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.4KG010900.1.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 NAC
Protein Properties Length: 395aa    MW: 45714.5 Da    PI: 6.711
Description NAC family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.4KG010900.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1NAM177.53.7e-55692031129
                  NAM   1 lppGfrFhPtdeelvveyLkkkvegkkleleevikevdiykvePwdLpk......kvkaeekewyfFskrdkkyatgkrknratksgyWk 84 
                          +ppGfrFhPtdeelv++yL+kkv++++++l +vik+vd+yk+ePwdL++        ++e++ewyfFs++dkky+tg+r+nrat++g+Wk
  Pavir.4KG010900.1.p  69 VPPGFRFHPTDEELVDYYLRKKVASRRIDL-NVIKDVDLYKIEPWDLQEkcrlggPGEEEQNEWYFFSHKDKKYPTGTRTNRATAAGFWK 157
                          69****************************.99**************953655542233677**************************** PP

                  NAM  85 atgkdkevlsk.kgelvglkktLvfykgrapkgektdWvmheyrle 129
                          atg+dk+++++ +++lvg++ktLv+ykgrap+g+k+dW+mheyrle
  Pavir.4KG010900.1.p 158 ATGRDKPIYANkQRQLVGMRKTLVYYKGRAPNGHKSDWIMHEYRLE 203
                          *********9856777****************************85 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019411.57E-6060223IPR003441NAC domain
PROSITE profilePS5100560.32369223IPR003441NAC domain
PfamPF023652.0E-2870202IPR003441NAC domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 395 aa     Download sequence    Send to blast
MLASFELLLF ICPLLSHACM RPIYDLIASL IQNMHAYDLS ISDRSINRDP SQLIKMGMSS  60
TQAQTQQLVP PGFRFHPTDE ELVDYYLRKK VASRRIDLNV IKDVDLYKIE PWDLQEKCRL  120
GGPGEEEQNE WYFFSHKDKK YPTGTRTNRA TAAGFWKATG RDKPIYANKQ RQLVGMRKTL  180
VYYKGRAPNG HKSDWIMHEY RLETNENGPP QEEGWVVCRV FKKRLPTTRR ESDHDAPCWY  240
LDEDGPFMHD LNSPMSRMPP HHAMSQLQEQ HLQMLNNTYK RELKLQFQMP SHHVLNTIPH  300
ELESPSFHSL LVSPDHQSNS HHAHQHVQLM DDAVDQVTDW RVLDKFVASQ LSHDATKGVD  360
YTDEGDIIQV NEKQEVATDY ASTSTSSSQV DPWK*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1ut4_A5e-52562244166NO APICAL MERISTEM PROTEIN
1ut4_B5e-52562244166NO APICAL MERISTEM PROTEIN
1ut7_A5e-52562244166NO APICAL MERISTEM PROTEIN
1ut7_B5e-52562244166NO APICAL MERISTEM PROTEIN
3swm_A5e-52562247169NAC domain-containing protein 19
3swm_B5e-52562247169NAC domain-containing protein 19
3swm_C5e-52562247169NAC domain-containing protein 19
3swm_D5e-52562247169NAC domain-containing protein 19
3swp_A5e-52562247169NAC domain-containing protein 19
3swp_B5e-52562247169NAC domain-containing protein 19
3swp_C5e-52562247169NAC domain-containing protein 19
3swp_D5e-52562247169NAC domain-containing protein 19
4dul_A5e-52562244166NAC domain-containing protein 19
4dul_B5e-52562244166NAC domain-containing protein 19
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Pvr.297290.0callus| leaf
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Up-regulated during xylem vessel element formation. Expressed preferentially in procambial cells adjacent to root meristem. {ECO:0000269|PubMed:16103214, ECO:0000269|PubMed:25148240}.
UniprotTISSUE SPECIFICITY: Expressed in root, shoot and hypocotyl vascular elements, columella root caps, epidermal and cortex root cells and root-hypocotyl junctions. Observed predominantly in root imature xylem vessels (PubMed:18445131). Present in root developing xylems (PubMed:16103214, PubMed:17565617). Specifically expressed in vessels in the secondary xylem of the root-hypocotyl region, and in vessels but not in interfascicular fibers in stems (PubMed:25148240). {ECO:0000269|PubMed:16103214, ECO:0000269|PubMed:17565617, ECO:0000269|PubMed:18445131, ECO:0000269|PubMed:25148240}.
Functional Description ? help Back to Top
Source Description
UniProtTranscription activator that binds to the secondary wall NAC binding element (SNBE), 5'-(T/A)NN(C/T)(T/C/G)TNNNNNNNA(A/C)GN(A/C/T)(A/T)-3', in the promoter of target genes (By similarity). Involved in xylem formation by promoting the expression of secondary wall-associated transcription factors and of genes involved in secondary wall biosynthesis and programmed cell death, genes driven by the secondary wall NAC binding element (SNBE). Triggers thickening of secondary walls (PubMed:16103214, PubMed:25148240). {ECO:0000250|UniProtKB:Q9LVA1, ECO:0000269|PubMed:16103214, ECO:0000269|PubMed:25148240}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapPavir.4KG010900.1.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
GenBankKT0750910.0KT075091.1 Panicum virgatum secondary wall NAC master switch (SWN7B) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_004964278.10.0NAC domain-containing protein 105
SwissprotQ9FWX21e-106NAC7_ARATH; NAC domain-containing protein 7
TrEMBLA0A0K1TPD70.0A0A0K1TPD7_PANVG; Secondary wall NAC master switch
STRINGPavir.Da02426.1.p0.0(Panicum virgatum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP121023039
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G12260.11e-95NAC 007
Publications ? help Back to Top
  1. Duarte JM, et al.
    Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis.
    Mol. Biol. Evol., 2006. 23(2): p. 469-78
    [PMID:16280546]
  2. Heyndrickx KS,Vandepoele K
    Systematic identification of functional plant modules through the integration of complementary data sources.
    Plant Physiol., 2012. 159(3): p. 884-901
    [PMID:22589469]