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.4KG024100.1.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: 301aa    MW: 31664.4 Da    PI: 9.1762
Description HD-ZIP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.4KG024100.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox60.23.3e-19125179256
                          T--SS--HHHHHHHHHHHHHSSS--HHHHHHHHHHCTS-HHHHHHHHHHHHHHHH CS
             Homeobox   2 rkRttftkeqleeLeelFeknrypsaeereeLAkklgLterqVkvWFqNrRakek 56 
                          rk+ +++k+q  +Le++F+ +++++ +++  LA++lgL  rqV vWFqNrRa+ k
  Pavir.4KG024100.1.p 125 RKKLRLSKDQAAVLEDCFKTHSTLNPKQKVALANRLGLRPRQVEVWFQNRRARTK 179
                          678899***********************************************98 PP
2HD-ZIP_I/II125.13.2e-40125215192
          HD-ZIP_I/II   1 ekkrrlskeqvklLEesFeeeekLeperKvelareLglqprqvavWFqnrRARtktkqlEkdyeaLkraydalkeenerLekeveeLree 90 
                          +kk+rlsk+q+++LE++F+++++L+p++Kv+la++Lgl+prqv+vWFqnrRARtk+kq+E+d+e+Lkr++++l++en+rLeke ++Lr +
  Pavir.4KG024100.1.p 125 RKKLRLSKDQAAVLEDCFKTHSTLNPKQKVALANRLGLRPRQVEVWFQNRRARTKLKQTEVDCEYLKRWCERLADENKRLEKELADLR-A 213
                          69*************************************************************************************9.5 PP

          HD-ZIP_I/II  91 lk 92 
                          lk
  Pavir.4KG024100.1.p 214 LK 215
                          55 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:1.10.10.607.9E-18106179IPR009057Homeodomain-like
PROSITE profilePS5007116.439121181IPR001356Homeobox domain
SuperFamilySSF466894.6E-18123190IPR009057Homeodomain-like
SMARTSM003891.1E-16123185IPR001356Homeobox domain
PfamPF000461.7E-16125179IPR001356Homeobox domain
CDDcd000861.78E-14125182No hitNo description
PRINTSPR000314.2E-5152161IPR000047Helix-turn-helix motif
PROSITE patternPS000270156179IPR017970Homeobox, conserved site
PRINTSPR000314.2E-5161177IPR000047Helix-turn-helix motif
SMARTSM003405.2E-21181224IPR003106Leucine zipper, homeobox-associated
PfamPF021831.4E-9181215IPR003106Leucine zipper, homeobox-associated
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0043565Molecular Functionsequence-specific DNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 301 aa     Download sequence    Send to blast
MMMPQSGGSL DLGLSLGLTS QGSLSSSTTS GALSPWAAAL SSVDGDAMTR RDAHAQQQQQ  60
HGAAAAAMDP DRAAMRASTS PDSAAALSSG ASGDNNKRER GELERTGSGG VRSDEEDGAD  120
GAGGRKKLRL SKDQAAVLED CFKTHSTLNP KQKVALANRL GLRPRQVEVW FQNRRARTKL  180
KQTEVDCEYL KRWCERLADE NKRLEKELAD LRALKAAPSP AAQPASPAAT LTMCPSCRRV  240
AAAAGAPAAN HHQQCHPKSN AAAAGNVVPS HCQFFPAAVD RTGQSTWNAA AAPLVTRELF  300
*
Nucleic Localization Signal ? help Back to Top
NLS
No. Start End Sequence
1173181RRARTKLKQ
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Pvr.147240.0root
Expression -- Description ? help Back to Top
Source Description
UniprotTISSUE SPECIFICITY: Expressed in seedlings, roots, leaves, nodes, internodes, flowers and embryo. {ECO:0000269|PubMed:10732669, ECO:0000269|PubMed:17999151}.
UniprotTISSUE SPECIFICITY: Expressed in seedlings, roots, leaves, nodes, internodes, flowers and embryo. {ECO:0000269|PubMed:10732669, ECO:0000269|PubMed:17999151}.
Functional Description ? help Back to Top
Source Description
UniProtProbable transcription factor that binds to the DNA sequence 5'-CAAT[GC]ATTG-3'. {ECO:0000269|PubMed:10732669}.
UniProtProbable transcription factor that binds to the DNA sequence 5'-CAAT[GC]ATTG-3'. {ECO:0000269|PubMed:10732669}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapPavir.4KG024100.1.p
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankFP0932881e-152FP093288.1 Phyllostachys edulis cDNA clone: bphylf053m07, full insert sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_025811981.11e-150homeobox-leucine zipper protein HOX2-like
SwissprotQ5VPE35e-94HOX2_ORYSJ; Homeobox-leucine zipper protein HOX2
SwissprotQ84U865e-94HOX2_ORYSI; Homeobox-leucine zipper protein HOX2
TrEMBLA0A2S3HLX71e-149A0A2S3HLX7_9POAL; Uncharacterized protein
STRINGPavir.Da02253.1.p0.0(Panicum virgatum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP38423376
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT5G06710.17e-51homeobox from Arabidopsis thaliana
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]