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 SMil_00002054-RA_Salv
Organism
Salvia miltiorrhiza
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Lamiales; Lamiaceae; Nepetoideae; Mentheae; Salvia
Family ARF
Protein Properties Length: 694aa    MW: 76569.6 Da    PI: 7.7669
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
SMil_00002054-RA_SalvgenomeNDCTCMView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B362.28.3e-20161243178
                            EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT- CS
                     B3   1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegD 78 
                            f+k+lt sd++++g +++p++ ae++      + +++ s++l+ +d++g +W++++iyr++++r++lt+GW+ Fv+ ++L  gD
  SMil_00002054-RA_Salv 161 FCKTLTASDTSTHGGFSVPRRAAEDCfppldyK-QQRPSQELVAKDLHGIEWKFRHIYRGQPRRHLLTTGWSAFVNKKKLVGGD 243
                            99****************************963.3445679***************************************9998 PP
2Auxin_resp106.92.3e-35278359182
             Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsL 82 
                            +++a++t ++F+++YnPr+ +s+ +v+ +k+ k+l++++s GmRfk++fetedsserr+sG++vgvsd+dp rWp+SkW++L
  SMil_00002054-RA_Salv 278 VVNAITTWTTFDICYNPRMRSSDIIVPHHKFCKSLTQSFSCGMRFKIRFETEDSSERRCSGLIVGVSDVDPARWPGSKWKCL 359
                            6899*****************************************************************************9 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019361.44E-37157246IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.102.6E-32158243IPR015300DNA-binding pseudobarrel domain
CDDcd100176.16E-19159243No hitNo description
PROSITE profilePS508639.77161264IPR003340B3 DNA binding domain
PfamPF023627.1E-18161243IPR003340B3 DNA binding domain
SMARTSM010192.1E-16161254IPR003340B3 DNA binding domain
PfamPF065072.9E-30279359IPR010525Auxin 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: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: 694 aa     Download sequence    Send to blast
LLSLKKGLNM MNGLIDLNTV NNEDETASGC GSPSSSVASG NLELATASSS MPSVSMELWH  60
ACAGPLISLP KKGSAVVYFP QGHVEHLPEH PAVTYDLPPH VFCRVVDVKL HADTTSDEVY  120
AQVSLIPDQQ IEQKWREGIM ESEAEDEDLE GVVKTMTPHM FCKTLTASDT STHGGFSVPR  180
RAAEDCFPPL DYKQQRPSQE LVAKDLHGIE WKFRHIYRGQ PRRHLLTTGW SAFVNKKKLV  240
GGDGELRLGI RRAAQIKSGA TTLPTTSQLS NASGIAAVVN AITTWTTFDI CYNPRMRSSD  300
IIVPHHKFCK SLTQSFSCGM RFKIRFETED SSERRCSGLI VGVSDVDPAR WPGSKWKCLL  360
VRWDDMEVNR LNRVSPWEIE LAGPMSGPNS FALPGTKRNR IGFPPAVKPD APVHRDGNDV  420
SDFVEPLRFQ KVLQGQEVFP FGSQYAGAEA SRNHLSDIRG YPSLSGFHAG GNSIRQHHAD  480
ARNSLERTVV GESFQFRAQE WKLLVTPPQY NGSPHLSPSM VRGLSPSSVL LLQQSSPQNS  540
QIPSLIHGYQ NKHETSNQDS FRVSQRIPKK FAPCEISPRD DLQHGYRSSG APEAHSPPVL  600
THRPLLTQPL FRDNQNFVSM CKDSCRLFGF PLTEGINAIG KADSHAAASA SAYGHGSNEE  660
QLFQPPLVTK VMVSSCTKPS DMHAVRDRLL DIAL
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldy_A1e-1005738022353Auxin response factor 1
4ldy_B1e-1005738022353Auxin 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 -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankKX0367240.0KX036724.1 Salvia miltiorrhiza auxin response factor ARF4 (ARF) gene, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_020554020.10.0auxin response factor 3 isoform X1
SwissprotO236611e-176ARFC_ARATH; Auxin response factor 3
TrEMBLA0A191T8S50.0A0A191T8S5_SALMI; Auxin response factor
STRINGMigut.M01096.1.p0.0(Erythranthe guttata)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA61012333
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G33860.11e-177ARF 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]