PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Neem_28680_f_1
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Sapindales; Meliaceae; Azadirachta
Family ARF
Protein Properties Length: 388aa    MW: 43533.7 Da    PI: 8.587
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Neem_28680_f_1genomeNGDView Nucleic Acid
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B373.91.9e-23123224199
                     EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSE CS
              B3   1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrse 89 
                     f+k+lt sd++++g +++p++ ae++      +++++  ++l+ +d++  +W++++iyr++++r++lt+GW+ Fv+ ++L +gD+v+F   ++++
  Neem_28680_f_1 123 FCKTLTASDTSTHGGFSVPRRAAEKIfppldfSMQPPA-QELVARDLHDTTWTFRHIYRGQPKRHLLTTGWSVFVSTKRLFAGDSVLFI--RDEK 214
                     99*****************************9445444.38************************************************..4567 PP

                     E..EEEEE-S CS
              B3  90 felvvkvfrk 99 
                      +l+++++r+
  Neem_28680_f_1 215 SQLLLGIRRA 224
                     778**99997 PP

2Auxin_resp126.32e-41249331183
      Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                     aahaa+++s+F+++YnPras+seFv++++k++ka++++vs+GmRf+m+fete+s  rr++Gt++gvsd+dpvrW+nS+Wr+L+
  Neem_28680_f_1 249 AAHAAANNSPFTIFYNPRASPSEFVIPLAKYNKAVYTQVSLGMRFRMMFETEESGVRRYMGTITGVSDIDPVRWKNSHWRNLQ 331
                     79*******************************************************************************97 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019368.63E-46113252IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.102.5E-43115238IPR015300DNA-binding pseudobarrel domain
CDDcd100177.09E-21122223No hitNo description
PfamPF023621.5E-21123224IPR003340B3 DNA binding domain
PROSITE profilePS5086312.294123225IPR003340B3 DNA binding domain
SMARTSM010191.6E-23123225IPR003340B3 DNA binding domain
PfamPF065071.4E-36249331IPR010525Auxin 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:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 388 aa     Download sequence    Send to blast
MKAQSNGFLP NSAEGERKSI NSELWHACAG PLVSLPPVGS LVVYFPQGHS EQVAASMQKE  60
NDFIPSYPNL PSKLICMLHN VTLHADPETD EVYAQMTLQP YEKEALLASD MGLKQSRQPT  120
EFFCKTLTAS DTSTHGGFSV PRRAAEKIFP PLDFSMQPPA QELVARDLHD TTWTFRHIYR  180
GQPKRHLLTT GWSVFVSTKR LFAGDSVLFI RDEKSQLLLG IRRANRQQPA LSSSVISSDS  240
MHIGILAAAA HAAANNSPFT IFYNPRASPS EFVIPLAKYN KAVYTQVSLG MRFRMMFETE  300
ESGVRRYMGT ITGVSDIDPV RWKNSHWRNL QVGWDESTAG ERPSRVSIWE IEPVVTPFYI  360
CPPPFFRPKF PKQPGMPGIF FSPNNEPL
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldu_A1e-179935239388Auxin 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 -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAB6712251e-129AB671225.1 Melia azedarach DNA, microsatellite: MA-TC20_2.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_010273878.10.0PREDICTED: auxin response factor 7-like
RefseqXP_015867478.10.0auxin response factor 19-like isoform X1
RefseqXP_028782730.10.0auxin response factor 19-like
RefseqXP_028797210.10.0LOW QUALITY PROTEIN: auxin response factor 19-like
SwissprotQ8RYC80.0ARFS_ARATH; Auxin response factor 19
TrEMBLA0A0B0MNI00.0A0A0B0MNI0_GOSAR; Auxin response factor
TrEMBLA0A1U8BCB50.0A0A1U8BCB5_NELNU; Auxin response factor
STRINGXP_010273878.10.0(Nelumbo nucifera)
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]