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_009110292.1
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: 1020aa    MW: 112489 Da    PI: 6.8171
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009110292.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B371.88.7e-23126224196
                     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++       + +++  ++++ +d++  +W++++iyr++++r++lt+GW+ Fv+ ++L +gD+v+F +d+  
  XP_009110292.1 126 FCKTLTASDTSTHGGFSVPRRAAEKIfppldfsM-QPPA-QEIVAKDLHDTTWTFRHIYRGQPKRHLLTTGWSVFVSTKRLIAGDSVLFVRDE-- 216
                     99*****************************954.4444.48************************************************654.. PP

                     EE..EEEE CS
              B3  89 efelvvkv 96 
                     + +l++++
  XP_009110292.1 217 KSQLTLGL 224
                     44445554 PP
2Auxin_resp119.42.9e-39252334183
      Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                     aaha +++s+F++++nPras+seFvv+++k++kal+ +vs+GmRf+m+feted+  rr++Gtv+gvsdldpvrW++S+Wr+L+
  XP_009110292.1 252 AAHANANNSPFTIFFNPRASPSEFVVPLAKYNKALYAQVSLGMRFRMMFETEDCGVRRYMGTVTGVSDLDPVRWKGSQWRNLQ 334
                     799******************************************************************************97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019361.7E-43116255IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.106.8E-40120241IPR015300DNA-binding pseudobarrel domain
CDDcd100177.37E-21125218No hitNo description
SMARTSM010197.3E-23126228IPR003340B3 DNA binding domain
PfamPF023625.5E-21126225IPR003340B3 DNA binding domain
PROSITE profilePS5086312.097126228IPR003340B3 DNA binding domain
PfamPF065073.2E-34252334IPR010525Auxin response factor
PfamPF023094.3E-9890978IPR033389AUX/IAA domain
PROSITE profilePS5174524.774892985IPR000270PB1 domain
SuperFamilySSF542771.5E-8906970No hitNo description
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009723Biological Processresponse to ethylene
GO:0009733Biological Processresponse to auxin
GO:0010311Biological Processlateral root formation
GO:0048366Biological Processleaf development
GO:0005634Cellular Componentnucleus
GO:0043565Molecular Functionsequence-specific DNA binding
GO:0046983Molecular Functionprotein dimerization activity
Sequence ? help Back to Top
Protein Sequence    Length: 1020 aa     Download sequence    Send to blast
MKAPSNGFHP SSAEGEKKPI NSQLWHACAG PLVSLPPVGS LVVYFPQGHS EQVAASMQKQ  60
TDFIPNYPNL PSKLICLLHS VTLHADTETD EVYAQMTLQP VNKYDREALL ASDMGLKLNR  120
QPTEFFCKTL TASDTSTHGG FSVPRRAAEK IFPPLDFSMQ PPAQEIVAKD LHDTTWTFRH  180
IYRGQPKRHL LTTGWSVFVS TKRLIAGDSV LFVRDEKSQL TLGLRLANRQ TPTLSSSVIS  240
SDSMHIGILA AAAHANANNS PFTIFFNPRA SPSEFVVPLA KYNKALYAQV SLGMRFRMMF  300
ETEDCGVRRY MGTVTGVSDL DPVRWKGSQW RNLQVGWDES TAGDRPSRVS VWEIEPVITP  360
FYICPPPFFR PKYPRQPGMP DDELDMENAF KRAMPWMGEE FGMKDAQSSM FPGLSLVQWM  420
SMQQNNTLSA GAAATTQLPS AYNLPKNFAL NDPSKLLNFQ SPNLSPVNSQ FNKPNMVSSH  480
ISQQMQVQPA MVKSQQQVQI SHQQLQQGVY NAGSVNNGVS VVSCQNQSTG FSQSQLQQQS  540
MLSNGSAKMN HQSIVGNKSS SQMTSQELQF QQQMELHNSS QLLRTQQEQS SMHSLQQTPQ  600
QLQMQQQSST PSPSQQLQLQ LLQKLQQQQQ STPPVSSSLQ PQLSAALQQT QSHQLQQLLS  660
SQNQQPFSAP TFMQPPQVQV SHHQQQGHMN NKPLITAGGS HSGHTDGEVP TCSTSPSANN  720
TRHDNVSPTN FLSRSQQQGQ AASVPAPDPV QSRNNQGMVN LRSAADQINV STAGTTYCPD  780
AVGTAQQQQT FPLQSFGNCQ QRNNLAFAGN LEAVTTPDAL YSQKEFQNLV PNYGNAPRDI  840
ETELSSAAIS SQSFGIPSIP FKSGGSNEIG GVNDSGIMNG GGLWPNQAQR MRTYTKVQKR  900
GSVGRSIDVT RYSGYDELRN DLARMFGIEG QLEDPRPSDW KLVYTDHEND ILLVGDDPWE  960
EFVNCVQNIK ILSSVEVQQM SLDGDLAAIP ATNQVCSETD SGNAWKVHYE DTSAAASFNR
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldu_A1e-1701535545388Auxin 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. Involved in ethylene responses. Regulates lateral root formation through direct regulation of LBD16 and/or LBD29. Functionally redundant with ARF7. {ECO:0000269|PubMed:12036261, ECO:0000269|PubMed:16461383, ECO:0000269|PubMed:17259263}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapXP_009110292.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By auxin and ethylene. {ECO:0000269|PubMed:16461383}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankJN9794830.0JN979483.1 Brassica rapa subsp. pekinensis auxin response factor 19-1 (ARF19-1) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009110292.10.0PREDICTED: auxin response factor 19
SwissprotQ8RYC80.0ARFS_ARATH; Auxin response factor 19
TrEMBLH9B4E40.0H9B4E4_BRARP; Auxin response factor
STRINGBra016517.1-P0.0(Brassica rapa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM26292665
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G19220.10.0auxin response factor 19
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. Perilli S, et al.
    RETINOBLASTOMA-RELATED protein stimulates cell differentiation in the Arabidopsis root meristem by interacting with cytokinin signaling.
    Plant Cell, 2013. 25(11): p. 4469-78
    [PMID:24285791]
  3. Sun Y, et al.
    Manipulation of Auxin Response Factor 19 affects seed size in the woody perennial Jatropha curcas.
    Sci Rep, 2017. 7: p. 40844
    [PMID:28102350]
  4. 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]
  5. Olmo R, et al.
    Molecular Transducers from Roots Are Triggered in Arabidopsis Leaves by Root-Knot Nematodes for Successful Feeding Site Formation: A Conserved Post-Embryogenic De novo Organogenesis Program?
    Front Plant Sci, 2017. 8: p. 875
    [PMID:28603536]
  6. Lee K,Seo PJ
    High-temperature promotion of callus formation requires the BIN2-ARF-LBD axis in Arabidopsis.
    Planta, 2017. 246(4): p. 797-802
    [PMID:28766014]
  7. Ayala-Rodríguez JÁ,Barrera-Ortiz S,Ruiz-Herrera LF,López-Bucio J
    Folic acid orchestrates root development linking cell elongation with auxin response and acts independently of the TARGET OF RAPAMYCIN signaling in Arabidopsis thaliana.
    Plant Sci., 2017. 264: p. 168-178
    [PMID:28969797]
  8. Nakamura M, et al.
    Auxin and ROP GTPase Signaling of Polar Nuclear Migration in Root Epidermal Hair Cells.
    Plant Physiol., 2018. 176(1): p. 378-391
    [PMID:29084900]
  9. Hong L, et al.
    Alternative polyadenylation is involved in auxin-based plant growth and development.
    Plant J., 2018. 93(2): p. 246-258
    [PMID:29155478]
  10. Lee K,Park OS,Seo PJ
    Arabidopsis ATXR2 deposits H3K36me3 at the promoters of LBD genes to facilitate cellular dedifferentiation.
    Sci Signal, 2018.
    [PMID:29184030]
  11. Kimura T, et al.
    Asymmetric Auxin Distribution is Not Required to Establish Root Phototropism in Arabidopsis.
    Plant Cell Physiol., 2018. 59(4): p. 823-835
    [PMID:29401292]
  12. Schoenaers S, et al.
    The Auxin-Regulated CrRLK1L Kinase ERULUS Controls Cell Wall Composition during Root Hair Tip Growth.
    Curr. Biol., 2018. 28(5): p. 722-732.e6
    [PMID:29478854]
  13. Huang KL, et al.
    The ARF7 and ARF19 Transcription Factors Positively Regulate PHOSPHATE STARVATION RESPONSE1 in Arabidopsis Roots.
    Plant Physiol., 2018. 178(1): p. 413-427
    [PMID:30026290]