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 XP_009128129.1
Organism
Brassica rapa
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Brassiceae; Brassica
Family ARF
Protein Properties Length: 647aa    MW: 71523 Da    PI: 8.0689
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_009128129.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B378.29e-25118219199
                     EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE-SSS CS
              B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkldgrs 88 
                     f k+lt+sd+++ g +++p+ +ae++        +++ +  t+  +d +g++W++++iyr++++r++lt+GW++Fv++++L +gD++vF+  + +
  XP_009128129.1 118 FAKTLTQSDANNGGGFSVPRYCAETIfprldynAEPPVQ--TILAKDVHGEVWKFRHIYRGTPRRHLLTTGWSNFVNQKKLVAGDSIVFM--RAE 208
                     89****************************985444444..8999*********************************************..448 PP

                     EE..EEEEE-S CS
              B3  89 efelvvkvfrk 99 
                     ++ l+v+++r+
  XP_009128129.1 209 NGDLCVGIRRA 219
                     8999****997 PP
2Auxin_resp110.81.3e-36272355183
      Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrl.sGtvvgvsdldpvrWpnSkWrsLk 83 
                     aa+ a ++  FevvY+Pras+seF+vk+ + ++a++++++ GmRfkmafetedss++++ +Gtv++vs +dpvrWpnS+Wr+L+
  XP_009128129.1 272 AAKLAVSGRGFEVVYYPRASSSEFCVKALDARAAMRIPWCSGMRFKMAFETEDSSRISWfMGTVSAVSVSDPVRWPNSPWRLLQ 355
                     6778889999************************************************************************97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.103.0E-39109223IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019364.71E-30113221IPR015300DNA-binding pseudobarrel domain
CDDcd100171.53E-22116218No hitNo description
PfamPF023629.6E-23118219IPR003340B3 DNA binding domain
PROSITE profilePS5086313.437118220IPR003340B3 DNA binding domain
SMARTSM010194.1E-23118220IPR003340B3 DNA binding domain
PfamPF065071.1E-30272355IPR010525Auxin response factor
PROSITE profilePS5174516.933561641IPR000270PB1 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: 647 aa     Download sequence    Send to blast
MINVMNPMRS GSEKGLDPQL WHACAGGMVR MPPMNSKVFY FPQGHAENAY DHVDFKNLPI  60
PPMVLCRVLA IKYMADPESD EVFAKLKLIP LKDNDHEYRD GEESNGLGSN NSEKTPSFAK  120
TLTQSDANNG GGFSVPRYCA ETIFPRLDYN AEPPVQTILA KDVHGEVWKF RHIYRGTPRR  180
HLLTTGWSNF VNQKKLVAGD SIVFMRAENG DLCVGIRRAK RGGIGNNGLE YSAGWNPIGG  240
SYSSLLRDDE RRSSSSLADR KGKVTAESVV EAAKLAVSGR GFEVVYYPRA SSSEFCVKAL  300
DARAAMRIPW CSGMRFKMAF ETEDSSRISW FMGTVSAVSV SDPVRWPNSP WRLLQVAWDE  360
PDLLQYVKRV NPWLVELVSN VHPIIPSFSP PRKKMRLPQH PDYNTRISVP SFASNPLIRS  420
SPLSSVLDNV PVGLQGARHN AHQYYGLSSS DLHHYYLNRP HPPPPSSTLS VPPPLGFRNI  480
DSKNEKGFCF LTMGTSPCND TESKKSHIVL FGKLILPEEQ KGSEKTQLSS GGSNQNCVAG  540
SSSEEGSPCS NKAHDGLGLE TGHCKVFMES DDVGRTLDLS VLGSYEELGM KLSDMFGIQK  600
SEMLSSVLYR DASGAVKYPG NEPFSEFLKT ARRLTILSEQ GSESVVV
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldu_A4e-78937643388Auxin response factor 5
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Bra.287980.0leaf
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}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapXP_009128129.1
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_009128129.10.0PREDICTED: auxin response factor 16
SwissprotQ93YR90.0ARFP_ARATH; Auxin response factor 16
TrEMBLH9B4D80.0H9B4D8_BRARP; 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]