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.9KG307100.2.p
Common NameSWN4A
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: 354aa    MW: 38875.3 Da    PI: 6.0526
Description NAC family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.9KG307100.2.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1NAM171.32.9e-5351391129
                  NAM   1 lppGfrFhPtdeelvveyLkkkvegkkleleevikevdiykvePwdLpk..kvka.eekewyfFskrdkkyatgkrknratksgyWkatg 87 
                          +ppGfrFhPtdeelv +yL+kkv+++k++l +vi++vd+y++ePwdL++  k+   e+++wyfFs +d+ky+tg+r+nrat +g+Wkatg
  Pavir.9KG307100.2.p   5 VPPGFRFHPTDEELVGYYLRKKVASQKIDL-DVIRDVDLYRIEPWDLQEhcKIGYeEQSDWYFFSYKDRKYPTGTRTNRATLTGFWKATG 93 
                          69****************************.9***************953433332556******************************* PP

                  NAM  88 kdkevlsk....kgelvglkktLvfykgrapkgektdWvmheyrle 129
                          +dk+v ++    +g l+g++ktLvfy+grap+g+ktdW+mheyrle
  Pavir.9KG307100.2.p  94 RDKAVRDSkhghGGGLIGMRKTLVFYTGRAPNGRKTDWIMHEYRLE 139
                          ******9877766677****************************85 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019411.57E-583159IPR003441NAC domain
PROSITE profilePS5100559.0815159IPR003441NAC domain
PfamPF023653.3E-286138IPR003441NAC 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: 354 aa     Download sequence    Send to blast
MESCVPPGFR FHPTDEELVG YYLRKKVASQ KIDLDVIRDV DLYRIEPWDL QEHCKIGYEE  60
QSDWYFFSYK DRKYPTGTRT NRATLTGFWK ATGRDKAVRD SKHGHGGGLI GMRKTLVFYT  120
GRAPNGRKTD WIMHEYRLET DENAAPQEEG WVVCRAFKKR AMHPPRGVAG AWDPSYPYYH  180
DPVLAGAARF KQESPELDGG GAAAASAASC ALLHYSSRLA ELPQLESPPP LPNQEMSRHR  240
ASAADGEGDP AAATDWRALD RFVASQLIPP DEDHAAAAGQ GLQQQQEYYC GKAPPLGAAA  300
HAGDNSDQDA TDMVALLLLD GAARHEEAGL LGSVADPACP HRNAARFAGQ QEP*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
3ulx_A1e-46216012169Stress-induced transcription factor NAC1
Search in ModeBase
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 metaxylem pole and in shoot pre-procambium and procambium (PubMed:18445131). Present in root developing xylems (PubMed:16103214). Specifically expressed in vessels but not in interfascicular fibers in stems (PubMed:25148240). {ECO:0000269|PubMed:16103214, 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:25148240). {ECO:0000250|UniProtKB:Q9LVA1, ECO:0000269|PubMed:25148240}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapPavir.9KG307100.2.p
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: Induced by chitin (e.g. chitooctaose) (PubMed:17722694). Accumulates in plants exposed to callus induction medium (CIM) (PubMed:17581762). {ECO:0000269|PubMed:17581762, ECO:0000269|PubMed:17722694}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankKT0750850.0KT075085.1 Panicum virgatum secondary wall NAC master switch (SWN4A) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_025796895.10.0NAC domain-containing protein 105-like
SwissprotQ9SL411e-106NAC37_ARATH; NAC domain-containing protein 37
TrEMBLA0A0K1TPW90.0A0A0K1TPW9_PANVG; Secondary wall NAC master switch
STRINGPavir.Ib02477.1.p0.0(Panicum virgatum)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G18060.11e-101vascular related NAC-domain protein 1
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. Negi S,Tak H,Ganapathi TR
    Cloning and functional characterization of MusaVND1 using transgenic banana plants.
    Transgenic Res., 2015. 24(3): p. 571-85
    [PMID:25523085]
  3. Zhong R, et al.
    Functional Characterization of NAC and MYB Transcription Factors Involved in Regulation of Biomass Production in Switchgrass (Panicum virgatum).
    PLoS ONE, 2015. 10(8): p. e0134611
    [PMID:26248336]
  4. Tan TT, et al.
    Transcription Factors VND1-VND3 Contribute to Cotyledon Xylem Vessel Formation.
    Plant Physiol., 2018. 176(1): p. 773-789
    [PMID:29133368]