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.9NG493300.1.p
Common NameSWN4B
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: 338aa    MW: 37435.8 Da    PI: 6.1377
Description NAC family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.9NG493300.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1NAM172.21.6e-5351371129
                  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.9NG493300.1.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.9NG493300.1.p  94 RDKAVRDSkhGGGLIGMRKTLVFYTGRAPNGRKTDWIMHEYRLE 137
                          ******98777888****************************85 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019415.36E-593157IPR003441NAC domain
PROSITE profilePS5100559.4775157IPR003441NAC domain
PfamPF023652.6E-286136IPR003441NAC 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: 338 aa     Download sequence    Send to blast
MESCVPPGFR FHPTDEELVG YYLRKKVASQ KIDLDVIRDV DLYRIEPWDL QEHCKIGYEE  60
QSDWYFFSYK DRKYPTGTRT NRATLTGFWK ATGRDKAVRD SKHGGGLIGM RKTLVFYTGR  120
APNGRKTDWI MHEYRLETDE NAAPQEEGWV VCRAFKKRTM HPPRSVAGAW DPSYPYYHDP  180
VLAGAARFKQ ESPELDGGAA SAASALLQYS SRLAELPQLE SPPLPNQGSH RASADGEGDP  240
AAATDWRALD RFVASQLIPP DEDHAAAGQG GLQQQEYYCG KPPLGAAHAE DSTDQDATDM  300
VALLLLDGAA RHEEAGLLGS VADPACLHKN AARFRKP*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
3ulx_A3e-47215912170Stress-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: Detected in root protoxylem and metaxylem poles and in vessels of protoxylems, outermost metaxylems, inner metaxylems, shoots and hypocotyls (PubMed:18445131). Expressed in roots, hypocotyls, cotyledons and leaves. Present in developing xylems (PubMed:16103214, PubMed:16581911). Specifically expressed in vessels but not in interfascicular fibers in stems (PubMed:25148240). {ECO:0000269|PubMed:16103214, ECO:0000269|PubMed:16581911, 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.9NG493300.1.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
GenBankKT0750860.0KT075086.1 Panicum virgatum secondary wall NAC master switch (SWN4B) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_025796895.10.0NAC domain-containing protein 105-like
SwissprotO655081e-109NAC76_ARATH; NAC domain-containing protein 76
TrEMBLA0A0K1TPD50.0A0A0K1TPD5_PANVG; Secondary wall NAC master switch
STRINGPavir.Ia02924.1.p0.0(Panicum virgatum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP36253768
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT4G36160.11e-106NAC domain containing protein 76
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. Ding Y, et al.
    Four distinct types of dehydration stress memory genes in Arabidopsis thaliana.
    BMC Plant Biol., 2013. 13: p. 229
    [PMID:24377444]
  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]