PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Cotton_A_11311_BGI-A2_v1.0
Common NameF383_05647
Organism
Gossypium arboreum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Malvales; Malvaceae; Malvoideae; Gossypium
Family ARF
Protein Properties Length: 705aa    MW: 77249.1 Da    PI: 7.0431
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Cotton_A_11311_BGI-A2_v1.0genomeBGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B377.51.4e-24148249199
                                 EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT CS
                          B3   1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkeg 77 
                                 f+k+lt sd++++g +++p++ ae++      + +++ s++l+ +d++g +W++++iyr++++r++lt+GW+ Fv+ ++L +g
  Cotton_A_11311_BGI-A2_v1.0 148 FCKTLTASDTSTHGGFSVPRRAAEDCfppldyN-QQRPSQELVAKDLHGLEWRFRHIYRGQPRRHLLTTGWSAFVNKKKLVSG 229
                                 99****************************963.3445679****************************************** PP

                                 -EEEEEE-SSSEE..EEEEE-S CS
                          B3  78 DfvvFkldgrsefelvvkvfrk 99 
                                 D v+F   + +++el+++++r+
  Cotton_A_11311_BGI-A2_v1.0 230 DAVLFL--RGENGELRLGIRRA 249
                                 ******..4499999****996 PP
2Auxin_resp120.41.4e-39274355182
                  Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsL 82 
                                 ++ha+s+ksvF+++YnPras+seF+++v+k+ k+l++++svGmRfkm+fe+ed++e r++G+v+g+s++dpvrW++SkWr+L
  Cotton_A_11311_BGI-A2_v1.0 274 VVHAISMKSVFSIYYNPRASSSEFIIPVHKFWKSLDHSFSVGMRFKMRFESEDAAEGRYTGVVTGISEMDPVRWSGSKWRCL 355
                                 689******************************************************************************9 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019361.44E-42141258IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.102.6E-40142252IPR015300DNA-binding pseudobarrel domain
CDDcd100171.05E-22146248No hitNo description
SMARTSM010191.2E-23148250IPR003340B3 DNA binding domain
PROSITE profilePS5086313.549148250IPR003340B3 DNA binding domain
PfamPF023621.8E-22148249IPR003340B3 DNA binding domain
PfamPF065073.5E-34274355IPR010525Auxin response factor
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009734Biological Processauxin-activated signaling pathway
GO:0010050Biological Processvegetative phase change
GO:0010158Biological Processabaxial cell fate specification
GO:0010582Biological Processfloral meristem determinacy
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 705 aa     Download sequence    Send to blast
LIDLNTTEDE ETPSYGSLSP SSSSASVLSA SGSASSSPVC LELWHACAGP LISLPKRGSV  60
VVYFPQGHLE QVSDFSGVAP AYDLPPHVFC RVVDVKLHAE GATDEVYAQV SLVPENEQIE  120
QKLKEGNIEV DGEEDAEADI KSTTPHMFCK TLTASDTSTH GGFSVPRRAA EDCFPPLDYN  180
QQRPSQELVA KDLHGLEWRF RHIYRGQPRR HLLTTGWSAF VNKKKLVSGD AVLFLRGENG  240
ELRLGIRRAA HIKNGTSFHS LCTQQLNRSN FADVVHAISM KSVFSIYYNP RASSSEFIIP  300
VHKFWKSLDH SFSVGMRFKM RFESEDAAEG RYTGVVTGIS EMDPVRWSGS KWRCLLVRWD  360
DIETNRHIRV SPWEIEPSSS ISSSNSLLSP GSKRNRVGLP SGKPEFMVPE GIGASDFGES  420
LRFQKVLQGQ EILGFNTHND GANSQIMHRS DISRRFPCSN GSGIAAIRNI GRDTLVNPDI  480
SYKGVGFEES FRFQKVLQGQ ETFVSPPCRR GPTVDDTRES DSPGAPDVGQ LSGTRSGWSS  540
LMQSYNTHSR IGPSAQVSSP SSVLKFQHAS NPFANVNPIH NLNSQEKEQR VHKSSSFHAP  600
ETYGDGIPSS TGGHGSRRRT SQELAASCKS SCRLFGFSLT EGGHDAAKED NMVQATSSLG  660
AGAFLPRIGE QFNTQPPAVT NTVGSSYTKV SNLYAVRDIV YDIAL
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldy_A1e-1213238412361Auxin response factor 1
4ldy_B1e-1213238412361Auxin 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}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00021PBMTransfer from AT2G33860Download
Motif logo
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Negatively regulated by AHL21/GIK. {ECO:0000269|PubMed:19956801}.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_017607332.10.0PREDICTED: auxin response factor 3-like isoform X2
SwissprotO236610.0ARFC_ARATH; Auxin response factor 3
TrEMBLA0A0B0PK950.0A0A0B0PK95_GOSAR; Auxin response factor
STRINGGorai.009G166100.10.0(Gossypium raimondii)
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]