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.1KG411800.1.p
Common NameSWN8B
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: 39845.5 Da    PI: 6.574
Description NAC family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.1KG411800.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1NAM1806.2e-5671361129
                  NAM   1 lppGfrFhPtdeelvveyLkkkvegkkleleevikevdiykvePwdLpk..kvka.eekewyfFskrdkkyatgkrknratksgyWkatg 87 
                          +ppGfrFhPtdeelv++yL+kkv+++k++l +vik++d+yk+ePwdL++  k+   e++ewyfFs++dkky+tg+r+nrat++g+Wkatg
  Pavir.1KG411800.1.p   7 VPPGFRFHPTDEELVDYYLRKKVASNKIDL-DVIKDIDLYKIEPWDLQEkcKIGMeEQNEWYFFSHKDKKYPTGTRTNRATTAGFWKATG 95 
                          69****************************.9***************952433333556******************************* PP

                  NAM  88 kdkevlskkgelvglkktLvfykgrapkgektdWvmheyrle 129
                          +dk++++ k+ lvg++ktLvfy+grap+g+k+dW+mheyrle
  Pavir.1KG411800.1.p  96 RDKPIYT-KNCLVGMRKTLVFYRGRAPNGQKSDWIMHEYRLE 136
                          *******.999*****************************85 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019411.96E-615156IPR003441NAC domain
PROSITE profilePS5100560.0357156IPR003441NAC domain
PfamPF023651.1E-288135IPR003441NAC domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0048759Biological Processxylem vessel member cell differentiation
GO:1901348Biological Processpositive regulation of secondary cell wall biogenesis
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
Sequence ? help Back to Top
Protein Sequence    Length: 354 aa     Download sequence    Send to blast
MDTFSHVPPG FRFHPTDEEL VDYYLRKKVA SNKIDLDVIK DIDLYKIEPW DLQEKCKIGM  60
EEQNEWYFFS HKDKKYPTGT RTNRATTAGF WKATGRDKPI YTKNCLVGMR KTLVFYRGRA  120
PNGQKSDWIM HEYRLETAEN GTTPEEGWVV CRVFKKRVAT VRRMADGAPC WFDDHVAGFM  180
PDLGSPRQLM MQHHHHPSTS AAAAAYGGQQ QLYHCKPELE YHHLLPSQEA AFLQQLPQLE  240
SPKPPAYIAQ GSSSLQSSDE ASIRYTAAQQ PDIEAAYMAA AGDDDSVTDW RVLDKFVASQ  300
LFSHGDGTTK EAAYSNPTQV FQAGRNKQRE EALDYASTSA NGGGGGSEAD MWK*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1ut4_A1e-51715717166NO APICAL MERISTEM PROTEIN
1ut4_B1e-51715717166NO APICAL MERISTEM PROTEIN
1ut7_A1e-51715717166NO APICAL MERISTEM PROTEIN
1ut7_B1e-51715717166NO APICAL MERISTEM PROTEIN
3swm_A2e-51715720169NAC domain-containing protein 19
3swm_B2e-51715720169NAC domain-containing protein 19
3swm_C2e-51715720169NAC domain-containing protein 19
3swm_D2e-51715720169NAC domain-containing protein 19
3swp_A2e-51715720169NAC domain-containing protein 19
3swp_B2e-51715720169NAC domain-containing protein 19
3swp_C2e-51715720169NAC domain-containing protein 19
3swp_D2e-51715720169NAC domain-containing protein 19
4dul_A1e-51715717166NAC domain-containing protein 19
4dul_B1e-51715717166NAC domain-containing protein 19
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, 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}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00136DAPTransfer from AT1G12260Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapPavir.1KG411800.1.p
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankKT0750930.0KT075093.1 Panicum virgatum secondary wall NAC master switch (SWN8B) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_025825485.10.0NAC domain-containing protein 7-like
SwissprotQ9FWX21e-126NAC7_ARATH; NAC domain-containing protein 7
TrEMBLA0A0K1TPH70.0A0A0K1TPH7_PANVG; Secondary wall NAC master switch
STRINGPavir.J39804.1.p0.0(Panicum virgatum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP23703892
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G12260.11e-105NAC 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]
  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]