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.9KG334700.1.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 HD-ZIP
Protein Properties Length: 317aa    MW: 34285.6 Da    PI: 8.7112
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.9KG334700.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox61.21.6e-19169223256
                          T--SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHH CS
             Homeobox   2 rkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakek 56 
                          rk+ +++k+q  +Lee F+++++++ ++++ LAk+l+L+ rqV vWFqNrRa+ k
  Pavir.9KG334700.1.p 169 RKKLRLSKDQAAVLEESFKEHNTLNPKQKAALAKQLNLKPRQVEVWFQNRRARTK 223
                          788899***********************************************98 PP
2HD-ZIP_I/II127.84.6e-41169258191
          HD-ZIP_I/II   1 ekkrrlskeqvklLEesFeeeekLeperKvelareLglqprqvavWFqnrRARtktkqlEkdyeaLkraydalkeenerLekeveeLree 90 
                          +kk+rlsk+q+++LEesF+e+++L+p++K++la++L+l+prqv+vWFqnrRARtk+kq+E+d+e+Lkr++++l+een+rL++ev+eLr +
  Pavir.9KG334700.1.p 169 RKKLRLSKDQAAVLEESFKEHNTLNPKQKAALAKQLNLKPRQVEVWFQNRRARTKLKQTEVDCEFLKRCCETLTEENRRLQREVAELR-A 257
                          69*************************************************************************************9.5 PP

          HD-ZIP_I/II  91 l 91 
                          l
  Pavir.9KG334700.1.p 258 L 258
                          5 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF046181.8E-2714138IPR006712HD-ZIP protein, N-terminal
Gene3DG3DSA:1.10.10.609.8E-20153219IPR009057Homeodomain-like
SuperFamilySSF466897.52E-19156226IPR009057Homeodomain-like
PROSITE profilePS5007117.281165225IPR001356Homeobox domain
SMARTSM003894.0E-17167229IPR001356Homeobox domain
PfamPF000467.1E-17169223IPR001356Homeobox domain
CDDcd000865.21E-17169226No hitNo description
PROSITE patternPS000270200223IPR017970Homeobox, conserved site
SMARTSM003409.5E-23225268IPR003106Leucine zipper, homeobox-associated
PfamPF021831.3E-10225259IPR003106Leucine zipper, homeobox-associated
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0005634Cellular Componentnucleus
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0043565Molecular Functionsequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 317 aa     Download sequence    Send to blast
MEMTVNARDQ EQHGLGLGLS LSLSIATAHP VEPPPQRAIS VAPISSHPAP PMPPQPQWWS  60
GAGLFFSHSS GTDRSLERKQ QPAALAACHG HEMPFLRGID VNRAPAGEAR RGSCSEDEEP  120
AASSPNSTLS SLSGKRAAAT RSGELEGDHT PRTGGGSDDE DSGAGGGSRK KLRLSKDQAA  180
VLEESFKEHN TLNPKQKAAL AKQLNLKPRQ VEVWFQNRRA RTKLKQTEVD CEFLKRCCET  240
LTEENRRLQR EVAELRALKL IAPHQYARMP PPTTLTMCPS CERLATADEA ARPAPTGPWG  300
PVPVRPVFVD GPARRS*
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1167173SRKKLRL
2217225RRARTKLKQ
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Pvr.24040.0stem
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in root provascular and vascular cylinder, provascular and vascular strands of leaves, provascular and vascular strands of the whole panicle, in mature embryo provascular bundles of scutellum and embryonic axis and provascular and vascular strands of young immature spikelet organs. Expressed in differentiating and differentiated xylem and phloem elements, and in outer and inner bundle sheath cells of all vascular bundles. Expressed in auricles, ligules, culm, guard cells brac hairs and pollen. {ECO:0000269|PubMed:10732669, ECO:0000269|PubMed:17999151, ECO:0000269|PubMed:9076993}.
UniprotTISSUE SPECIFICITY: Expressed in root provascular and vascular cylinder, provascular and vascular strands of leaves, provascular and vascular strands of the whole panicle, in mature embryo provascular bundles of scutellum and embryonic axis and provascular and vascular strands of young immature spikelet organs. Expressed in differentiating and differentiated xylem and phloem elements, and in outer and inner bundle sheath cells of all vascular bundles. Expressed in auricles, ligules, culm, guard cells brac hairs and pollen. {ECO:0000269|PubMed:10934011, ECO:0000269|PubMed:17999151, ECO:0000269|PubMed:9076993}.
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription repressor involved leaf development. Binds to the DNA sequence 5'-CAAT[GC]ATTG-3'. May act as a regulatory switch to specify provascular cell fate. {ECO:0000269|PubMed:10732669, ECO:0000269|PubMed:10934011, ECO:0000269|PubMed:9076993}.
UniProtProbable transcription repressor involved leaf development. Binds to the DNA sequence 5'-CAAT[GC]ATTG-3'. May act as a regulatory switch to specify provascular cell fate. {ECO:0000269|PubMed:10732669, ECO:0000269|PubMed:9076993}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapPavir.9KG334700.1.p
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By auxin and sucrose in primary root apical region. By wounding in leaves. {ECO:0000269|PubMed:10732669}.
UniProtINDUCTION: By auxin and sucrose in primary root apical region. By wounding in leaves. {ECO:0000269|PubMed:10934011}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankEU9424520.0EU942452.1 Zea mays clone 1503625 mRNA sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_025795353.10.0homeobox-leucine zipper protein HOX1-like
SwissprotQ406911e-84HOX1_ORYSI; Homeobox-leucine zipper protein HOX1
SwissprotQ7XC541e-84HOX1_ORYSJ; Homeobox-leucine zipper protein HOX1
TrEMBLA0A3L6SDQ60.0A0A3L6SDQ6_PANMI; Homeobox-leucine zipper protein HOX1 isoform X2
STRINGPavir.J12300.1.p0.0(Panicum virgatum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP25873889
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G60390.17e-67homeobox-leucine zipper protein 3
Publications ? help Back to Top
  1. Scarpella E,Boot KJ,Rueb S,Meijer AH
    The procambium specification gene Oshox1 promotes polar auxin transport capacity and reduces its sensitivity toward inhibition.
    Plant Physiol., 2002. 130(3): p. 1349-60
    [PMID:12428000]
  2. Scarpella E,Rueb S,Meijer AH
    The RADICLELESS1 gene is required for vascular pattern formation in rice.
    Development, 2003. 130(4): p. 645-58
    [PMID:12505996]
  3. Rice Chromosome 10 Sequencing Consortium
    In-depth view of structure, activity, and evolution of rice chromosome 10.
    Science, 2003. 300(5625): p. 1566-9
    [PMID:12791992]
  4. 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]
  5. Scarpella E,Simons EJ,Meijer AH
    Multiple regulatory elements contribute to the vascular-specific expression of the rice HD-Zip gene Oshox1 in Arabidopsis.
    Plant Cell Physiol., 2005. 46(8): p. 1400-10
    [PMID:15964905]
  6. Meijer AH,Ouwerkerk PB,Hoge JH
    Vectors for transcription factor cloning and target site identification by means of genetic selection in yeast.
    Yeast, 1998. 14(15): p. 1407-15
    [PMID:9848232]