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.3KG300900.4.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: 572aa    MW: 63348.3 Da    PI: 9.335
Description ARF family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.3KG300900.4.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1B3764.3e-245104197
                          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.3KG300900.4.p   5 FCKTLTASDTSTHGGFSVPRRAAEDCfppldyS-QQRPSQELVAKDLHGTEWRFRHIYRGQPRRHLLTTGWSAFVNKKKLVSGDAVLFLR 93 
                          99****************************963.3445679************************************************3 PP

                          -SSSEE..EEEEE CS
                   B3  85 dgrsefelvvkvf 97 
                             +++el+++v+
  Pavir.3KG300900.4.p  94 --GDDGELRLGVR 104
                          ..37888888876 PP
2Auxin_resp110.32e-36132211282
           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.3KG300900.4.p 132 AHAVATKSVFHIYYNPRLSQSEFIIPYSKFMKSFSQPFSAGLRFKMRYESDDATERRYTGIIAGIGDADP-MWRGSKWKCL 211
                          89********************************************************************.9********9 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:2.40.330.102.3E-402108IPR015300DNA-binding pseudobarrel domain
CDDcd100178.84E-233105No hitNo description
SuperFamilySSF1019362.09E-423118IPR015300DNA-binding pseudobarrel domain
PfamPF023624.6E-225104IPR003340B3 DNA binding domain
SMARTSM010195.8E-215107IPR003340B3 DNA binding domain
PROSITE profilePS5086313.1125107IPR003340B3 DNA binding domain
PfamPF065077.8E-31132211IPR010525Auxin 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: 572 aa     Download sequence    Send to blast
MPHMFCKTLT ASDTSTHGGF SVPRRAAEDC FPPLDYSQQR PSQELVAKDL HGTEWRFRHI  60
YRGQPRRHLL TTGWSAFVNK KKLVSGDAVL FLRGDDGELR LGVRCAAQLK NGSAFPALYN  120
QCSNLGSLAN IAHAVATKSV FHIYYNPRLS QSEFIIPYSK FMKSFSQPFS AGLRFKMRYE  180
SDDATERRYT GIIAGIGDAD PMWRGSKWKC LMVRWDDDVD FRRPNRISPW EIELTSSVSG  240
SHLSAPNVKR LKPCLPHVNP DYLVPNGSGH PDFAESAQFH KVLQGQELLG YRTRDSAAVA  300
TSQSCEARNM QYIDERSCSN DASNNIPGVP RHGVRTPLGN PGFSYHCSGF GESQRFQKVL  360
QGQEVFRPYR GTLTDSCLRN NAFHQQDGSH APSVANKWHT QLHGCAFRGP PAPLNPSQSS  420
SPPSVLTFQR GNSKMTHFEF GLGPLDKNVD GRPAVLGHAG GIGGTEQTLM LQPHPVSEEV  480
RNRHATVEKF HSVGKEGADN REVNTNSCKV FGISLAEKVP SSKQKECGDA NYPSPFLSLK  540
QQVPKSLGSS CATVHEQRPV VGRVIDLSRW I*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4ldv_A2e-883241122361Auxin response factor 1
4ldw_A2e-883241122361Auxin response factor 1
4ldw_B2e-883241122361Auxin response factor 1
4ldx_A3e-883241122361Auxin response factor 1
4ldx_B3e-883241122361Auxin 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).
Cis-element ? help Back to Top
SourceLink
PlantRegMapPavir.3KG300900.4.p
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
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
TrEMBLA0A3L6SWS70.0A0A3L6SWS7_PANMI; Auxin response factor
STRINGPavir.Ca00928.1.p0.0(Panicum virgatum)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G33860.11e-126ARF 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]