PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Previous version: v3.0 v4.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Solyc08g006020.2.1
Common NameLOC101256693
Organism
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; asterids; lamiids; Solanales; Solanaceae; Solanoideae; Solaneae; Solanum; Lycopersicon
Family NAC
Protein Properties Length: 303aa    MW: 34863.8 Da    PI: 9.4857
Description NAC family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Solyc08g006020.2.1genomeITAGView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1NAM173.75.3e-54101431128
                 NAM   1 lppGfrFhPtdeelvveyLkkkvegkkleleevikevdiykvePwdLpkkvkaeekewyfFskrdkkyatgkrknratksgyWkatgkdke 91 
                         lppGfrFhPtdeel+++yL +k+++ +++  ++i++vd++k+ePwdLp k+k + kewyfFs rd+ky+tg r+nrat+sgyWk+tgkdke
  Solyc08g006020.2.1  10 LPPGFRFHPTDEELITYYLVNKINDANFTG-RAIADVDLNKSEPWDLPGKAKMGGKEWYFFSLRDRKYPTGVRTNRATNSGYWKTTGKDKE 99 
                         79*************************999.89***************999999************************************* PP

                 NAM  92 vlsk..kgel.......vglkktLvfykgrapkgektdWvmheyrl 128
                         ++++  +  +       +g+kktLvfykgrap+gek++Wvmheyr+
  Solyc08g006020.2.1 100 IFNSknN--NnnnnlelIGMKKTLVFYKGRAPRGEKSNWVMHEYRI 143
                         ***8551..34556677***************************97 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019416.28E-635165IPR003441NAC domain
PROSITE profilePS5100559.99910165IPR003441NAC domain
PfamPF023655.2E-2911143IPR003441NAC 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: 303 aa     Download sequence    Send to blast
MEEVKEETQL PPGFRFHPTD EELITYYLVN KINDANFTGR AIADVDLNKS EPWDLPGKAK  60
MGGKEWYFFS LRDRKYPTGV RTNRATNSGY WKTTGKDKEI FNSKNNNNNN NLELIGMKKT  120
LVFYKGRAPR GEKSNWVMHE YRIRSKSSYK TNKQDEWVVC RIFQKSVGLK KYPTSQYSRA  180
TYSLNNTQNN ASIMSSQMMQ LPNDHQGFQL AMGRNNNNNN NYMNNHGHEI QDVNNRVIFQ  240
SGSSSMINNF PTQPQMSYNI TSYGGEMNNA NTSYGGEMNN ANTMNSGVMD HCVDLHNYWT  300
TY*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1ut4_A2e-5411716171NO APICAL MERISTEM PROTEIN
1ut4_B2e-5411716171NO APICAL MERISTEM PROTEIN
1ut7_A2e-5411716171NO APICAL MERISTEM PROTEIN
1ut7_B2e-5411716171NO APICAL MERISTEM PROTEIN
3swm_A2e-5411719174NAC domain-containing protein 19
3swm_B2e-5411719174NAC domain-containing protein 19
3swm_C2e-5411719174NAC domain-containing protein 19
3swm_D2e-5411719174NAC domain-containing protein 19
3swp_A2e-5411719174NAC domain-containing protein 19
3swp_B2e-5411719174NAC domain-containing protein 19
3swp_C2e-5411719174NAC domain-containing protein 19
3swp_D2e-5411719174NAC domain-containing protein 19
4dul_A2e-5411716171NAC domain-containing protein 19
4dul_B2e-5411716171NAC domain-containing protein 19
Search in ModeBase
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: First expressed in early to mid-globular-stage embryos. In late globular stage, detected as a stripe running medially across the top of the embryo. In heart stage embryo, expression is restricted to a stripe between the cotyledon primordia, but confined to hypodermal cells. In the bending-cotyledon stage, localized in a region surrounding the SAM, that correspond to the boundary region of cotyledon margins (BCM) and the boundaries between SAM and cotyledons, including protoderm cells. Observed in the margins of leaf primordia, and later restricted to the leaf sinus region, with a diminution in outgrowing teeth. Restricted to the proximal part of mature leaves. Expressed at the boundaries between the inflorescence meristem (IM) and flower primordia. Once the flower starts to grow out and the internode begin to elongates, restricted to the axils of the floral pedicels through several nodes. Detected within floral primordia, between sepal primordia and the floral meristem. Also present at the boundaries of individual sepal primordia, as well as in the region surrounding each petal and stamen primordium. Later detected transiently at the boundaries between locules of each theca in anthers. Expression at the inner part of presumtive septal regions that raises to include presumptive placenta, at the tips of septal primordia, as septum grow. Localized in the fused region of the septum. Found at the boundaries of ovule primordia, and later at the boundary between the nucellus and the chalaza. {ECO:0000269|PubMed:10079219, ECO:0000269|PubMed:10750709, ECO:0000269|PubMed:17098808, ECO:0000269|PubMed:17251269}.
UniprotTISSUE SPECIFICITY: Mostly expressed in buds and flowers, and, to a lower extent, in the aerial parts of seedling, inflorescence and old silique. In a general manner, present at the boundaries between mersitems and araising primordia. {ECO:0000269|PubMed:10750709, ECO:0000269|PubMed:15053771, ECO:0000269|PubMed:9212461}.
Functional Description ? help Back to Top
Source Description
UniProtTranscription activator of STM and KNAT6. Involved in molecular mechanisms regulating shoot apical meristem (SAM) formation during embryogenesis and organ separation. Required for the fusion of septa of gynoecia along the length of the ovaries. Activates the shoot formation in callus in a STM-dependent manner. Controls leaf margin development and required for leaf serration. Involved in axillary meristem initiation and separation of the meristem from the main stem. Regulates the phyllotaxy throughout the plant development. Seems to act as an inhibitor of cell division. {ECO:0000269|PubMed:10079219, ECO:0000269|PubMed:10750709, ECO:0000269|PubMed:12163400, ECO:0000269|PubMed:12492830, ECO:0000269|PubMed:12610213, ECO:0000269|PubMed:15202996, ECO:0000269|PubMed:15294871, ECO:0000269|PubMed:15500463, ECO:0000269|PubMed:15723790, ECO:0000269|PubMed:16798887, ECO:0000269|PubMed:17098808, ECO:0000269|PubMed:17122068, ECO:0000269|PubMed:17251269, ECO:0000269|PubMed:17287247, ECO:0000269|PubMed:9212461}.
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00277DAPTransfer from AT2G24430Download
Motif logo
Cis-element ? help Back to Top
SourceLink
PlantRegMapSolyc08g006020.2.1
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By BRM and SYD, at the chromatin level, and conferring a very specific spatial expression pattern. Precise spatial regulation by post-transcriptional repression directed by the microRNA miR164. {ECO:0000269|PubMed:15202996, ECO:0000269|PubMed:15294871, ECO:0000269|PubMed:15723790, ECO:0000269|PubMed:16854978, ECO:0000269|PubMed:17251269, ECO:0000269|PubMed:17287247}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieveRetrieve
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAP0093570.0Solanum lycopersicum genomic DNA, chromosome 8, clone: C08HBa0025I17, complete sequence
GenBankAP0094830.0Solanum lycopersicum DNA, chromosome 8, clone: C08SLm0116H03, complete sequence
GenBankAP0107840.0Solanum lycopersicum DNA, chromosome 8, clone: C08HBa0021H05, complete sequence
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_004244460.10.0NAC domain-containing protein 100-like
SwissprotO040171e-79NAC98_ARATH; Protein CUP-SHAPED COTYLEDON 2
TrEMBLM1B6X01e-164M1B6X0_SOLTU; Uncharacterized protein
STRINGSolyc08g006020.2.10.0(Solanum lycopersicum)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
AsteridsOGEA15224279
Representative plantOGRP1715800
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT2G24430.21e-105NAC domain containing protein 38
Publications ? help Back to Top
  1. Wang Y,van der Hoeven RS,Nielsen R,Mueller LA,Tanksley SD
    Characteristics of the tomato nuclear genome as determined by sequencing undermethylated EcoRI digested fragments.
    Theor. Appl. Genet., 2005. 112(1): p. 72-84
    [PMID:16208505]
  2. Wang YX
    Characterization of a novel Medicago sativa NAC transcription factor gene involved in response to drought stress.
    Mol. Biol. Rep., 2013. 40(11): p. 6451-8
    [PMID:24057250]
  3. Kamiuchi Y,Yamamoto K,Furutani M,Tasaka M,Aida M
    The CUC1 and CUC2 genes promote carpel margin meristem formation during Arabidopsis gynoecium development.
    Front Plant Sci, 2014. 5: p. 165
    [PMID:24817871]
  4. Gonçalves B, et al.
    A conserved role for CUP-SHAPED COTYLEDON genes during ovule development.
    Plant J., 2015. 83(4): p. 732-42
    [PMID:26119568]
  5. Du Q,Wang H
    The role of HD-ZIP III transcription factors and miR165/166 in vascular development and secondary cell wall formation.
    Plant Signal Behav, 2015. 10(10): p. e1078955
    [PMID:26340415]
  6. Vialette-Guiraud AC, et al.
    A Conserved Role for the NAM/miR164 Developmental Module Reveals a Common Mechanism Underlying Carpel Margin Fusion in Monocarpous and Syncarpous Eurosids.
    Front Plant Sci, 2015. 6: p. 1239
    [PMID:26793217]
  7. Cui X, et al.
    REF6 recognizes a specific DNA sequence to demethylate H3K27me3 and regulate organ boundary formation in Arabidopsis.
    Nat. Genet., 2016. 48(6): p. 694-9
    [PMID:27111035]
  8. Blein T,Pautot V,Laufs P
    Combinations of Mutations Sufficient to Alter Arabidopsis Leaf Dissection.
    Plants (Basel), 2013. 2(2): p. 230-47
    [PMID:27137374]
  9. Biot E, et al.
    Multiscale quantification of morphodynamics: MorphoLeaf software for 2D shape analysis.
    Development, 2016. 143(18): p. 3417-28
    [PMID:27387872]
  10. Zheng M, et al.
    Chloroplast Translation Initiation Factors Regulate Leaf Variegation and Development.
    Plant Physiol., 2016. 172(2): p. 1117-1130
    [PMID:27535792]
  11. Balkunde R,Kitagawa M,Xu XM,Wang J,Jackson D
    SHOOT MERISTEMLESS trafficking controls axillary meristem formation, meristem size and organ boundaries in Arabidopsis.
    Plant J., 2017. 90(3): p. 435-446
    [PMID:28161901]
  12. Koyama T,Sato F,Ohme-Takagi M
    Roles of miR319 and TCP Transcription Factors in Leaf Development.
    Plant Physiol., 2017. 175(2): p. 874-885
    [PMID:28842549]
  13. González-Carranza ZH, et al.
    HAWAIIAN SKIRT controls size and floral organ number by modulating CUC1 and CUC2 expression.
    PLoS ONE, 2017. 12(9): p. e0185106
    [PMID:28934292]
  14. Wilson-Sánchez D,Martínez-López S,Navarro-Cartagena S,Jover-Gil S,Micol JL
    Members of the DEAL subfamily of the DUF1218 gene family are required for bilateral symmetry but not for dorsoventrality in Arabidopsis leaves.
    New Phytol., 2018. 217(3): p. 1307-1321
    [PMID:29139551]
  15. Gonçalves B, et al.
    GDP-L-fucose is required for boundary definition in plants.
    J. Exp. Bot., 2017. 68(21-22): p. 5801-5811
    [PMID:29186469]
  16. Sha S, et al.
    To be serrate or pinnate: diverse leaf forms of yarrows (Achillea) are linked to differential expression patterns of NAM genes.
    Ann. Bot., 2018. 121(2): p. 255-266
    [PMID:29267935]
  17. Maugarny-Calès A, et al.
    Dissecting the pathways coordinating patterning and growth by plant boundary domains.
    PLoS Genet., 2019. 15(1): p. e1007913
    [PMID:30677017]