PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Sp_038740_sosp.t1
Common NameSOVF_038740
Organism
Spinacia oleracea
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; Caryophyllales; Chenopodiaceae; Chenopodioideae; Anserineae; Spinacia
Family ARF
Protein Properties Length: 692aa    MW: 76787.3 Da    PI: 6.9682
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Sp_038740_sosp.t1genomeTBVRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B377.61.3e-24170271199
                        EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-S CS
                 B3   1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldg 86 
                        f+k+lt sd++++g +++p++ ae++      + +++ s++l+ +d++g +W++++iyr++++r++lt+GW+ Fv+ ++L +gD v+F   +
  Sp_038740_sosp.t1 170 FCKTLTASDTSTHGGFSVPRRAAEDCfppldyK-QQRPSQELVAKDLHGLEWRFRHIYRGQPRRHLLTTGWSAFVNKKKLVSGDAVLFL--R 258
                        99****************************963.3445679************************************************..3 PP

                        SSEE..EEEEE-S CS
                 B3  87 rsefelvvkvfrk 99 
                         +++el+++++r+
  Sp_038740_sosp.t1 259 GDDGELRLGIRRA 271
                        489999****996 PP
2Auxin_resp115.83.8e-38297377282
         Auxin_resp   2 ahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsL 82 
                         +a+s++ vF+v+YnPras+seFvv++++++k+l++++ vGmRfkm+fe ed+ err++G+v+g+ +ldpvrWp+SkWr+L
  Sp_038740_sosp.t1 297 LDAVSSGRVFNVCYNPRASSSEFVVPIRRFLKSLDTSFNVGMRFKMRFEAEDAGERRYTGVVTGMAELDPVRWPGSKWRCL 377
                        6799****************************************************************************9 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019364.97E-43163280IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.108.5E-40165273IPR015300DNA-binding pseudobarrel domain
CDDcd100173.13E-22168270No hitNo description
PfamPF023621.1E-22170271IPR003340B3 DNA binding domain
SMARTSM010192.9E-23170272IPR003340B3 DNA binding domain
PROSITE profilePS5086313.126170272IPR003340B3 DNA binding domain
PfamPF065075.4E-33296377IPR010525Auxin 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: 692 aa     Download sequence    Send to blast
MMGVLIDLNT VNEDEEDNNS NISNNNYNYQ NTLQNHLQNS SSSVCMELWH ACAGPLISLP  60
KKGNLVVYLP QGHLEEHHQQ NNLPGFDFSR GINSNNHNFD SHQSNIPPHV FCRVLDVKLH  120
AEVATDEVYA QVSLIPESQI EEKLKESEAD IEGDEEDFED LVKSTTPHMF CKTLTASDTS  180
THGGFSVPRR AAEDCFPPLD YKQQRPSQEL VAKDLHGLEW RFRHIYRGQP RRHLLTTGWS  240
AFVNKKKLVS GDAVLFLRGD DGELRLGIRR AVQLKGSGSF PALPTRPMSN NSVSAALDAV  300
SSGRVFNVCY NPRASSSEFV VPIRRFLKSL DTSFNVGMRF KMRFEAEDAG ERRYTGVVTG  360
MAELDPVRWP GSKWRCLMVR WDDVEVNRHG RVSPWEIELT GSFPSPSSIM ASGLKRSRIG  420
LPLSKPEFPI PSGVGMADFG ESMGFRKVLQ GQEKLGCRSA CDGNDNPHLP PSDPGRRFHS  480
SVPPGEFGRT AKGGIGFRES FRFQKVLQGQ EIHHLSPAHL DGLTSSLNRG GHEGCGGPLE  540
IYEGVQVPNS CGTGWLKAQV SSPSSILMFP HPSIQQQARS SFRPPMSQPR LMNYSGVPAA  600
YNFLSKASDE LVPSGKASCR LFGFSLTEGE HDHRVDNERK HSNSFQPPES SFWPLVEGQP  660
CYKSPSVNKV GSNCPGTNDL YAVRDMLLDI AL
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A1e-1114140316358Auxin response factor 1
4ldw_A1e-1114140316358Auxin response factor 1
4ldw_B1e-1114140316358Auxin response factor 1
4ldx_A1e-1114140316358Auxin response factor 1
4ldx_B1e-1114140316358Auxin response factor 1
4ldy_A1e-1114140316358Auxin response factor 1
4ldy_B1e-1114140316358Auxin 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}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_021844131.10.0auxin response factor 3
SwissprotO236610.0ARFC_ARATH; Auxin response factor 3
TrEMBLA0A0K9RQW40.0A0A0K9RQW4_SPIOL; Auxin response factor
STRINGXP_010686390.10.0(Beta vulgaris)
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]