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.6NG005700.1.p
Common NameSWN3A
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: 250aa    MW: 28062.3 Da    PI: 7.8249
Description NAC family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Pavir.6NG005700.1.pgenomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1NAM161.33.7e-50131571128
                  NAM   1 lppGfrFhPtdeelvveyLkkkvegkkleleevikevdiykvePwdLpk..............kvkaeekewyfFskrdkkyatgkrknr 76 
                          +ppGfrFhPt+eelv +yL++kv+++k++l ++i+evd+y++ePwdL++                ++e +e+yfFs +d+ky++g+r+nr
  Pavir.6NG005700.1.p  13 VPPGFRFHPTEEELVGYYLARKVAAQKIDL-DIIREVDLYRIEPWDLQErcciyyggagtgsgGQEEEPTEYYFFSYKDRKYPSGTRTNR 101
                          69****************************.99**************9558999998877653223344499****************** PP

                  NAM  77 atksgyWkatgkdkevlskkgel....vglkktLvfykgrapkgektdWvmheyrl 128
                          at++g+Wkatg+dk+vls+++++    +g++ktLvfy+grap+g+ktdW++heyrl
  Pavir.6NG005700.1.p 102 ATAAGFWKATGRDKPVLSSRSAAplsvIGMRKTLVFYRGRAPNGRKTDWIIHEYRL 157
                          ******************855556777***************************98 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019416.41E-547178IPR003441NAC domain
PROSITE profilePS5100554.50713178IPR003441NAC domain
PfamPF023659.3E-2614157IPR003441NAC 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: 250 aa     Download sequence    Send to blast
MDHQQQQQQT PCVPPGFRFH PTEEELVGYY LARKVAAQKI DLDIIREVDL YRIEPWDLQE  60
RCCIYYGGAG TGSGGQEEEP TEYYFFSYKD RKYPSGTRTN RATAAGFWKA TGRDKPVLSS  120
RSAAPLSVIG MRKTLVFYRG RAPNGRKTDW IIHEYRLQNN EHAPAQEEGW VVCRAFQKPM  180
PNQQQQRHGC YAGGFPYPSS YDQSAAASAE SSAVDWNLLS SLLPAAQLNF HQPPASPASC  240
SKNSNDLVM*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
3ulx_A2e-4711783168Stress-induced transcription factor NAC1
Search in ModeBase
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Predominantly expressed in immature xylem vessels, only in some cells just beside xylem vessels. Also present in various vascular cells of older part of the roots, near the location of emergence of the lateral roots. {ECO:0000269|PubMed:16103214, ECO:0000269|PubMed:18445131}.
UniprotTISSUE SPECIFICITY: Expressed in developing protoxylems in roots and shoots (PubMed:16103214, PubMed:16581911, PubMed:17565617, PubMed:18952777). Detected in root protoxylem poles and in vessels of protoxylems, outermost metaxylems, inner metaxylems, shoots and hypocotyls. Expressed in roots, hypocotyls, cotyledons and leaves (PubMed:18445131). Accumulates in the xylem but not in interfascicular fibers or pith cells in inflorescence stems. Present in developing vessels of the secondary xylem in roots undergoing secondary growth (PubMed:18952777). {ECO:0000269|PubMed:16103214, ECO:0000269|PubMed:16581911, ECO:0000269|PubMed:17565617, ECO:0000269|PubMed:18445131, ECO:0000269|PubMed:18952777}.
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 (e.g. genes involved in secondary wall biosynthesis, cell wall modification such as xylan accumulation, and programmed cell death) (PubMed:20935069, PubMed:20488898, PubMed:22037706, PubMed:21284754). Involved in xylem formation in roots and shoots, especially regulating protoxylem vessel differentiation by promoting immature xylem vessel-specific genes expression (PubMed:16103214, PubMed:18445131, PubMed:20488898, PubMed:21498679, PubMed:21284754). Can activate the expression of several genes including XCP1, MYB46, NAC010/SND3, MYB103, MYB58, MYB63, MYB83, KNAT7, ASL19 and ASL20 (PubMed:17890373, PubMed:19088331, PubMed:18952777, PubMed:19122102, PubMed:19808805, PubMed:20935069, PubMed:21284754). {ECO:0000269|PubMed:16103214, ECO:0000269|PubMed:17890373, ECO:0000269|PubMed:18445131, ECO:0000269|PubMed:18952777, ECO:0000269|PubMed:19088331, ECO:0000269|PubMed:19122102, ECO:0000269|PubMed:19808805, ECO:0000269|PubMed:20488898, ECO:0000269|PubMed:20935069, ECO:0000269|PubMed:21284754, ECO:0000269|PubMed:21498679, ECO:0000269|PubMed:22037706}.; FUNCTION: Required for the soilborne fungal pathogen Verticillium longisporum-induced transdifferentiation of chloroplast-containing bundle sheath cells to functional xylem elements leading to stunted growth, vein clearing, and leaf chloroses, as well as xylem hyperplasia within the vasculature of leaves, hypocotyls, and roots due to reinitiation of cambial activity and transdifferentiation of xylem parenchyma cells. This developmental reprogramming mediates also an increased drought stress tolerance. {ECO:0000269|PubMed:23023171}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapPavir.6NG005700.1.p
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By brassinosteroids (e.g. brassinolide BL), auxin (e.g. 2,4-dichlorphenoxyacetic acid 2,4-D) and cytokinin (e.g. kinetin), with a synergistic effect (PubMed:16103214, PubMed:22345435). Up-regulated in a feed-back loop by ASL20 (PubMed:19088331). Levels are monitored by proteasome-mediated degradation (PubMed:18445131). Repressed by WEE1 upon replication stress to prevent premature tracheary element differentiation (PubMed:21498679). Accumulates during infection by the soilborne fungal pathogen Verticillium longisporum, especially in tissues undergoing de novo xylem formation (PubMed:23023171). {ECO:0000269|PubMed:16103214, ECO:0000269|PubMed:18445131, ECO:0000269|PubMed:19088331, ECO:0000269|PubMed:21498679, ECO:0000269|PubMed:22345435, ECO:0000269|PubMed:23023171}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankKT0750830.0KT075083.1 Panicum virgatum secondary wall NAC master switch (SWN3A) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_025821657.11e-146NAC domain-containing protein 30-like
RefseqXP_025821658.11e-146NAC domain-containing protein 30-like
SwissprotQ9C8W98e-85NAC30_ARATH; NAC domain-containing protein 30
TrEMBLA0A0K1TPG91e-155A0A0K1TPG9_PANVG; Secondary wall NAC master switch
STRINGPavir.J20890.1.p1e-156(Panicum virgatum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
MonocotsOGMP25943791
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT1G71930.13e-86vascular related NAC-domain protein 7
Publications ? help Back to Top
  1. 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]
  2. Kakehi J, et al.
    Mutations in ribosomal proteins, RPL4 and RACK1, suppress the phenotype of a thermospermine-deficient mutant of Arabidopsis thaliana.
    PLoS ONE, 2015. 10(1): p. e0117309
    [PMID:25625317]
  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. Li Z, et al.
    A Transcriptional and Metabolic Framework for Secondary Wall Formation in Arabidopsis.
    Plant Physiol., 2016. 172(2): p. 1334-1351
    [PMID:27566165]
  5. de Lucas M, et al.
    Transcriptional Regulation of Arabidopsis Polycomb Repressive Complex 2 Coordinates Cell-Type Proliferation and Differentiation.
    Plant Cell, 2016. 28(10): p. 2616-2631
    [PMID:27650334]
  6. Tan TT, et al.
    Transcription Factors VND1-VND3 Contribute to Cotyledon Xylem Vessel Formation.
    Plant Physiol., 2018. 176(1): p. 773-789
    [PMID:29133368]
  7. Ohashi-Ito K,Iwamoto K,Fukuda H
    LOB DOMAIN-CONTAINING PROTEIN 15 Positively Regulates Expression of VND7, a Master Regulator of Tracheary Elements.
    Plant Cell Physiol., 2018. 59(5): p. 989-996
    [PMID:29444288]