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 RrC1226_p4
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: 617aa    MW: 68226.5 Da    PI: 7.9427
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
RrC1226_p4genomeMSUView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B377.51.5e-24120221199
                 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
  RrC1226_p4 120 FAKTLTQSDANNGGGFSVPRYCAETIfprldynAEPPVQ--TILAKDVHGDVWKFRHIYRGTPRRHLLTTGWSNFVNQKKLVAGDSIVFM--RAENGDL 214
                 89****************************985444444..8999*********************************************..4488999 PP

                 EEEEE-S CS
          B3  93 vvkvfrk 99 
                 +v+++r+
  RrC1226_p4 215 CVGIRRA 221
                 ****997 PP
2Auxin_resp821.3e-27275342268
  Auxin_resp   2 ahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrl.sGtvvgvsd 68 
                 a  a ++ +FevvY+Pras+seF+vk+ + ++a++++++ GmRfkmafetedss++++ +Gtv++v  
  RrC1226_p4 275 AALAVSGRAFEVVYYPRASSSEFCVKALDARAAMRIPWCSGMRFKMAFETEDSSRISWfMGTVSAVAW 342
                 66788999********************************************************9865 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.102.6E-39110225IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019366.8E-30115223IPR015300DNA-binding pseudobarrel domain
CDDcd100173.23E-22118220No hitNo description
SMARTSM010197.1E-23120222IPR003340B3 DNA binding domain
PROSITE profilePS5086313.352120222IPR003340B3 DNA binding domain
PfamPF023621.6E-22120221IPR003340B3 DNA binding domain
PfamPF065076.5E-22274341IPR010525Auxin response factor
PROSITE profilePS5174517.716531611IPR000270PB1 domain
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:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0005515Molecular Functionprotein binding
Sequence ? help Back to Top
Protein Sequence    Length: 617 aa     Download sequence    Send to blast
MINVMNPMRS GSEKGLDPQL WHACAGGMVR MPPMNSKVFY FPQGHAENAY DRVDFKNLPL  60
PPMVLCRVLA IKYMADPESD EVFAKLRLIP LKDDDFVDHE YIDGRQDSNE SNNSEKTPSF  120
AKTLTQSDAN NGGGFSVPRY CAETIFPRLD YNAEPPVQTI LAKDVHGDVW KFRHIYRGTP  180
RRHLLTTGWS NFVNQKKLVA GDSIVFMRAE NGDLCVGIRR AKRGGIGGNG PEYSAGWNPI  240
GGSCGGYSSL LRDDSSSSLA DRKGKVTAES VVEAAALAVS GRAFEVVYYP RASSSEFCVK  300
ALDARAAMRI PWCSGMRFKM AFETEDSSRI SWFMGTVSAV AWDEPDLLQN VKRVNPWLVE  360
LVSNVHPMPL PSFSPPRKKM RVPQHQDYNN ARISVPSFPS NPLIRSSSPL GSVLDNVPVG  420
LQGARHNAHQ YYGLSSSDLH HYYLNRPPPP PPSSTPPPLG FRNIDSKNEK GFCFLTMGTS  480
PGSDTESKKS HIVLFGKLIL PEEQKGSTDV EKTQIPPVCS NKAHEALGLE TGHCKVFMES  540
DDVGRTLDLS VLGSYEELSR KLSDMFGIQK SEMLSSVLYR DASGAIKYPG KEPFSEFLKT  600
ARRLTIMTEQ GSESVVV
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldu_A2e-64936043388Auxin 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}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankJN9794770.0JN979477.1 Brassica rapa subsp. pekinensis auxin response factor 16-1 (ARF16-1) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_018470497.10.0PREDICTED: auxin response factor 16-like
SwissprotQ93YR90.0ARFP_ARATH; Auxin response factor 16
TrEMBLA0A398AJP50.0A0A398AJP5_BRACM; Auxin response factor
STRINGBra011162.1-P0.0(Brassica rapa)
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]