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 RrC5488_p1
Organism
Raphanus raphanistrum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Raphanus
Family ARF
Protein Properties Length: 660aa    MW: 73017.8 Da    PI: 7.5439
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC5488_p1genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B377.51.4e-24121222199
                 EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSSEE.. CS
          B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrsefel 92 
                 f k+lt+sd+++ g +++p+ +ae++        +++ +  t+  +d +g +W++++iyr++++r++lt+GW++Fv++++L +gD++vF+  + +++ l
  RrC5488_p1 121 FAKTLTQSDANNGGGFSVPRYCAETIfprldynAEPPVQ--TILAKDVHGDVWKFRHIYRGTPRRHLLTTGWSNFVNQKKLVAGDSIVFM--RAESGDL 215
                 89****************************985444444..8999*********************************************..4489999 PP

                 EEEEE-S CS
          B3  93 vvkvfrk 99 
                 +v+++r+
  RrC5488_p1 216 CVGIRRA 222
                 *****97 PP
2Auxin_resp111.86.7e-37280363183
  Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrl.sGtvvgvsdldpvrWpnSkWrsLk 83 
                 aa+ a ++  FevvY+PrastseF+vk+ + ++a++++++ GmRfkmafetedss++++ +Gtv++vs +dp+rWpnS+Wr+L+
  RrC5488_p1 280 AATLAINGRGFEVVYYPRASTSEFCVKALDARAAMRIPWCSGMRFKMAFETEDSSRISWfMGTVSAVSVSDPIRWPNSPWRLLQ 363
                 6778889999************************************************************************97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019366.67E-30111222IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.102.1E-38114228IPR015300DNA-binding pseudobarrel domain
CDDcd100174.54E-22119221No hitNo description
SMARTSM010191.7E-22121223IPR003340B3 DNA binding domain
PfamPF023621.6E-22121222IPR003340B3 DNA binding domain
PROSITE profilePS5086313.267121223IPR003340B3 DNA binding domain
PfamPF065078.4E-31280363IPR010525Auxin response factor
PROSITE profilePS5174518.234574660IPR000270PB1 domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0007389Biological Processpattern specification process
GO:0009733Biological Processresponse to auxin
GO:0048829Biological Processroot cap development
GO:0051301Biological Processcell division
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0005515Molecular Functionprotein binding
Sequence ? help Back to Top
Protein Sequence    Length: 660 aa     Download sequence    Send to blast
MINVMDPMKS GSEKGLDPQL WHACAGGMVR MPPMNSKVFY FPQGHAENAY DHVDFKNLPI  60
PPMVLCRVLA IKYMADPESD EVFAKLRLVP LKDDDHREYG DNGQVVEGQG FETNSEKTPS  120
FAKTLTQSDA NNGGGFSVPR YCAETIFPRL DYNAEPPVQT ILAKDVHGDV WKFRHIYRGT  180
PRRHLLTTGW SNFVNQKKLV AGDSIVFMRA ESGDLCVGIR RAKRGGIGNG PEYSAGWNPI  240
GGSCGYSSLL REDESNNLRR SNCSLADRKG KVTAESVIEA ATLAINGRGF EVVYYPRAST  300
SEFCVKALDA RAAMRIPWCS GMRFKMAFET EDSSRISWFM GTVSAVSVSD PIRWPNSPWR  360
LLQVAWDEPD LLQNVKRVNP WLVELVSNVH PIPLTSFSPP RKKMRLPQHP DYNNLINSIP  420
VPSFPSNPLI RSNPLSSVLD NVPVGLQGAR HNAHQYYGLS SSDLHHYYLN RPPPPPPQPS  480
STLPLPQPLG LRNIDSRNEK GFCFLTMGTT PCNDTESKKS QHIVLFGKLI LPEEQISEKG  540
STDTASTSGG SKLSSSDEGS PCSNKAHDAA GLETGHCKVF MESDDVGRTL DLSVLGSYEE  600
LSRKLSDMFG IQKAEMLSSV LYRDASGAIK YAGNEPFSEF LKTARRLTIL TEQGRESVVV
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldu_A7e-76938443388Auxin response factor 5
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. {ECO:0000269|PubMed:12036261}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00461DAPTransfer from AT4G30080Download
Motif logo
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankJN9794780.0JN979478.1 Brassica rapa subsp. pekinensis auxin response factor 16-2 (ARF16-2) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018477677.10.0PREDICTED: auxin response factor 16
SwissprotQ93YR90.0ARFP_ARATH; Auxin response factor 16
TrEMBLA0A3P5ZU720.0A0A3P5ZU72_BRACM; Auxin response factor
STRINGBo7g114200.10.0(Brassica oleracea)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MalvidsOGEM58027130
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G30080.10.0auxin response factor 16
Publications ? help Back to Top
  1. Yang ZB, et al.
    TAA1-regulated local auxin biosynthesis in the root-apex transition zone mediates the aluminum-induced inhibition of root growth in Arabidopsis.
    Plant Cell, 2014. 26(7): p. 2889-904
    [PMID:25052716]
  2. Bennett T,van den Toorn A,Willemsen V,Scheres B
    Precise control of plant stem cell activity through parallel regulatory inputs.
    Development, 2014. 141(21): p. 4055-64
    [PMID:25256342]
  3. Zhang GZ, et al.
    Ectopic expression of UGT75D1, a glycosyltransferase preferring indole-3-butyric acid, modulates cotyledon development and stress tolerance in seed germination of Arabidopsis thaliana.
    Plant Mol. Biol., 2016. 90(1-2): p. 77-93
    [PMID:26496910]
  4. Ye Y, et al.
    Germostatin resistance locus 1 encodes a PHD finger protein involved in auxin-mediated seed dormancy and germination.
    Plant J., 2016. 85(1): p. 3-15
    [PMID:26611158]
  5. Liu Z, et al.
    Repression of callus initiation by the miRNA-directed interaction of auxin-cytokinin in Arabidopsis thaliana.
    Plant J., 2016. 87(4): p. 391-402
    [PMID:27189514]
  6. 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]
  7. Wójcik AM,Nodine MD,Gaj MD
    miR160 and miR166/165 Contribute to the LEC2-Mediated Auxin Response Involved in the Somatic Embryogenesis Induction in Arabidopsis.
    Front Plant Sci, 2017. 8: p. 2024
    [PMID:29321785]
  8. Lin JS, et al.
    MicroRNA160 Modulates Plant Development and Heat Shock Protein Gene Expression to Mediate Heat Tolerance in Arabidopsis.
    Front Plant Sci, 2018. 9: p. 68
    [PMID:29449855]