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.3KG305900.1.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: 738aa    MW: 80457.1 Da    PI: 7.4782
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.3KG305900.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B377.91.1e-24168269199
                          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.3KG305900.1.p 168 FCKTLTASDTSTHGGFSVPRRAAEDCfppldyS-QQRPSQELVAKDLHGTEWRFRHIYRGQPRRHLLTTGWSAFVNKKKLVSGDAVLFL- 255
                          99****************************963.3445679************************************************. PP

                          -SSSEE..EEEEE-S CS
                   B3  85 dgrsefelvvkvfrk 99 
                           + +++el+++v+r+
  Pavir.3KG305900.1.p 256 -RGDDGELRLGVRRA 269
                          .3489999***9996 PP
2Auxin_resp109.82.9e-36295374282
           Auxin_resp   2 ahaastksvFevvYnPrastseFvvkvekvekalkvkvsvGmRfkmafetedsserrlsGtvvgvsdldpvrWpnSkWrsL 82 
                          aha++tksvF+++YnPr s+seF+++++k++k++++++s+G Rfkm++e++d+ err++G+++g+ d+dp  W++SkW++L
  Pavir.3KG305900.1.p 295 AHAVATKSVFHIYYNPRLSQSEFIIPYSKFMKSFSQPFSAGLRFKMRYESDDATERRYTGIIAGIGDADP-MWRGSKWKCL 374
                          89********************************************************************.9********9 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019361.83E-43160284IPR015300DNA-binding pseudobarrel domain
Gene3DG3DSA:2.40.330.108.1E-41161271IPR015300DNA-binding pseudobarrel domain
CDDcd100175.73E-23166268No hitNo description
SMARTSM010195.3E-23168270IPR003340B3 DNA binding domain
PROSITE profilePS5086313.493168270IPR003340B3 DNA binding domain
PfamPF023621.4E-22168269IPR003340B3 DNA binding domain
PfamPF065071.1E-30295374IPR010525Auxin 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:0010050Biological Processvegetative phase change
GO:0010158Biological Processabaxial cell fate specification
GO:0010582Biological Processfloral meristem determinacy
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 738 aa     Download sequence    Send to blast
MTGIDLNDSV EDDEEEAEAG HACSQQSRSS SAATGTGTPP PPQPGPGAAV CVCLELWHAC  60
AGPVASLPRK GSAVVYLPQG HLEHLGDAAS AAAGGGAVPP HVFCRVVDLT LHADASTDEV  120
YAQLALVAEN EEVARRLRGG SEDGSGGDGD GEDGDNVRQR FSRMPHMFCK TLTASDTSTH  180
GGFSVPRRAA EDCFPPLDYS QQRPSQELVA KDLHGTEWRF RHIYRGQPRR HLLTTGWSAF  240
VNKKKLVSGD AVLFLRGDDG ELRLGVRRAA QLKNGSAFPA LYNQCSNLGS LANIAHAVAT  300
KSVFHIYYNP RLSQSEFIIP YSKFMKSFSQ PFSAGLRFKM RYESDDATER RYTGIIAGIG  360
DADPMWRGSK WKCLMVRWDD DVDFRRPNRI SPWEIELTSS VSGSHLSAPN AKRLKPCLPH  420
VNPDYLVPNG SGRPDFAESA QFHKVLQGQE LLGYRTRDNA AIATSQSCEA RNMQYIDERS  480
CSNDASNNIP GVPRHGVRTP LGNPGFSYHC SGFGESQRFQ KVLQGQEVFR PYRGTLADAC  540
LRNNAFHQQD GYHAPSVANK WHTQLHGCAF RGPPAPMNPS QSSFPPSVLM FQQGNSKMAQ  600
YEFGHGPLDK NVDARPAMLG QAGGIGGTEQ TLLLQPHHVS EEARNRHAPV EKFHSVGKEG  660
ADNREVNPNS CKVFGISLAE KVPSSKQKEC GDANYPSPFL SLKQQVPKSL GNSCATVHEQ  720
RPVVGRVIDL STMDMMI*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A1e-1124340410361Auxin response factor 1
4ldw_A1e-1124340410361Auxin response factor 1
4ldw_B1e-1124340410361Auxin response factor 1
4ldx_A1e-1124340410361Auxin response factor 1
4ldx_B1e-1124340410361Auxin response factor 1
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Pvr.91140.0callus| leaf| root| 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).
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00021PBMTransfer from AT2G33860Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapPavir.3KG305900.1.p
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_025807170.10.0auxin response factor 15-like
SwissprotQ8S9850.0ARFO_ORYSJ; Auxin response factor 15
TrEMBLA0A3L6R7K40.0A0A3L6R7K4_PANMI; Auxin response factor
STRINGPavir.J08401.1.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-163ARF family protein
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. Cheng CH, et al.
    A fine physical map of the rice chromosome 5.
    Mol. Genet. Genomics, 2005. 274(4): p. 337-45
    [PMID:16261349]
  3. 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]