: p. 2024
    [PMID:29321785]
  8. Lin JS, et al.
    MicroRNA160 Modulates Plant Development and Heat Shock Protein Gene Expression to Mediate Heat Tolerance in Arabidopsis.
    Front Plant Sci, 2018. 9: p. 68
    [PMID:29449855]