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 Csa13g024650.1
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Camelina
Family ARF
Protein Properties Length: 898aa    MW: 98685.5 Da    PI: 6.2989
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Csa13g024650.1genomeCSGPView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B371.97.9e-23127228199
                     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 +  + +
  Csa13g024650.1 127 FCKTLTASDTSTHGGFSVPRRAAEKIfpaldfSMQPPCQ-ELVAKDIHDSTWTFRHIYRGQPKRHLLTTGWSVFVSTKRLFAGDSVLFIR--DGK 218
                     99*****************************98888885.9************************************************5..467 PP

                     E..EEEEE-S CS
              B3  90 felvvkvfrk 99 
                     ++l+++++r+
  Csa13g024650.1 219 AQLLLGIRRA 228
                     8889999997 PP

2Auxin_resp1188e-39253335183
      Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                     aaha +++s+F+++YnPra+++eFvv+++k+ ka++ +vs+GmRf+m fete++  rr++Gtv+g+sdldpvrW+nS+Wr+L+
  Csa13g024650.1 253 AAHANANNSPFTIFYNPRAAPAEFVVPLAKYTKAMYAQVSLGMRFRMIFETEECGVRRYMGTVTGISDLDPVRWKNSQWRNLQ 335
                     799******************************************************************************97 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019362.35E-42117256IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.102.3E-41121242IPR015300DNA-binding pseudobarrel domain
CDDcd100172.29E-19126227No hitNo description
SMARTSM010193.1E-22127229IPR003340B3 DNA binding domain
PfamPF023624.5E-21127228IPR003340B3 DNA binding domain
PROSITE profilePS5086312.055127229IPR003340B3 DNA binding domain
PfamPF065077.2E-34253335IPR010525Auxin response factor
PfamPF023091.1E-9768856IPR033389AUX/IAA domain
PROSITE profilePS5174526.956770863IPR000270PB1 domain
SuperFamilySSF542777.36E-9783848No hitNo description
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
GO:0005515Molecular Functionprotein binding
Sequence ? help Back to Top
Protein Sequence    Length: 898 aa     Download sequence    Send to blast
MKAPSSNGVS PNPVEGERRN INSELWHACA GPLISLPPAG SLVVYFPQGH SEQVAASMQK  60
QTDCIPSYPN LPSKLICMLH NVTLNADPET DEVYAQMTLQ PVNKYDRDAL LASDMGLKLN  120
RQPNEFFCKT LTASDTSTHG GFSVPRRAAE KIFPALDFSM QPPCQELVAK DIHDSTWTFR  180
HIYRGQPKRH LLTTGWSVFV STKRLFAGDS VLFIRDGKAQ LLLGIRRANR QQPALSSSVI  240
SSDSMHIGVL AAAAHANANN SPFTIFYNPR AAPAEFVVPL AKYTKAMYAQ VSLGMRFRMI  300
FETEECGVRR YMGTVTGISD LDPVRWKNSQ WRNLQIGWDE SAAGDRPSRV SVWDIEPVLT  360
PFYICPPPFF RPRFGGQPGM PDDETDMESA LKRAMPWLDN SSEMKDASST IFPGLSLVQW  420
MNMQQQNGQL PSAAAQPETQ FPRQVEQQQP PGLKGQNQQT LLQQKAHQAQ AQQIFQQSLL  480
EQPHLQFQLL QRLQQQQQQQ FLSPQSQLPH HQLQSQQLPA LSQGHQFPSS CTNNGLSTLQ  540
PPQMLVNRPQ EKQNPPVGGG VKAYSGITDG GDAPSSSTSP STNNCQISSS GFLNRSQSGP  600
AILIPDAAID MSGNLVQDLY GKSDMRLKQE LVGQQKSKAS LTDHHLEASA SGTSYGLDGG  660
DNNRQQNFLA PTFGLDGDSR NSLLGGPNVD NGFVPDTLLS RGYDSQKDLQ NMLSNYGGVT  720
NDIGTEMSTS AVRTQSFGVP NVPAISNDLA VNDAGVLGAG LWPAQTQRMR TYTKVQKRGS  780
VGRSIDVNRY RGYDELRHDL ARMFGIEGQL EDPQTSDWKL VYVDHENDIL LVGDDPWEEF  840
VNCVQSIKIL SSAEVQQMSL DGNFAGVPVT NQACSGGDSG NAWRGHYDDN SATSFNR*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldu_A1e-1682135651388Auxin 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). Act as a transcriptional activator of several tropic stimulus-induced (TSI) genes, including SAUR50. Formation of heterodimers with Aux/IAA proteins may alter their ability to modulate early auxin response genes expression. Required for differential growth responses of aerial tissues. Involved in ethylene responses. Regulates lateral root formation through direct regulation of LBD16 and/or LBD29. Functionally redundant with ARF19. Mediates embryo axis formation and vascular tissues differentiation. Functionally redundant with ARF5. {ECO:0000269|PubMed:12036261, ECO:0000269|PubMed:14973283, ECO:0000269|PubMed:16371470, ECO:0000269|PubMed:16461383, ECO:0000269|PubMed:17259263}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapCsa13g024650.1
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAF0421950.0AF042195.1 Arabidopsis thaliana auxin response factor 7 (ARF7) mRNA, complete cds.
GenBankAY6697890.0AY669789.1 Arabidopsis thaliana clone C105344 ARF7 (At5g20730) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_012851206.10.0PREDICTED: auxin response factor 19-like
SwissprotP930220.0ARFG_ARATH; Auxin response factor 7
TrEMBLA0A3N6QIU70.0A0A3N6QIU7_BRACR; Auxin response factor
STRINGOMERI03G31460.10.0(Oryza meridionalis)
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
AT5G20730.20.0ARF family protein
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. Hu J,Zhang Y,Wang J,Zhou Y
    Glycerol affects root development through regulation of multiple pathways in Arabidopsis.
    PLoS ONE, 2014. 9(1): p. e86269
    [PMID:24465999]
  3. Mellor N, et al.
    Modelling of Arabidopsis LAX3 expression suggests auxin homeostasis.
    J. Theor. Biol., 2015. 366: p. 57-70
    [PMID:25446711]
  4. Gupta A,Singh M,Laxmi A
    Interaction between glucose and brassinosteroid during the regulation of lateral root development in Arabidopsis.
    Plant Physiol., 2015. 168(1): p. 307-20
    [PMID:25810094]
  5. Youn JH, et al.
    ARF7 increases the endogenous contents of castasterone through suppression of BAS1 expression in Arabidopsis thaliana.
    Phytochemistry, 2016. 122: p. 34-44
    [PMID:26608667]
  6. Porco S, et al.
    Lateral root emergence in Arabidopsis is dependent on transcription factor LBD29 regulation of auxin influx carrier LAX3.
    Development, 2016. 143(18): p. 3340-9
    [PMID:27578783]
  7. Carey NS,Krogan NT
    The role of AUXIN RESPONSE FACTORs in the development and differential growth of inflorescence stems.
    Plant Signal Behav, 2017. 12(4): p. e1307492
    [PMID:28340328]
  8. 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]
  9. Sheng L, et al.
    Non-canonical WOX11-mediated root branching contributes to plasticity in Arabidopsis root system architecture.
    Development, 2017. 144(17): p. 3126-3133
    [PMID:28743799]
  10. 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]
  11. 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]
  12. 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]
  13. 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]
  14. 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]
  15. Prát T, et al.
    WRKY23 is a component of the transcriptional network mediating auxin feedback on PIN polarity.
    PLoS Genet., 2018. 14(1): p. e1007177
    [PMID:29377885]
  16. 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]
  17. 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]
  18. 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]
  19. Hablak SG
    Features inheritance of root system Arabidopsis thaliana (L.) Heynh. the interaction of genes CTR1 AND ALF3, NPH4 and IAR2.
    Tsitol. Genet., 2019.
    [PMID:30484609]
  20. Orosa-Puente B, et al.
    Root branching toward water involves posttranslational modification of transcription factor ARF7.
    Science, 2018. 362(6421): p. 1407-1410
    [PMID:30573626]