PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Cagra.1744s0020.1.p
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Capsella
Family ARF
Protein Properties Length: 671aa    MW: 73941.7 Da    PI: 7.2025
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Cagra.1744s0020.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B377.31.7e-24120221199
                          EEEE-..-HHHHTT-EE--HHH.HTT.......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEE CS
                   B3   1 ffkvltpsdvlksgrlvlpkkfaeeh.......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFk 83 
                          f k+lt+sd+++ g +++p+ +ae++        +++ +  t+  +d +g +W++++iyr++++r++lt+GW++Fv++++L +gD++vF+
  Cagra.1744s0020.1.p 120 FAKTLTQSDANNGGGFSVPRYCAETIfprldynAEPPVQ--TILAKDVHGDVWKFRHIYRGTPRRHLLTTGWSNFVNQKKLVAGDSIVFM 207
                          89****************************985444444..8999********************************************* PP

                          E-SSSEE..EEEEE-S CS
                   B3  84 ldgrsefelvvkvfrk 99 
                            + +++ l+v+++r+
  Cagra.1744s0020.1.p 208 --RAENGDLCVGIRRA 221
                          ..4488999****997 PP

2Auxin_resp113.71.7e-37279362183
           Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrl.sGtvvgvsdldpvrWpnSkWrsLk 83 
                          aa+ a ++ +FevvY+PrastseF+vk+ + ++a++++++ GmRfkmafetedss++++ +Gtv++v+ +dp+rWpnS+Wr+L+
  Cagra.1744s0020.1.p 279 AATLAISGRPFEVVYYPRASTSEFCVKALDARAAMRIPWCSGMRFKMAFETEDSSRISWfMGTVSAVNVSDPIRWPNSPWRLLQ 362
                          67788899**************************************************************************97 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.105.5E-39112227IPR015300DNA-binding pseudobarrel domain
SuperFamilySSF1019367.72E-30115223IPR015300DNA-binding pseudobarrel domain
CDDcd100171.96E-22118220No hitNo description
PfamPF023621.8E-22120221IPR003340B3 DNA binding domain
SMARTSM010197.1E-23120222IPR003340B3 DNA binding domain
PROSITE profilePS5086313.352120222IPR003340B3 DNA binding domain
PfamPF065072.7E-31279362IPR010525Auxin response factor
PROSITE profilePS5174517.488584664IPR000270PB1 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: 671 aa     Download sequence    Send to blast
MINVMNPLKG GSEKGLDPQL WHACAGGMVR MPPMNSKVFY FPQGHAENAY DCVDFGNMPI  60
HPMVLCRVLA IKYMADAESD EVFAKLRLIP LKEDDYVDHE YTDGDDSNGF ESNSEKTPSF  120
AKTLTQSDAN NGGGFSVPRY CAETIFPRLD YNAEPPVQTI LAKDVHGDVW KFRHIYRGTP  180
RRHLLTTGWS NFVNQKKLVA GDSIVFMRAE NGDLCVGIRR AKRGGIGNGP EYSAGWNPIG  240
GSCGYSSLLR EDESNTLRRS NCSLADRKGK VTAESVIEAA TLAISGRPFE VVYYPRASTS  300
EFCVKALDAR AAMRIPWCSG MRFKMAFETE DSSRISWFMG TVSAVNVSDP IRWPNSPWRL  360
LQVAWDEPDL LQNVKRVNPW LVELVSNVHP IPLTSFSPPR KKMRLPQHPD YNNLINSIPI  420
PSFPSNPLIR SSPLSSVLDN VPVGLQGARH NAHQYYGLSS SDLHHYYLNR PPPPPPSSLP  480
LSPSLGLRNI DSKNEKGFCF LTMGTTPCND TASKKSHIVL FGKLILPEEQ LSEKGSTDTA  540
NVEKTQISSG GSNQNNGIAG RDLSSSDEGS PCSKKVHDAS GLETGHCKVF MESDEVGRTL  600
DLSVLGSYDE LSRKLSDMFG IKKSEMLSSV LYKDASGAIK YPGNEPFSEF LKTARRLTIL  660
TEQGSESVVI *
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldu_A2e-76238337388Auxin 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
PlantRegMapCagra.1744s0020.1.p
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAY0597920.0AY059792.1 Arabidopsis thaliana putative transcription factor (At4g30080) mRNA, complete cds.
GenBankAY0911980.0AY091198.1 Arabidopsis thaliana putative transcription factor (At4g30080) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_023635190.10.0auxin response factor 16
SwissprotQ93YR90.0ARFP_ARATH; Auxin response factor 16
TrEMBLR0GY890.0R0GY89_9BRAS; Auxin response factor
STRINGXP_006283190.10.0(Capsella rubella)
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]