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 Potri.003G163600.3
Common NamePOPTR_0003s16210g
Organism
Populus trichocarpa
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus
Family ARF
Protein Properties Length: 769aa    MW: 87566.4 Da    PI: 7.2516
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Potri.003G163600.3genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B371.98.2e-23159260199
                         EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE- CS
                  B3   1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkld 85 
                         f+k lt sd++++g +++ k++a+e+      +++++  ++l+ +d++g++W++++i+r++++r++l++GW+ Fv+a++L +gD ++F   
  Potri.003G163600.3 159 FCKMLTASDTSTHGGFSVLKRHADEClppldmSLQPPV-QELVAKDLHGNEWRFRHIFRGQPRRHLLQSGWSLFVSAKKLVAGDAFIFL-- 246
                         89*****************************9666655.49************************************************.. PP

                         SSSEE..EEEEE-S CS
                  B3  86 grsefelvvkvfrk 99 
                         + +++el+v+v+r+
  Potri.003G163600.3 247 RGETEELRVGVRRA 260
                         3489999****985 PP
2Auxin_resp119.23.4e-39285367183
          Auxin_resp   1 aahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsLk 83 
                         a+ha+st+s+F+v+Y+Pr+s++eF+++v+k+++++k+++++GmRfkm+fe +d++e+r+sGtv+gv+++dp +Wp+S+Wr+Lk
  Potri.003G163600.3 285 AWHAVSTGSMFTVYYKPRTSPAEFIIPVDKYMESVKINYAIGMRFKMRFEADDAPEQRFSGTVIGVEEADPKKWPRSNWRCLK 367
                         89*******************************************************************************96 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019365.49E-39152288IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.108.0E-39153274IPR015300DNA-binding pseudobarrel domain
CDDcd100178.84E-20157259No hitNo description
PROSITE profilePS5086311.42159261IPR003340B3 DNA binding domain
PfamPF023629.2E-21159260IPR003340B3 DNA binding domain
SMARTSM010191.4E-21159261IPR003340B3 DNA binding domain
PfamPF065079.3E-36285367IPR010525Auxin response factor
PROSITE profilePS5174524.355626719IPR000270PB1 domain
SuperFamilySSF542775.1E-11626703No hitNo description
PfamPF023094.8E-6672717IPR033389AUX/IAA domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009734Biological Processauxin-activated signaling pathway
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0005515Molecular Functionprotein binding
Sequence ? help Back to Top
Protein Sequence    Length: 769 aa     Download sequence    Send to blast
MELRAGAGVF RWLVKVPMII HNDFLSFSFD FFRFYWIIAV VVLARVGSED ALYKELWHAC  60
AGPLVTVPRQ GELVYYFPQG HIEQVEASTN QVADDQQMPA YNLSPKILCR VVNVQLKAEL  120
DTDEVFAQVI LLPETQQDVE LVEEEDLPPL PARPRVHSFC KMLTASDTST HGGFSVLKRH  180
ADECLPPLDM SLQPPVQELV AKDLHGNEWR FRHIFRGQPR RHLLQSGWSL FVSAKKLVAG  240
DAFIFLRGET EELRVGVRRA LRQPSKIPSS LISSHSMHIG ILATAWHAVS TGSMFTVYYK  300
PRTSPAEFII PVDKYMESVK INYAIGMRFK MRFEADDAPE QRFSGTVIGV EEADPKKWPR  360
SNWRCLKVHW DETSPVHRPD RVSPWKVEPA LAPSMDPVSG CRLKRHRPNT VTSSADSSAL  420
TKKDNGPSRH MQHQEILTLR NTPTGKNYSD NNHNPPWVLS QDEKSMFNWH SAPMMYTGHP  480
FNMLASSMEV QVAKDKDTQQ QHGSRFLPFP YADSSPHPSR SKPQHLPFQQ CNERTAKDDN  540
YKLFGVSLFR NSKALEPATI HRHSADKPQH QINVASDHLQ LLGSDRYLEQ LKHPKHARCE  600
EQENIFQASS LYSKDVQGKP EGGSARRCVK VHKQGTAVGR SLDLAKFNGY NELTAELDQI  660
FEFNGELVAP NKDWLIVFTD DEDDMMLVGD DPWQEFCSMA RRIFIYTKEE INRMEPRSLN  720
REAEGNSRST DQMVDLENRI SKHLPAVSPS ECQGLCYMTG SKVMRPER*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A1e-1665038917354Auxin response factor 1
4ldw_A1e-1665038917354Auxin response factor 1
4ldw_B1e-1665038917354Auxin response factor 1
4ldx_A1e-1665038917354Auxin response factor 1
4ldx_B1e-1665038917354Auxin response factor 1
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Pth.117330.0bud
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in roots, culms, leaves and young panicles. {ECO:0000269|PubMed:17408882}.
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).
Cis-element ? help Back to Top
SourceLink
PlantRegMapPotri.003G163600.3
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC2084820.0AC208482.1 Populus trichocarpa clone JGIACSB13-H05, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_024453973.10.0auxin response factor 4 isoform X3
SwissprotQ5JK200.0ARFD_ORYSJ; Auxin response factor 4
TrEMBLA0A385JHW80.0A0A385JHW8_POPTO; Auxin response factor
STRINGPOPTR_0003s16210.10.0(Populus trichocarpa)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G62000.30.0auxin response factor 2
Publications ? help Back to Top
  1. Kikuchi S, et al.
    Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice.
    Science, 2003. 301(5631): p. 376-9
    [PMID:12869764]
  2. Song X, et al.
    Rice RNA-dependent RNA polymerase 6 acts in small RNA biogenesis and spikelet development.
    Plant J., 2012. 71(3): p. 378-89
    [PMID:22443269]
  3. Kishimoto N, et al.
    Identification of the duplicated segments in rice chromosomes 1 and 5 by linkage analysis of cDNA markers of known functions.
    Theor. Appl. Genet., 1994. 88(6-7): p. 722-6
    [PMID:24186168]