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 Araha.6310s0002.1.p
Organism
Arabidopsis halleri
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
Family ARF
Protein Properties Length: 1071aa    MW: 118516 Da    PI: 6.6625
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Araha.6310s0002.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B373.23.2e-23126227199
                          EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEE CS
                   B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFk 83 
                          f+k+lt sd++++g +++p++ ae++       + +++  ++++ +d++  +W++++iyr++++r++lt+GW+ Fv+ ++L +gD+v+F 
  Araha.6310s0002.1.p 126 FCKTLTASDTSTHGGFSVPRRAAEKIfppldfsM-QPPA-QEIVAKDLHDTTWTFRHIYRGQPKRHLLTTGWSVFVSTKRLFAGDSVLFV 213
                          99*****************************954.4444.48************************************************ PP

                          E-SSSEE..EEEEE-S CS
                   B3  84 ldgrsefelvvkvfrk 99 
                            ++++ +l+++++r+
  Araha.6310s0002.1.p 214 --RDEKSQLMLGIRRA 227
                          ..4567778****997 PP
2Auxin_resp118.55.3e-39252334183
           Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                          aaha +++s+F++++nPras+seFvv+++k++kal+ +vs+GmRf+m+feted+  rr++Gtv+g+sdldpvrW++S+Wr+L+
  Araha.6310s0002.1.p 252 AAHANANSSPFTIFFNPRASPSEFVVPLAKYNKALYAQVSLGMRFRMMFETEDCGVRRYMGTVTGISDLDPVRWKGSQWRNLQ 334
                          799******************************************************************************97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019363.4E-44116255IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.107.9E-42120241IPR015300DNA-binding pseudobarrel domain
CDDcd100176.63E-21125226No hitNo description
SMARTSM010191.0E-24126228IPR003340B3 DNA binding domain
PROSITE profilePS5086312.534126228IPR003340B3 DNA binding domain
PfamPF023621.5E-21126227IPR003340B3 DNA binding domain
PfamPF065077.4E-34252334IPR010525Auxin response factor
PfamPF023092.6E-99401028IPR033389AUX/IAA domain
PROSITE profilePS5174524.8019421035IPR000270PB1 domain
SuperFamilySSF542771.57E-89561020No 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: 1071 aa     Download sequence    Send to blast
MKAPSNGFLP TSNEGEKKPI NSQLWHACAG PLVSLPPVGS LVVYFPQGHS EQVAASMQKQ  60
TDFIPNYPNL PSKLICLLHS VTLHADTETD EVYAQMTLQP VNKYDREALL ASDMGLKLNR  120
QPTEFFCKTL TASDTSTHGG FSVPRRAAEK IFPPLDFSMQ PPAQEIVAKD LHDTTWTFRH  180
IYRGQPKRHL LTTGWSVFVS TKRLFAGDSV LFVRDEKSQL MLGIRRANRQ TPTLSSSVIS  240
SDSMHIGILA AAAHANANSS PFTIFFNPRA SPSEFVVPLA KYNKALYAQV SLGMRFRMMF  300
ETEDCGVRRY MGTVTGISDL DPVRWKGSQW RNLQVGWDES TAGDRPSRVS IWEIEPVITP  360
FYICPPPFFR PKYPRQPGMP DDELDMENAF KRAMPWMGDD FGMKDAQSSM FPGLSLVQWM  420
SMQQNNPLSG SATPQLPSAL SSYNLPNNFA SNDPSKLLNF QSPNLSSANS QFNKSNTVNH  480
ISQQMQAQPA MVKSLQQQQQ QQQLQMSHQQ LQQQGNYNNG ASAVANQVSC QNPNQPTGFS  540
QSQLQQQSML PTGAKMIHQN INSVGNKVSS QMTSFAQEMQ FQQQLELHNS SQLLRNQQEQ  600
SSLHSLQQNL SQNPQQLQMQ QQSSKPSPSQ QLQLQLLQKL QQQQQQQSVP PVSSSLQPQL  660
SALQQTQSHQ LQQLLSSQNQ QSLAHGNNSF SASTFMQPPQ IQVSHQQQGQ MNNKNLVAAG  720
RSHSGHTDGE APSCSTSPSA NNTGHDNVSP TNFLSRNQQQ GQASSVSASD SVFERASNPV  780
QEHYTKNESR INQGMVNLKS AGEQFRFKGA VTDQIDVSTA GVTYCPDVVA QQQQTFPLPS  840
FGFDGDCQSH HPRNNLAFPG NLEAVTSDAL YSQKDFQNLV PNYGNAPRDI ETELSSAAIS  900
SQSFGIPSIP FKSGCSNEVG GINDSGIMNG GGLWPNQTQR MRTYTKVQKR GSVGRSIDVT  960
RYSGYDELRH DLARMFGIEG QLEDPLTSDW KLVYTDHEND ILLVGDDPWE EFVNCVQNIK  1020
ILSSVEVQQM SLDGDLAAIP TTNQACSETD SGNAWKVHYE DTSAAASFNR *
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldu_A1e-1721535545388Auxin 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
PlantRegMapAraha.6310s0002.1.p
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
GenBankATU536720.0U53672.2 Arabidopsis thaliana early auxin-induced IAA22 mRNA, complete cds.
GenBankAY6697940.0AY669794.1 Arabidopsis thaliana clone C105352 ARF19 (At1g19220) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_020870042.10.0auxin response factor 19
SwissprotQ8RYC80.0ARFS_ARATH; Auxin response factor 19
TrEMBLD7KHB30.0D7KHB3_ARALL; Auxin response factor
STRINGfgenesh1_pg.C_scaffold_10017390.0(Arabidopsis lyrata)
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]