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_5632_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: 455aa    MW: 51219.4 Da    PI: 8.5783
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Neem_5632_f_1genomeNGDView Nucleic Acid
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B373.52.5e-23123224199
                    EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE CS
             B3   1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsef 90 
                    f+k+lt sd++++g +++p++ ae++      +++++  ++l+ +d++  +W++++iyr++++r++lt+GW+ Fv+ ++L +gD+v+F   ++++ 
  Neem_5632_f_1 123 FCKTLTASDTSTHGGFSVPRRAAEKIfppldfSMQPPA-QELVARDLHDTTWTFRHIYRGQPKRHLLTTGWSVFVSTKRLFAGDSVLFI--RDEKS 215
                    99*****************************9445444.38************************************************..45677 PP

                    ..EEEEE-S CS
             B3  91 elvvkvfrk 99 
                    +l+++++r+
  Neem_5632_f_1 216 QLLLGIRRA 224
                    78**99997 PP

2Auxin_resp1262.5e-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_5632_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
SuperFamilySSF1019361.2E-45113252IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.103.3E-43115238IPR015300DNA-binding pseudobarrel domain
CDDcd100172.44E-20122223No hitNo description
PROSITE profilePS5086312.294123225IPR003340B3 DNA binding domain
PfamPF023621.9E-21123224IPR003340B3 DNA binding domain
SMARTSM010191.6E-23123225IPR003340B3 DNA binding domain
PfamPF065071.8E-36249331IPR010525Auxin response factor
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: 455 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 PKQPGMPDDE SDIENAFKRA MPWLGDDFGM KDGTSSIFPG LSLVQWMSMQ  420
QNHQFPAAQS GFFPSMLLQY LHQISSLTKR IHKTK
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldu_A1e-1781535245388Auxin 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-128AB671225.1 Melia azedarach DNA, microsatellite: MA-TC20_2.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_015867478.10.0auxin response factor 19-like isoform X1
RefseqXP_028797210.10.0LOW QUALITY PROTEIN: auxin response factor 19-like
SwissprotQ8RYC80.0ARFS_ARATH; Auxin response factor 19
TrEMBLA0A2H5NBP80.0A0A2H5NBP8_CITUN; Auxin response factor
STRINGXP_010089663.10.0(Morus notabilis)
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]