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 Csa07g007410.1
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: 608aa    MW: 66706.8 Da    PI: 7.0583
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Csa07g007410.1genomeCSGPView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B376.52.9e-24158259199
                     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++      ++++ s++l  +d++g +W++++iyr++++r++lt+GW+ Fv+ ++L +gD v+F   + +++
  Csa07g007410.1 158 FCKTLTASDTSTHGGFSVPRRAAEDCfppldYSQPRPSQELLARDLHGLEWRFRHIYRGQPRRHLLTTGWSAFVNKKKLVSGDAVLFL--RGDDG 250
                     99****************************955566778*************************************************..34899 PP

                     ..EEEEE-S CS
              B3  91 elvvkvfrk 99 
                     +l+++v+r+
  Csa07g007410.1 251 KLRLGVRRA 259
                     99****997 PP

2Auxin_resp1111.2e-36284365182
      Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsL 82 
                     +aha+st svF+++YnP+as+s+F++++ k++k ++ ++++GmRfk ++e+ed+serr  G+++g+sdldp+rWp+SkWr+L
  Csa07g007410.1 284 VAHAISTYSVFSIYYNPKASWSNFIIPAPKFLKIVDYPFCIGMRFKARVESEDASERRSPGIITGISDLDPIRWPGSKWRCL 365
                     79*******************************************************************************9 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019363.14E-42149277IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.103.1E-39152267IPR015300DNA-binding pseudobarrel domain
CDDcd100177.04E-22156258No hitNo description
SMARTSM010191.9E-22158260IPR003340B3 DNA binding domain
PROSITE profilePS5086313.324158260IPR003340B3 DNA binding domain
PfamPF023623.5E-22158259IPR003340B3 DNA binding domain
PfamPF065073.3E-30284365IPR010525Auxin 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: 608 aa     Download sequence    Send to blast
MGGLIDLNVM EAEEEETQTQ TPSSASGSVS PTSSSSASAS VVSSSSGGGV CLELWHACAG  60
PLISLPKRGS LVLYFPQGHL EQAPDFSAAI YGLPPHVFCR ILDVKLHAET TTDEVYAQVS  120
LLPESEDIER KVREGIIDVD AGEEDYEVLK RSSTPHMFCK TLTASDTSTH GGFSVPRRAA  180
EDCFPPLDYS QPRPSQELLA RDLHGLEWRF RHIYRGQPRR HLLTTGWSAF VNKKKLVSGD  240
AVLFLRGDDG KLRLGVRRAS QIEGTAALSA KYNQNMNHNN FSEVAHAIST YSVFSIYYNP  300
KASWSNFIIP APKFLKIVDY PFCIGMRFKA RVESEDASER RSPGIITGIS DLDPIRWPGS  360
KWRCLLVRWD DIEANGHQQR VSPWEIEPSG SISNSGSFVT TGPKRSRIGF SSGKPDIPVS  420
EGIRATDFEE SMRFQRVLQG QEILPGFINT SSDGGAGARR GRFKGTEFND SYGFHKVLQG  480
QETVPAYSIT DHHRQHGLSQ RNIWCGPFQN FSTRILPPSA SSSPSSVLLT NSNSPNARLE  540
DHHGGSGRCR LFGFPLTEET TSVASATVVP CVEGNSMKGA SAVQNNHHRS QGRDIYAMKD  600
MLLDIAL*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A1e-111383952361Auxin response factor 1
4ldw_A1e-111383952361Auxin response factor 1
4ldw_B1e-111383952361Auxin response factor 1
4ldx_A1e-111383952361Auxin response factor 1
4ldx_B1e-111383952361Auxin response factor 1
4ldy_A1e-111383952361Auxin response factor 1
4ldy_B1e-111383952361Auxin response factor 1
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 the establishment or elaboration of tissue patterning during gynoecial development. {ECO:0000269|PubMed:10952886, ECO:0000269|PubMed:12036261}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapCsa07g007410.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Negatively regulated by AHL21/GIK. {ECO:0000269|PubMed:19956801}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAF3603130.0AF360313.1 Arabidopsis thaliana auxin response transcription factor 3 (ETTIN/ARF3) (At2g33860) mRNA, complete cds.
GenBankAY0563650.0AY056365.1 Arabidopsis thaliana auxin response transcription factor 3 (At2g33860) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_010413793.10.0PREDICTED: auxin response factor 3
SwissprotO236610.0ARFC_ARATH; Auxin response factor 3
TrEMBLR0G0L10.0R0G0L1_9BRAS; Auxin response factor
STRINGXP_010413793.10.0(Camelina sativa)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM49242849
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G33860.10.0ARF family protein
Publications ? help Back to Top
  1. Ozerova LV,Krasnikova MS,Troitsky AV,Solovyev AG,Morozov SY
    TAS3 Genes for small ta-siARF RNAs in plants belonging to subtribe Senecioninae: occurrence of prematurely terminated RNA precursors.
    Mol. Gen. Mikrobiol. Virusol., 2013.
    [PMID:24003511]
  2. Thoma R,Chandler JW
    Polarity in the early floral meristem of Arabidopsis.
    Plant Signal Behav, 2015. 10(4): p. e992733
    [PMID:25806573]
  3. Lora J,Hormaza JI,Herrero M
    Transition from two to one integument in Prunus species: expression pattern of INNER NO OUTER (INO), ABERRANT TESTA SHAPE (ATS) and ETTIN (ETT).
    New Phytol., 2015. 208(2): p. 584-95
    [PMID:25991552]
  4. Machida C,Nakagawa A,Kojima S,Takahashi H,Machida Y
    The complex of ASYMMETRIC LEAVES (AS) proteins plays a central role in antagonistic interactions of genes for leaf polarity specification in Arabidopsis.
    Wiley Interdiscip Rev Dev Biol, 2015 Nov-Dec. 4(6): p. 655-71
    [PMID:26108442]
  5. Cabrera J, et al.
    Differentially expressed small RNAs in Arabidopsis galls formed by Meloidogyne javanica: a functional role for miR390 and its TAS3-derived tasiRNAs.
    New Phytol., 2016. 209(4): p. 1625-40
    [PMID:26542733]
  6. Husbands AY,Benkovics AH,Nogueira FT,Lodha M,Timmermans MC
    The ASYMMETRIC LEAVES Complex Employs Multiple Modes of Regulation to Affect Adaxial-Abaxial Patterning and Leaf Complexity.
    Plant Cell, 2015. 27(12): p. 3321-35
    [PMID:26589551]
  7. Yamaguchi N,Wu MF,Winter CM,Wagner D
    LEAFY and Polar Auxin Transport Coordinately Regulate Arabidopsis Flower Development.
    Plants (Basel), 2014. 3(2): p. 251-65
    [PMID:27135503]
  8. Matsumura Y, et al.
    A genetic link between epigenetic repressor AS1-AS2 and a putative small subunit processome in leaf polarity establishment of Arabidopsis.
    Biol Open, 2016. 5(7): p. 942-54
    [PMID:27334696]
  9. Simonini S, et al.
    A noncanonical auxin-sensing mechanism is required for organ morphogenesis in Arabidopsis.
    Genes Dev., 2016. 30(20): p. 2286-2296
    [PMID:27898393]
  10. Pfannebecker KC,Lange M,Rupp O,Becker A
    An Evolutionary Framework for Carpel Developmental Control Genes.
    Mol. Biol. Evol., 2017. 34(2): p. 330-348
    [PMID:28049761]
  11. 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]
  12. Su Z, et al.
    The THO Complex Non-Cell-Autonomously Represses Female Germline Specification through the TAS3-ARF3 Module.
    Curr. Biol., 2017. 27(11): p. 1597-1609.e2
    [PMID:28552357]
  13. Simonini S,Bencivenga S,Trick M,Østergaard L
    Auxin-Induced Modulation of ETTIN Activity Orchestrates Gene Expression in Arabidopsis.
    Plant Cell, 2017. 29(8): p. 1864-1882
    [PMID:28804059]
  14. Guan C, et al.
    Spatial Auxin Signaling Controls Leaf Flattening in Arabidopsis.
    Curr. Biol., 2017. 27(19): p. 2940-2950.e4
    [PMID:28943086]
  15. Simonini S, et al.
    Corrigendum: A noncanonical auxin-sensing mechanism is required for organ morphogenesis in Arabidopsis.
    Genes Dev., 2017. 31(17): p. 1821
    [PMID:28982764]
  16. Zhang K, et al.
    AUXIN RESPONSE FACTOR3 Regulates Floral Meristem Determinacy by Repressing Cytokinin Biosynthesis and Signaling.
    Plant Cell, 2018. 30(2): p. 324-346
    [PMID:29371438]
  17. Vial-Pradel S, et al.
    Arabidopsis Zinc-Finger-Like Protein ASYMMETRIC LEAVES2 (AS2) and Two Nucleolar Proteins Maintain Gene Body DNA Methylation in the Leaf Polarity Gene ETTIN (ARF3).
    Plant Cell Physiol., 2018. 59(7): p. 1385-1397
    [PMID:29415182]
  18. Simonini S,Stephenson P,Østergaard L
    A molecular framework controlling style morphology in Brassicaceae.
    Development, 2018.
    [PMID:29440299]
  19. Andres-Robin A, et al.
    Evidence for the Regulation of Gynoecium Morphogenesis by ETTIN via Cell Wall Dynamics.
    Plant Physiol., 2018. 178(3): p. 1222-1232
    [PMID:30237208]
  20. 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]