PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT1G76420.1
Common NameANAC031, CUC3, F14G6.2, F15M4.8, NAC031, NAC368
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis
Family NAC
Protein Properties Length: 334aa    MW: 38017.6 Da    PI: 6.4644
Description NAC family protein
Gene Model
Gene Model ID Type Source Coding Sequence
AT1G76420.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
          NAM   1 97 
                  lppGfrFhPtdeel+++yL+ k+ +  l+   +i+evd++++ePw+Lp+++k +e+ewyf+s rd+ky+tg r+nrat++gyWkatgkdkev+s  +g
                  79*************************999.78***************9889999***************************************9788 PP

          NAM  98 elvglkktLvfykgrapkgektdWvmheyrle 129
                  +lvg+kktLvfykgrap+g kt+Wvmheyrle
                  89****************************85 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019411.15E-6317171IPR003441NAC domain
PROSITE profilePS5100559.63922171IPR003441NAC domain
PfamPF023651.0E-2623149IPR003441NAC domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0010014Biological Processmeristem initiation
GO:0010199Biological Processorgan boundary specification between lateral organs and the meristem
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000037anatomyshoot apex
PO:0009009anatomyplant embryo
PO:0009025anatomyvascular leaf
PO:0009052anatomyflower pedicel
PO:0025022anatomycollective leaf structure
PO:0001078developmental stageplant embryo cotyledonary stage
PO:0001081developmental stagemature plant embryo stage
PO:0001185developmental stageplant embryo globular stage
PO:0004507developmental stageplant embryo bilateral stage
PO:0007611developmental stagepetal differentiation and expansion stage
PO:0007616developmental stageflowering stage
Sequence ? help Back to Top
Protein Sequence    Length: 334 aa     Download sequence    Send to blast
3D Structure ? help Back to Top
PDB ID Evalue Query Start Query End Hit Start Hit End Description
3swm_A2e-502217120168NAC domain-containing protein 19
3swm_B2e-502217120168NAC domain-containing protein 19
3swm_C2e-502217120168NAC domain-containing protein 19
3swm_D2e-502217120168NAC domain-containing protein 19
3swp_A2e-502217120168NAC domain-containing protein 19
3swp_B2e-502217120168NAC domain-containing protein 19
3swp_C2e-502217120168NAC domain-containing protein 19
3swp_D2e-502217120168NAC domain-containing protein 19
Search in ModeBase
Expression -- Microarray ? help Back to Top
Source ID E-value
Expression AtlasAT1G76420-
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: First expressed at the globular stage, mostly in the apical part of the embryo. During the triangular stage, confined to the boundary of emerging cotyledons. Later restricted to the center of the apical part of the embryo and to seedling apex, at the boundaries of the cotyledon margins and the boundaries between the SAM and the cotyledons. Localized in a one-cell-wide ring at the boundary between trichomes or lateral roots and epidermis. Accumulates at the boundaries between leaf primordia and the shoot meristem and between floral primordia and the inflorescence meristem. Found in the adaxial axils of secondary inflorescences and pedicels, and in axiallary buds. In flowers, expressed in a ring at the bases of sepals and petals. In carpels, confined to the boundaries between ovule primordia. In ovules, localized in a ring at the boundary between the nucellus and the chalaza. In the mature embryo sac, detected in the two polar nuclei of the central cell. {ECO:0000269|PubMed:12837947, ECO:0000269|PubMed:17122068}.
UniprotTISSUE SPECIFICITY: In a general manner, present at the boundaries between mersitems and araising primordia. {ECO:0000269|PubMed:12837947}.
Functional Description ? help Back to Top
Source Description
TAIRIdentified in an enhancer trap line; member of the NAC family of proteins. Expressed at the boundary between the shoot meristem and lateral organs and the polar nuclei in the embryo sac.
UniProtTranscription activator. Involved in molecular mechanisms regulating shoot apical meristem (SAM) formation during embryogenesis and organ separation. Required for axillary meristem initiation and separation of the meristem from the main stem. May act as an inhibitor of cell division. {ECO:0000269|PubMed:12837947, ECO:0000269|PubMed:17122068}.
Function -- GeneRIF ? help Back to Top
  1. These results reveal that redundant but partially distinct functions of CUC1, CUC2, and CUC3 are responsible for shoot organ boundary and meristem formation throughout the life cycle in Arabidopsis.
    [PMID: 17122068]
  2. Overexpression of miR164 in the cuc3-2 mutant caused an almost complete block of axillary meristem formation.
    [PMID: 18346190]
  3. CUC2 and CUC3 expression mediated by AHK2 and AHK3 signaling may play roles in regulation of flower development.
    [PMID: 19913077]
  4. CUC2 and CUC3 are expressed in leaf primordia and are required for wild-type serration.
    [PMID: 21258003]
  5. The cuc2 cuc3 double mutant displays irregular phyllotaxis in the mature shoot but not in the shoot apex, thus showing a post-meristematic effect of the mutations on phyllotaxis.
    [PMID: 25681504]
  6. cuc1 grf1/2/3, cuc2 grf1/2/3, and cuc3 grf1/2/3 quadruple mutants showed dramatic increases in cotyledon fusion as well as floral organ fusion.
    [PMID: 25761011]
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
Motif logo
Cis-element ? help Back to Top
Regulation -- Description ? help Back to Top
Source Description
UniProtINDUCTION: By BRM, at the chromatin level, and conferring a very specific spatial expression pattern. {ECO:0000269|PubMed:16854978}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
Regulation -- ATRM (Manually Curated Upstream Regulators) ? help Back to Top
Source Upstream Regulator (A: Activate/R: Repress)
ATRM AT1G62360 (R), AT3G15170 (A), AT5G53950 (A), AT5G61850 (A)
Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source Target Gene (A: Activate/R: Repress)
ATRM AT1G62360(A), AT5G61850(A)
Regulation -- Hormone ? help Back to Top
Source Hormone
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT1G76420
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC0123940.0AC012394.3 Arabidopsis thaliana chromosome 1 BAC F15M4 genomic sequence, complete sequence.
GenBankAC0154500.0AC015450.5 Arabidopsis thaliana chromosome 1 BAC F14G6 genomic sequence, complete sequence.
GenBankAF5431940.0AF543194.1 Arabidopsis thaliana cup-shaped cotyledon 3 (CUC3) gene, complete cds.
GenBankCP0026840.0CP002684.1 Arabidopsis thaliana chromosome 1 sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_177768.10.0NAC (No Apical Meristem) domain transcriptional regulator superfamily protein
SwissprotQ9S8510.0NAC31_ARATH; Protein CUP-SHAPED COTYLEDON 3
TrEMBLA0A178W1E70.0A0A178W1E7_ARATH; NAC368
STRINGAT1G76420.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
Representative plantOGRP1715800
Publications ? help Back to Top
  1. Riechmann JL, et al.
    Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
    Science, 2000. 290(5499): p. 2105-10
  2. Vroemen CW,Mordhorst AP,Albrecht C,Kwaaitaal MA,de Vries SC
    The CUP-SHAPED COTYLEDON3 gene is required for boundary and shoot meristem formation in Arabidopsis.
    Plant Cell, 2003. 15(7): p. 1563-77
  3. Ooka H, et al.
    Comprehensive analysis of NAC family genes in Oryza sativa and Arabidopsis thaliana.
    DNA Res., 2003. 10(6): p. 239-47
  4. Laufs P,Peaucelle A,Morin H,Traas J
    MicroRNA regulation of the CUC genes is required for boundary size control in Arabidopsis meristems.
    Development, 2004. 131(17): p. 4311-22
  5. Zimmermann R,Werr W
    Pattern formation in the monocot embryo as revealed by NAM and CUC3 orthologues from Zea mays L.
    Plant Mol. Biol., 2005. 58(5): p. 669-85
  6. Belles-Boix E, et al.
    KNAT6: an Arabidopsis homeobox gene involved in meristem activity and organ separation.
    Plant Cell, 2006. 18(8): p. 1900-7
  7. Kwon CS, et al.
    A role for chromatin remodeling in regulation of CUC gene expression in the Arabidopsis cotyledon boundary.
    Development, 2006. 133(16): p. 3223-30
  8. Nikovics K, et al.
    The balance between the MIR164A and CUC2 genes controls leaf margin serration in Arabidopsis.
    Plant Cell, 2006. 18(11): p. 2929-45
  9. Hibara K, et al.
    Arabidopsis CUP-SHAPED COTYLEDON3 regulates postembryonic shoot meristem and organ boundary formation.
    Plant Cell, 2006. 18(11): p. 2946-57
  10. Raman S, et al.
    Interplay of miR164, CUP-SHAPED COTYLEDON genes and LATERAL SUPPRESSOR controls axillary meristem formation in Arabidopsis thaliana.
    Plant J., 2008. 55(1): p. 65-76
  11. Blein T, et al.
    A conserved molecular framework for compound leaf development.
    Science, 2008. 322(5909): p. 1835-9
  12. Lee DK,Geisler M,Springer PS
    LATERAL ORGAN FUSION1 and LATERAL ORGAN FUSION2 function in lateral organ separation and axillary meristem formation in Arabidopsis.
    Development, 2009. 136(14): p. 2423-32
  13. Li XG, et al.
    Cytokinin overproduction-caused alteration of flower development is partially mediated by CUC2 and CUC3 in Arabidopsis.
    Gene, 2010. 450(1-2): p. 109-20
  14. Hasson A, et al.
    Evolution and diverse roles of the CUP-SHAPED COTYLEDON genes in Arabidopsis leaf development.
    Plant Cell, 2011. 23(1): p. 54-68
  15. Lie C,Kelsom C,Wu X
    WOX2 and STIMPY-LIKE/WOX8 promote cotyledon boundary formation in Arabidopsis.
    Plant J., 2012. 72(4): p. 674-82
  16. Stirnberg P,Liu JP,Ward S,Kendall SL,Leyser O
    Mutation of the cytosolic ribosomal protein-encoding RPS10B gene affects shoot meristematic function in Arabidopsis.
    BMC Plant Biol., 2012. 12: p. 160
  17. Pei H, et al.
    An NAC transcription factor controls ethylene-regulated cell expansion in flower petals.
    Plant Physiol., 2013. 163(2): p. 775-91
  18. Chen C, et al.
    Transcriptome profiling reveals roles of meristem regulators and polarity genes during fruit trichome development in cucumber (Cucumis sativus L.).
    J. Exp. Bot., 2014. 65(17): p. 4943-58
  19. Burian A, et al.
    The CUP-SHAPED COTYLEDON2 and 3 genes have a post-meristematic effect on Arabidopsis thaliana phyllotaxis.
    Ann. Bot., 2015. 115(5): p. 807-20
  20. Jin J, et al.
    An Arabidopsis Transcriptional Regulatory Map Reveals Distinct Functional and Evolutionary Features of Novel Transcription Factors.
    Mol. Biol. Evol., 2015. 32(7): p. 1767-73
  21. Lee BH,Jeon JO,Lee MM,Kim JH
    Genetic interaction between GROWTH-REGULATING FACTOR and CUP-SHAPED COTYLEDON in organ separation.
    Plant Signal Behav, 2015. 10(2): p. e988071
  22. Huang D, et al.
    A Gibberellin-Mediated DELLA-NAC Signaling Cascade Regulates Cellulose Synthesis in Rice.
    Plant Cell, 2015. 27(6): p. 1681-96
  23. Gonçalves B, et al.
    A conserved role for CUP-SHAPED COTYLEDON genes during ovule development.
    Plant J., 2015. 83(4): p. 732-42
  24. 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
  25. Espinosa-Ruiz A, et al.
    TOPLESS mediates brassinosteroid control of shoot boundaries and root meristem development in Arabidopsis thaliana.
    Development, 2017. 144(9): p. 1619-1628
  26. 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