PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Home  TFext  BLAST  Prediction  Download  Help  About  Links  PlantRegMap
(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID XP_009104599.1
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: 546aa    MW: 59807.9 Da    PI: 5.019
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009104599.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B373.13.3e-23123224199
                     EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSS CS
              B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrs 88 
                     f k+ltpsd+++ g +++p+ +a++          ++ +  +l ++d +g +W++++iyr++++r++lt+GW++Fv+ ++L +gD+vvF+  ++s
  XP_009104599.1 123 FAKILTPSDANNGGGFSVPRYCADSVfppldfhADPPVQ--KLFITDIHGVVWDFRHIYRGTPRRHLLTTGWSKFVNGKKLIAGDSVVFM--RKS 213
                     89*********************999*****97555555..7************************************************..447 PP

                     EE..EEEEE-S CS
              B3  89 efelvvkvfrk 99 
                       e++++v+r+
  XP_009104599.1 214 VDEMFIGVRRA 224
                     88899***997 PP
2Auxin_resp69.88.7e-24257331175
      Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrl.sGtvvgvsdldpvrWp 75 
                     a+++a ++ +FevvY+P a++s+Fvv++e+ve ++   +s+G+R+kma+etedss+ ++ +G+v+++ + ++  W+
  XP_009104599.1 257 AVNKAVQGYPFEVVYYPTAGWSDFVVRAEDVEVSMAGYWSPGTRVKMAMETEDSSRVTWfQGVVSSTFQ-ETGLWK 331
                     6789999****************************************************9999998876.444554 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.103.1E-33113224IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019367.85E-29116230IPR015300DNA-binding pseudobarrel domain
PfamPF023621.7E-20123224IPR003340B3 DNA binding domain
CDDcd100177.61E-20123219No hitNo description
SMARTSM010194.2E-20123225IPR003340B3 DNA binding domain
PROSITE profilePS5086312.647123225IPR003340B3 DNA binding domain
PfamPF065071.1E-18257331IPR010525Auxin response factor
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:0010208Biological Processpollen wall assembly
GO:0048830Biological Processadventitious root development
GO:0052543Biological Processcallose deposition in cell wall
GO:0005634Cellular Componentnucleus
GO:0000987Molecular Functioncore promoter proximal region sequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 546 aa     Download sequence    Send to blast
MSPPPSATAD FLREVDPQIW RACAGASVQI PSLYSRVYYF PQGHVEHSCP SSLISSFSTA  60
APVPCVVSAV ELLADPITDE VFAHLALQPI SPEHFSPSNF SGFGSDDDDD NNSNSNKNKV  120
VTFAKILTPS DANNGGGFSV PRYCADSVFP PLDFHADPPV QKLFITDIHG VVWDFRHIYR  180
GTPRRHLLTT GWSKFVNGKK LIAGDSVVFM RKSVDEMFIG VRRAPISNHG DEYYGGGKKG  240
FRRIGMGKLT AEAVSEAVNK AVQGYPFEVV YYPTAGWSDF VVRAEDVEVS MAGYWSPGTR  300
VKMAMETEDS SRVTWFQGVV SSTFQETGLW KQLQITWDEP EILQNLKRVN PWQVEVVANS  360
SHLLAIYPPA KRLKPSSSAS GFLSGEGEML YSGRGQQAVD PSPYLFSYTT FPAGMQGARH  420
YEFGSFNSIG FIGENTPQLC TNNFFSPLPG LRKVSTEMVN YGSPLSDDLS PNSNTTNVSS  480
GNELVGNRGH AVRVSSIQLF GQIINVQELT ESGLAEGLYE EDGSKESSDN EVVNETQLSL  540
TYAQGM
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldu_A2e-621535651389Auxin response factor 5
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
PlantRegMapXP_009104599.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankJN9794790.0JN979479.1 Brassica rapa subsp. pekinensis auxin response factor 17-1 (ARF17-1) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009104599.10.0PREDICTED: auxin response factor 17
SwissprotQ84WU60.0ARFQ_ARATH; Auxin response factor 17
TrEMBLM4CHI20.0M4CHI2_BRARP; Auxin response factor
STRINGBra003665.1-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
AT1G77850.10.0auxin response factor 17
Publications ? help Back to Top
  1. Shi ZH, et al.
    Overexpression of AtTTP affects ARF17 expression and leads to male sterility in Arabidopsis.
    PLoS ONE, 2015. 10(3): p. e0117317
    [PMID:25822980]
  2. de Lucas M, et al.
    Transcriptional Regulation of Arabidopsis Polycomb Repressive Complex 2 Coordinates Cell-Type Proliferation and Differentiation.
    Plant Cell, 2016. 28(10): p. 2616-2631
    [PMID:27650334]
  3. 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]
  4. Wang B, et al.
    Fine regulation of ARF17 for anther development and pollen formation.
    BMC Plant Biol., 2017. 17(1): p. 243
    [PMID:29258431]
  5. 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]
  6. 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]