PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID XP_013593026.1
Organism
Brassica oleracea
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: 654aa    MW: 72137.6 Da    PI: 7.0666
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
XP_013593026.1genomeNCBIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B377.51.4e-24117218199
                     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_013593026.1 117 FAKTLTQSDANNGGGFSVPRYCAETIfprldynAEPPVQ--TILAKDVHGDVWKFRHIYRGTPRRHLLTTGWSNFVNQKKLVAGDSIVFM--RAE 207
                     89****************************985444444..8999*********************************************..448 PP

                     EE..EEEEE-S CS
              B3  89 efelvvkvfrk 99 
                     ++ l+v+++r+
  XP_013593026.1 208 SGDLCVGIRRA 218
                     9999*****97 PP
2Auxin_resp111.21.1e-36276359183
      Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrl.sGtvvgvsdldpvrWpnSkWrsLk 83 
                     aa+ a ++  FevvY+PrastseF+vk+ + ++a++++++ GmRfkmafetedss++++ +Gtv++vs +dp+rWpnS+Wr+L+
  XP_013593026.1 276 AATLALSGRGFEVVYYPRASTSEFCVKALDARAAMRIPWCSGMRFKMAFETEDSSRISWfMGTVSAVSVSDPIRWPNSPWRLLQ 359
                     5677788999************************************************************************97 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019361.44E-29108219IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.101.1E-38109223IPR015300DNA-binding pseudobarrel domain
CDDcd100174.44E-22115217No hitNo description
PROSITE profilePS5086313.267117219IPR003340B3 DNA binding domain
SMARTSM010191.7E-22117219IPR003340B3 DNA binding domain
PfamPF023621.6E-22117218IPR003340B3 DNA binding domain
PfamPF065071.8E-30276359IPR010525Auxin response factor
PROSITE profilePS5174517.352568646IPR000270PB1 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: 654 aa     Download sequence    Send to blast
MINVMDPMKS GSEKGLDPQL WHACAGGMVR MPPVNSKVFY FPQGHAENAY DHVDFKNLPI  60
PPMVLCRVLA IKYMADPESD EVFAKLRLIP LKDDDHEYGD GQEGNGFESN SEKTPSFAKT  120
LTQSDANNGG GFSVPRYCAE TIFPRLDYNA EPPVQTILAK DVHGDVWKFR HIYRGTPRRH  180
LLTTGWSNFV NQKKLVAGDS IVFMRAESGD LCVGIRRAKR GGIGNGPDYS PGWNPIGGSC  240
GYSSLLREDE SNSLRRSNCS LADRKGKVAA ESVIEAATLA LSGRGFEVVY YPRASTSEFC  300
VKALDARAAM RIPWCSGMRF KMAFETEDSS RISWFMGTVS AVSVSDPIRW PNSPWRLLQV  360
AWDEPDLLQN VKRVNPWLVE LVSNVHPIPL TSFSPPRKKM RLPQHPDYNN LINSIPVPSF  420
PSNPLIRSNP LSSVLDNVPV GLQGARHNAH QYYGLSSSDL HHYYLNRPPP PPQPSALPLS  480
QPLGLRNIDS RNEKGFCFLT MGTTPCNDDT ESKKSHIVLF GKLILPEEQI SEKGSTDTAN  540
TSGGSKLSSS DEGSPCSNKA HDAAGLETGH CKVFMESDDV GRTLDLSVLG SYEELSRKLS  600
DMFGIQKAEM LSSVLYRDAS GAIKYAGNEP FSEFLKTARR LTIVTEQGSE SVVV
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldu_A1e-76938043388Auxin 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
Cis-element ? help Back to Top
SourceLink
PlantRegMapXP_013593026.1
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_013593026.10.0PREDICTED: auxin response factor 16
SwissprotQ93YR90.0ARFP_ARATH; Auxin response factor 16
TrEMBLA0A0D3DGX20.0A0A0D3DGX2_BRAOL; 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]