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 Niben101Scf02744g00012.1
Organism
Nicotiana benthamiana
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Nicotianoideae; Nicotianeae; Nicotiana
Family ARF
Protein Properties Length: 916aa    MW: 102679 Da    PI: 6.5139
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Niben101Scf02744g00012.1genomeBTI-
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B371.51.1e-22126227199
                               EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT- CS
                        B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegD 78 
                               f+k+lt sd++++g +++p++ ae++       + +++  ++l+ +d++ + W++++iyr++++r++lt+GW+ F ++++L++gD
  Niben101Scf02744g00012.1 126 FCKTLTASDTSTHGGFSVPRRAAEKIfppldfsM-QPPA-QELMARDLHDQAWTFRHIYRGQPKRHLLTTGWSVFISSKRLCAGD 208
                               99*****************************954.5444.48******************************************* PP

                               EEEEEE-SSSEE..EEEEE-S CS
                        B3  79 fvvFkldgrsefelvvkvfrk 99 
                               +v+F +  +++ +l++++ r+
  Niben101Scf02744g00012.1 209 SVLFIR--DEKSQLLLGIKRA 227
                               *****4..4666678888765 PP
2Auxin_resp123.21.9e-40252334183
                Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                               aahaa+++s+F+++YnPras+seFv++++k++ka++ +vs+GmRf+m+fete+s  rr++Gtv+gvsdldp+rW+ S+Wr+L+
  Niben101Scf02744g00012.1 252 AAHAAANNSPFSIFYNPRASPSEFVIPLAKYNKAMYAQVSLGMRFRMMFETEESGVRRYMGTVTGVSDLDPIRWKSSQWRNLQ 334
                               79*******************************************************************************97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019362.09E-43114255IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.103.1E-40118241IPR015300DNA-binding pseudobarrel domain
CDDcd100179.86E-18125226No hitNo description
PfamPF023624.0E-20126227IPR003340B3 DNA binding domain
SMARTSM010194.5E-21126228IPR003340B3 DNA binding domain
PROSITE profilePS5086311.97126228IPR003340B3 DNA binding domain
PfamPF065072.9E-35252334IPR010525Auxin response factor
SuperFamilySSF542772.85E-9781867No hitNo description
PROSITE profilePS5174525.947789873IPR000270PB1 domain
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: 916 aa     Download sequence    Send to blast
MKAPSNGYIA NSGEGERKVL NSELWHACAG PLVSLPPIGS LVVYFPQGHS EQVAASMQKE  60
TDGIPSYPNL PSKLICMLHN VTLHADPETD EVYAQMTLQP VNKYDQEALI LSDMGLKQNR  120
QPAEFFCKTL TASDTSTHGG FSVPRRAAEK IFPPLDFSMQ PPAQELMARD LHDQAWTFRH  180
IYRGQPKRHL LTTGWSVFIS SKRLCAGDSV LFIRDEKSQL LLGIKRANRQ QPALSSSVIS  240
SDSMHIGILA AAAHAAANNS PFSIFYNPRA SPSEFVIPLA KYNKAMYAQV SLGMRFRMMF  300
ETEESGVRRY MGTVTGVSDL DPIRWKSSQW RNLQVGWDES TAGERPSRVS IWDIEPVVTP  360
FYICPPPFFR PKFPKQPGFP GDESDIENAL KRGMPWVSDE FGLKDAPSSI FPGLSLVQWM  420
SMQQNNHNPV AQSGLPNVLH SNIGTDDHSK LLSFQSPTPA PQFNKPNLLN QQFAQIQQPQ  480
LAWPQQQQQS LRSPPSAQQQ QNTQQQQQQP PQHMLQQVPQ PQPQIHQQAQ QQLHQQQRGP  540
QQQLYQQQRG TQQQQLTVNS PPVNNCVSPD QIPNQIFPQT SIYAQLQQQQ LLSASNQSQQ  600
NVPVNKNPFL SASSAQDFPF QQQAEQQSNL LQKSQPQQQI IPQQAPLQLL QQSLIQRPQV  660
QTPNQGQAIL VDESVVDPSQ EQNKSEFQMK HDLPFSKGSE QSKYKGNGTE NLEAASSTTS  720
YGKDMQNLFS PFGSTPRDIE TELSAAGINS QQFGVPNMSY QPRCSNDLAV NDNGVLNNNS  780
WMNQTQRMRT YTKVQKRGSV GRTIDVTRYK GYDELRHDLA RMFGIEGQLE DPQRTEWKLV  840
YVDHENDILL VGDDPWEEFV SCVQSVKILS SAEVQQMSLD GDLGNVPVPN QASSGTDSGN  900
AWRGHYDDNS VASFNR
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldu_A1e-1731535545388Auxin 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}.
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By auxin and ethylene. {ECO:0000269|PubMed:16461383}.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_009620963.10.0PREDICTED: auxin response factor 19-like isoform X1
SwissprotQ8RYC80.0ARFS_ARATH; Auxin response factor 19
TrEMBLA0A1S4CS510.0A0A1S4CS51_TOBAC; Auxin response factor
STRINGXP_009620963.10.0(Nicotiana tomentosiformis)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA13022465
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]