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.2NG401700.1.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: 277aa    MW: 29542.7 Da    PI: 4.5123
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.2NG401700.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox60.13.4e-1949102356
                          --SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHH CS
             Homeobox   3 kRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakek 56 
                          k++++++eq+++Le+ Fe ++++  e++++LA+ lgL+ rqV vWFqNrRa++k
  Pavir.2NG401700.1.p  49 KKRRLSAEQVRALERSFEVENKLEPERKARLARDLGLQPRQVAVWFQNRRARWK 102
                          45689************************************************9 PP
2HD-ZIP_I/II133.76.9e-4348140193
          HD-ZIP_I/II   1 ekkrrlskeqvklLEesFeeeekLeperKvelareLglqprqvavWFqnrRARtktkqlEkdyeaLkraydalkeenerLekeveeLree 90 
                          ekkrrls+eqv++LE+sFe e+kLeperK++lar+LglqprqvavWFqnrRAR+ktkqlE+dy+aL+++ydal++++++L++++++L +e
  Pavir.2NG401700.1.p  48 EKKRRLSAEQVRALERSFEVENKLEPERKARLARDLGLQPRQVAVWFQNRRARWKTKQLERDYAALRHSYDALRRDHDALRRDKDALLAE 137
                          69**************************************************************************************99 PP

          HD-ZIP_I/II  91 lke 93 
                          +ke
  Pavir.2NG401700.1.p 138 IKE 140
                          987 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF466891.03E-1941106IPR009057Homeodomain-like
PROSITE profilePS5007117.47544104IPR001356Homeobox domain
SMARTSM003891.5E-1847108IPR001356Homeobox domain
PfamPF000461.6E-1649102IPR001356Homeobox domain
CDDcd000869.96E-1949105No hitNo description
Gene3DG3DSA:1.10.10.603.0E-2050111IPR009057Homeodomain-like
PRINTSPR000319.4E-67584IPR000047Helix-turn-helix motif
PROSITE patternPS00027079102IPR017970Homeobox, conserved site
PRINTSPR000319.4E-684100IPR000047Helix-turn-helix motif
PfamPF021833.9E-17104145IPR003106Leucine zipper, homeobox-associated
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0009637Biological Processresponse to blue light
GO:0030308Biological Processnegative regulation of cell growth
GO:0045893Biological Processpositive regulation of transcription, DNA-templated
GO:0048510Biological Processregulation of timing of transition from vegetative to reproductive phase
GO:0048573Biological Processphotoperiodism, flowering
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0043565Molecular Functionsequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 277 aa     Download sequence    Send to blast
MKRPRAGSPS LLPTASPDDD GYGAAAGMET EGDAEEEMVA CGGGGGGEKK RRLSAEQVRA  60
LERSFEVENK LEPERKARLA RDLGLQPRQV AVWFQNRRAR WKTKQLERDY AALRHSYDAL  120
RRDHDALRRD KDALLAEIKE LKAKLGDEEA AASFTSVKAE PAASDGPPAA GVGSSESDSS  180
AVLNDADPAV GAAEAPVPEV QGALLPAPTG AAATSHGGAF FHGGFLKVEE DETGFLDDDE  240
PCGGFFAVEQ PPPMAWWTEP TAGTELGWMR AQTWDL*
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
17379ERKARLA
296104RRARWKTKQ
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Pvr.16230.0callus| leaf| root| stem
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in leaf and floral organ primordia, floral meristems, embryonic axis and cells surrounding the vascular bundles. Expressed in the vasculature of roots, stem, leaves and spikelets, and in the vascular bundle of the scutellum in embryos. {ECO:0000269|PubMed:10732669, ECO:0000269|PubMed:17999151, ECO:0000269|PubMed:18049796}.
UniprotTISSUE SPECIFICITY: Expressed in leaf and floral organ primordia, floral meristems, embryonic axis and cells surrounding the vascular bundles. Expressed in the vasculature of roots, stem, leaves and spikelets, and in the vascular bundle of the scutellum in embryos. {ECO:0000269|PubMed:10732669, ECO:0000269|PubMed:17999151, ECO:0000269|PubMed:18049796}.
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription activator that binds to the DNA sequence 5'-CAAT[AT]ATTG-3'. May be involved in the regulation of gibberellin signaling. {ECO:0000269|PubMed:10732669, ECO:0000269|PubMed:18049796}.
UniProtProbable transcription activator that binds to the DNA sequence 5'-CAAT[AT]ATTG-3'. May be involved in the regulation of gibberellin signaling. {ECO:0000269|PubMed:10732669, ECO:0000269|PubMed:18049796}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00051PBMTransfer from AT4G40060Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapPavir.2NG401700.1.p
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By gibberellin. Down-regulated in leaves by drought stress. {ECO:0000269|PubMed:17999151, ECO:0000269|PubMed:18049796}.
UniProtINDUCTION: By gibberellin. Down-regulated in leaves by drought stress. {ECO:0000269|PubMed:17999151, ECO:0000269|PubMed:18049796}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankBT0342570.0BT034257.1 Zea mays full-length cDNA clone ZM_BFc0009H14 mRNA, complete cds.
GenBankBT0390620.0BT039062.1 Zea mays full-length cDNA clone ZM_BFb0367N11 mRNA, complete cds.
GenBankBT0553740.0BT055374.1 Zea mays full-length cDNA clone ZM_BFb0091J03 mRNA, complete cds.
GenBankJX4699290.0JX469929.1 Zea mays subsp. mays clone UT3187 HB-type transcription factor mRNA, partial cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_004957072.11e-162homeobox-leucine zipper protein HOX4
SwissprotQ6K4981e-123HOX4_ORYSJ; Homeobox-leucine zipper protein HOX4
SwissprotQ9XH371e-123HOX4_ORYSI; Homeobox-leucine zipper protein HOX4
TrEMBLK3ZW401e-160K3ZW40_SETIT; Uncharacterized protein
STRINGPavir.J27155.1.p0.0(Panicum virgatum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP30093482
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G01470.12e-33homeobox 1
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]