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 Phvul.003G290200.1
Common NamePHAVU_003G290200g
Organism
Phaseolus vulgaris
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Fabales; Fabaceae; Papilionoideae; Phaseoleae; Phaseolus
Family ARF
Protein Properties Length: 707aa    MW: 77658.9 Da    PI: 7.607
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Phvul.003G290200.1genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B376.92.2e-24134235199
                         EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE- CS
                  B3   1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkld 85 
                         f+k+lt sd++++g +++p++ ae++      + +++ s++l+ +d++g++W++++iyr++++r++lt+GW+ Fv+ ++L ++D v+F   
  Phvul.003G290200.1 134 FCKTLTASDTSTHGGFSVPRRAAEDCfppldyS-QQRPSQELVAKDLHGQEWRFRHIYRGQPRRHLLTTGWSAFVNKKKLVSRDAVLFL-- 221
                         99****************************963.3445679************************************************.. PP

                         SSSEE..EEEEE-S CS
                  B3  86 grsefelvvkvfrk 99 
                         + +++el+++++r+
  Phvul.003G290200.1 222 RGEDGELRLGIRRA 235
                         449999*****996 PP
2Auxin_resp114.59.6e-38260341182
          Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsL 82 
                         +++a+s +++F+v YnPr+s+seF+++++k++++l+ ++svG+Rf+m+feted++err++G++vg++d+dpvrWp+SkWr+L
  Phvul.003G290200.1 260 VVNALSARCAFSVHYNPRVSSSEFIIPIKKFLRSLDYSYSVGTRFRMRFETEDAAERRFTGLIVGITDVDPVRWPGSKWRCL 341
                         6899*****************************************************************************9 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019364.19E-41127245IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.101.9E-40128237IPR015300DNA-binding pseudobarrel domain
CDDcd100173.13E-22132234No hitNo description
PfamPF023621.7E-22134235IPR003340B3 DNA binding domain
PROSITE profilePS5086312.858134236IPR003340B3 DNA binding domain
SMARTSM010194.7E-22134236IPR003340B3 DNA binding domain
PfamPF065073.0E-32261341IPR010525Auxin 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:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 707 aa     Download sequence    Send to blast
MPALIDLNSA TEDHETPSSR PSSVCLELWH ACAGPMISLP KKGTLVVYFP QGHLEQHLHD  60
FPLPASANIP SHLFCRVLDV KLHSEEGSDE VYCQVVLVPE SEQGHQKLRE GEIDADGEEE  120
DAEAVMKSTT PHMFCKTLTA SDTSTHGGFS VPRRAAEDCF PPLDYSQQRP SQELVAKDLH  180
GQEWRFRHIY RGQPRRHLLT TGWSAFVNKK KLVSRDAVLF LRGEDGELRL GIRRAAQLKS  240
GSTISTFAGQ QLNHSSLLDV VNALSARCAF SVHYNPRVSS SEFIIPIKKF LRSLDYSYSV  300
GTRFRMRFET EDAAERRFTG LIVGITDVDP VRWPGSKWRC LMVRWDDLEA TRHNRVSPWE  360
IEPSGSASTA NNMISAGLKR TKIGLPSTKL DFQVSNAIGA SDFGESLRFQ KVLQGQEMLG  420
VNTTFDSTNG QGHQLSDLRR CYPGSNCSRI AATGNSIGIP QVSSNVSCNG IGFSESFRFQ  480
KVLQGQEILP SQPYGRALSV DEACGNGRFG PFDGYHTLRS RNGWSSHLSN SSSHLHPPVP  540
SGQVSSPSSV LMFQQAHNPV SNSDYNSKIS QVMEGKVQQR SSYTSEAKGG KFVSTPYEPL  600
RGLAQEGTNS YGVSNLHNQF ETSRSHDSIS ALRATQELVP TCKSRCRVFG FSLTEGAPVA  660
SKEVAGTDPS AVTCSGPSFA RHAEDDFHPV HSKAVGSYCT KGVLQY*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldy_A1e-1122336818359Auxin response factor 1
4ldy_B1e-1122336818359Auxin 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
PlantRegMapPhvul.003G290200.1
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
GenBankAP0150340.0AP015034.1 Vigna angularis var. angularis DNA, chromosome 1, almost complete sequence, cultivar: Shumari.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_007156488.10.0hypothetical protein PHAVU_003G290200g
SwissprotO236610.0ARFC_ARATH; Auxin response factor 3
TrEMBLV7CE540.0V7CE54_PHAVU; Auxin response factor
STRINGXP_007156488.10.0(Phaseolus vulgaris)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
FabidsOGEF45763355
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]