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 Pavir.5NG425700.1.p
Organism
Panicum virgatum
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; Liliopsida; Petrosaviidae; commelinids; Poales; Poaceae; PACMAD clade; Panicoideae; Panicodae; Paniceae; Panicinae; Panicum
Family ARF
Protein Properties Length: 711aa    MW: 78476 Da    PI: 6.6282
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.5NG425700.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B375.56.3e-24139240199
                          EEEE-..-HHHHTT-EE--HHH.HTT......---..--SEEEEEETTS-EEEEEE..EEETTEEEE-TTHHHHHHHHT--TT-EEEEEE CS
                   B3   1 ffkvltpsdvlksgrlvlpkkfaeeh......ggkkeesktltledesgrsWevkliyrkksgryvltkGWkeFvkangLkegDfvvFkl 84 
                          f+k+lt sd++++g +++p++ ae++      +++ + s++l+ +d++g +W++++iyr++++r++lt+GW+ Fv+ ++L +gD v+F  
  Pavir.5NG425700.1.p 139 FCKTLTASDTSTHGGFSVPRRAAEDCfppldySLQRP-SQELVAKDLHGTEWKFRHIYRGQPRRHLLTTGWSAFVNKKKLVSGDAVLFL- 226
                          99****************************9966654.569************************************************. PP

                          -SSSEE..EEEEE-S CS
                   B3  85 dgrsefelvvkvfrk 99 
                           + +++ l ++v+r+
  Pavir.5NG425700.1.p 227 -RGEDGVLQLGVRRA 240
                          .34889899999986 PP
2Auxin_resp102.55.5e-34266345282
           Auxin_resp   2 ahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsL 82 
                           +a++ ++vF+++YnPr s+seF+v+++k+++++++++svGmR +m++e++d+serr++G+++g ++++p  W++SkW+sL
  Pavir.5NG425700.1.p 266 TQAVALRTVFHICYNPRLSQSEFIVPYWKFMRSFNQPFSVGMRCRMRYESDDASERRCTGIIIGSREAEP-MWHGSKWKSL 345
                          6788999***************************************************************.9*******99 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019363.53E-42133256IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.103.9E-39135242IPR015300DNA-binding pseudobarrel domain
CDDcd100171.21E-22137239No hitNo description
PfamPF023629.4E-22139240IPR003340B3 DNA binding domain
SMARTSM010193.8E-22139241IPR003340B3 DNA binding domain
PROSITE profilePS5086313.296139241IPR003340B3 DNA binding domain
PfamPF065077.6E-29266345IPR010525Auxin response factor
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
Sequence ? help Back to Top
Protein Sequence    Length: 711 aa     Download sequence    Send to blast
MAGIDLNTVE GEEDEEEPEA PRADGAVCLD LWHACAGPVA PLPRKGSAVV YLPQGHLEHV  60
GGDAAPPAAV PPHVFCRVVD VNLHADGATD EVYARVSLLP EDEEAERRGR ARAREDEDAA  120
RDGEGGGAMK PLARTPHMFC KTLTASDTST HGGFSVPRRA AEDCFPPLDY SLQRPSQELV  180
AKDLHGTEWK FRHIYRGQPR RHLLTTGWSA FVNKKKLVSG DAVLFLRGED GVLQLGVRRA  240
AQLKNVNLIP ALHNQCSNHR NLGNVTQAVA LRTVFHICYN PRLSQSEFIV PYWKFMRSFN  300
QPFSVGMRCR MRYESDDASE RRCTGIIIGS REAEPMWHGS KWKSLAVRWD DDIERCRSNR  360
VSPWEIELTG SVSGSQSHLC VPNSKRLKPC LPQVNTEIVL PYGSVSSDFA GSARFHKVLQ  420
GQEFLGFKTH DDTAVSALQA TEARNLQYND EHSSSINNSN NILGVPRFGV RSPTGTPGFP  480
YHCSGFGESQ RFQKVLQGQE VFRSFRGALA DVHIRTSGMY QPDCMHATGA AYKWPTPQGC  540
DFRQPTKPVL LQASSPSSVL MFPQTSSKVP HLEYGYSCLD KDDTGRNDRA FPTQDMGRSN  600
QALSLWPHLV SGEAIDECTG TEKMHSPVSD AEHESNNEST VENGCKIFGI SLAEQVRSCD  660
EADSCNANCN SRFQPSEPQM SKSLGSCWAT VHEQRPTVGR VVDVSLMDMI *
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A1e-1052637518361Auxin response factor 1
4ldw_A1e-1052637518361Auxin response factor 1
4ldw_B1e-1052637518361Auxin response factor 1
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Pvr.183340.0callus| leaf| stem
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
PlantRegMapPavir.5NG425700.1.p
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By auxin under dark condition. {ECO:0000269|PubMed:17408882}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankBT0690050.0BT069005.1 Zea mays full-length cDNA clone ZM_BFb0119L19 mRNA, complete cds.
GenBankJX4285080.0JX428508.1 Zea mays subsp. mays clone pUT3106 ARF12 ARF type transcription factor mRNA, partial cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_025818787.10.0auxin response factor 2-like
SwissprotQ0JKI90.0ARFB_ORYSJ; Auxin response factor 2
TrEMBLA0A2T7DIM00.0A0A2T7DIM0_9POAL; Auxin response factor
STRINGPavir.Eb02716.1.p0.0(Panicum virgatum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP25373580
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G33860.11e-147ARF family protein
Publications ? help Back to Top
  1. Khanday I,Yadav SR,Vijayraghavan U
    Rice LHS1/OsMADS1 controls floret meristem specification by coordinated regulation of transcription factors and hormone signaling pathways.
    Plant Physiol., 2013. 161(4): p. 1970-83
    [PMID:23449645]