Plant Transcription Factor Database
Previous version: v3.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT3G15170.1
Common NameANAC054, ATNAC1, CUC1, F4B12.8, NAC054
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: 310aa    MW: 34232.8 Da    PI: 8.2019
Description NAC family protein
Gene Model
Gene Model ID Type Source Coding Sequence
AT3G15170.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
          NAM   1 97 
                  +ppGfrFhPtdeel+++yL kkv ++++++  +i++vd++k+ePw+Lp+k+k +ekewyfF+ rd+ky+tg r+nrat++gyWkatgkd+e++s+ ++
                  79****************************.88***************99999****************************************98566 PP

          NAM  98 elvglkktLvfykgrapkgektdWvmheyrl 128
                  +l g+kktLvfykgrapkgek+ Wvmheyrl
                  77***************************98 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF1019415.49E-6217172IPR003441NAC domain
PROSITE profilePS5100558.6320172IPR003441NAC domain
PfamPF023651.2E-2821147IPR003441NAC domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009793Biological Processembryo development ending in seed dormancy
GO:0010014Biological Processmeristem initiation
GO:0010072Biological Processprimary shoot apical meristem specification
GO:0010160Biological Processformation of organ boundary
GO:0010223Biological Processsecondary shoot formation
GO:0048467Biological Processgynoecium development
GO:0048527Biological Processlateral root development
GO:0051782Biological Processnegative regulation of cell division
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:0000003anatomywhole plant
PO:0000037anatomyshoot apex
PO:0009009anatomyplant embryo
PO:0025022anatomycollective leaf structure
PO:0001078developmental stageplant embryo cotyledonary stage
PO:0001081developmental stagemature plant embryo stage
PO:0004507developmental stageplant embryo bilateral stage
PO:0007611developmental stagepetal differentiation and expansion stage
Sequence ? help Back to Top
Protein Sequence    Length: 310 aa     Download sequence    Send to blast
3D Structure ? help Back to Top
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4dul_B2e-502017317166NAC domain-containing protein 19
4dul_A2e-502017317166NAC domain-containing protein 19
3swp_D3e-502017320169NAC domain-containing protein 19
3swp_C3e-502017320169NAC domain-containing protein 19
3swp_B3e-502017320169NAC domain-containing protein 19
3swp_A3e-502017320169NAC domain-containing protein 19
3swm_D3e-502017320169NAC domain-containing protein 19
3swm_C3e-502017320169NAC domain-containing protein 19
3swm_B3e-502017320169NAC domain-containing protein 19
3swm_A3e-502017320169NAC domain-containing protein 19
Search in ModeBase
Expression -- Microarray ? help Back to Top
Source ID E-value
Expression AtlasAT3G15170-
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: First observed in young embryonic SAM. Later confined to the boundaries between cotyledon primordia and the SAM. In mature embryos, localized around first leaves primordia. Only weakly present in vegetative SAM. In inflorescence, observed at the boundaries between floral organ primordia. In callus, expressed during transition to shoot development, with a progressive restriction to specific areas corresponding to future shoot apex. {ECO:0000269|PubMed:11245578, ECO:0000269|PubMed:12492830}.
UniprotTISSUE SPECIFICITY: Expressed in inflorescence stems, rosette leaves, aerial parts of seedlings, flowers, floral buds and roots. {ECO:0000269|PubMed:11245578}.
Functional Description ? help Back to Top
Source Description
TAIREncodes a transcription factor involved in shoot apical meristem formation and auxin-mediated lateral root formation. The gene is thought not to be involved in stress responses (NaCl, auxins, ethylene). Cuc mutant was first recognized at the heart stage, where embryos lacking two distinct bulges of cotyledonary primordia were observed.
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. Seems to act as an inhibitor of cell division. {ECO:0000269|PubMed:10079219, ECO:0000269|PubMed:10750709, ECO:0000269|PubMed:11245578, ECO:0000269|PubMed:12163400, ECO:0000269|PubMed:12492830, ECO:0000269|PubMed:12610213, ECO:0000269|PubMed:12787253, ECO:0000269|PubMed:14617069, ECO:0000269|PubMed:15202996, ECO:0000269|PubMed:15294871, ECO:0000269|PubMed:15500463, ECO:0000269|PubMed:15723790, ECO:0000269|PubMed:16798887, ECO:0000269|PubMed:17122068, ECO:0000269|PubMed:17287247, ECO:0000269|PubMed:9212461}.
Function -- GeneRIF ? help Back to Top
  1. The molecular basis for the activity of the protein.
    [PMID: 15500463]
  2. These results suggest that ESR2 plays a role in shoot regeneration through transcriptional regulation of CUC1.
    [PMID: 17056621]
  3. Regulation of axillary meristem formation by miR164 is mediated through CUC1 and CUC2, which in turn regulate LAS.
    [PMID: 18346190]
  4. CUC1 and CUC2 resulted from duplications of a unique ancestral gene and show different patterns of evolution.
    [PMID: 21258003]
  5. CUC1 directly activates transcription of the nuclear factor genes LSH4 and LSH3, which may suppress organ differentiation in the boundary region.
    [PMID: 21435050]
  6. The results bring new insights into the mechanistic links between KNOXI and CUC transcription factors and contribute to the understanding of the regulatory network controlled by STM.
    [PMID: 21685178]
  7. suppresses growth of sepal tissues from the boundary region
    [PMID: 22507233]
  8. SPT negatively regulates CUC1 and CUC2 expression in the apical part of the gynoecium.
    [PMID: 22514090]
  9. CUC1, CUC2, and AINTEGUMENTA have additive effects on ovule primordia formation.
    [PMID: 23941199]
  10. 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. Directly induced by ESR2 in response to cytokinins. 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:17056621, ECO:0000269|PubMed:17287247}.
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 AT1G24590 (A), AT1G65620 (R), AT2G37630 (R), AT4G32980 (A)
Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source Target Gene (A: Activate/R: Repress)
ATRM AT1G23380(A), AT1G55580(A), AT1G62360(A), AT1G76420(A), AT2G31160(A), AT3G23290(A)
Regulation -- Hormone ? help Back to Top
Source Hormone
AHDauxin, ethylene
Interaction ? help Back to Top
Source Intact With
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT3G15170
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAB0490690.0AB049069.1 Arabidopsis thaliana CUC1 mRNA, complete cds.
GenBankBT0260800.0BT026080.1 Arabidopsis thaliana At3g15170 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_188135.10.0protein CUP-SHAPED COTYLEDON 1
TrEMBLD7L3Z70.0D7L3Z7_ARALL; Cup-shaped cotyledon1
STRINGAT3G15170.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
Representative plantOGRP1715800
Publications ? help Back to Top
  1. Aida M,Ishida T,Tasaka M
    Shoot apical meristem and cotyledon formation during Arabidopsis embryogenesis: interaction among the CUP-SHAPED COTYLEDON and SHOOT MERISTEMLESS genes.
    Development, 1999. 126(8): p. 1563-70
  2. Ishida T,Aida M,Takada S,Tasaka M
    Involvement of CUP-SHAPED COTYLEDON genes in gynoecium and ovule development in Arabidopsis thaliana.
    Plant Cell Physiol., 2000. 41(1): p. 60-7
  3. Riechmann JL, et al.
    Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
    Science, 2000. 290(5499): p. 2105-10
  4. Takada S,Hibara K,Ishida T,Tasaka M
    The CUP-SHAPED COTYLEDON1 gene of Arabidopsis regulates shoot apical meristem formation.
    Development, 2001. 128(7): p. 1127-35
  5. Sharma VK,Fletcher JC
    Maintenance of shoot and floral meristem cell proliferation and fate.
    Plant Physiol., 2002. 129(1): p. 31-9
  6. Aida M,Vernoux T,Furutani M,Traas J,Tasaka M
    Roles of PIN-FORMED1 and MONOPTEROS in pattern formation of the apical region of the Arabidopsis embryo.
    Development, 2002. 129(17): p. 3965-74
  7. Cary AJ,Che P,Howell SH
    Developmental events and shoot apical meristem gene expression patterns during shoot development in Arabidopsis thaliana.
    Plant J., 2002. 32(6): p. 867-77
  8. Daimon Y,Takabe K,Tasaka M
    The CUP-SHAPED COTYLEDON genes promote adventitious shoot formation on calli.
    Plant Cell Physiol., 2003. 44(2): p. 113-21
  9. Hiratsu K,Matsui K,Koyama T,Ohme-Takagi M
    Dominant repression of target genes by chimeric repressors that include the EAR motif, a repression domain, in Arabidopsis.
    Plant J., 2003. 34(5): p. 733-9
  10. 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
  11. Hibara K,Takada S,Tasaka M
    CUC1 gene activates the expression of SAM-related genes to induce adventitious shoot formation.
    Plant J., 2003. 36(5): p. 687-96
  12. Ooka H, et al.
    Comprehensive analysis of NAC family genes in Oryza sativa and Arabidopsis thaliana.
    DNA Res., 2003. 10(6): p. 239-47
  13. Mallory AC,Dugas DV,Bartel DP,Bartel B
    MicroRNA regulation of NAC-domain targets is required for proper formation and separation of adjacent embryonic, vegetative, and floral organs.
    Curr. Biol., 2004. 14(12): p. 1035-46
  14. Brewer PB, et al.
    PETAL LOSS, a trihelix transcription factor gene, regulates perianth architecture in the Arabidopsis flower.
    Development, 2004. 131(16): p. 4035-45
  15. 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
  16. Furutani M, et al.
    PIN-FORMED1 and PINOID regulate boundary formation and cotyledon development in Arabidopsis embryogenesis.
    Development, 2004. 131(20): p. 5021-30
  17. Taoka K, et al.
    The NAC domain mediates functional specificity of CUP-SHAPED COTYLEDON proteins.
    Plant J., 2004. 40(4): p. 462-73
  18. Kajiwara T,Furutani M,Hibara K,Tasaka M
    The GURKE gene encoding an acetyl-CoA carboxylase is required for partitioning the embryo apex into three subregions in Arabidopsis.
    Plant Cell Physiol., 2004. 45(9): p. 1122-8
  19. Baker CC,Sieber P,Wellmer F,Meyerowitz EM
    The early extra petals1 mutant uncovers a role for microRNA miR164c in regulating petal number in Arabidopsis.
    Curr. Biol., 2005. 15(4): p. 303-15
  20. Kidner CA,Martienssen RA
    The role of ARGONAUTE1 (AGO1) in meristem formation and identity.
    Dev. Biol., 2005. 280(2): p. 504-17
  21. Yanai O, et al.
    Arabidopsis KNOXI proteins activate cytokinin biosynthesis.
    Curr. Biol., 2005. 15(17): p. 1566-71
  22. He XJ, et al.
    AtNAC2, a transcription factor downstream of ethylene and auxin signaling pathways, is involved in salt stress response and lateral root development.
    Plant J., 2005. 44(6): p. 903-16
  23. 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
  24. 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
  25. Ikeda Y,Banno H,Niu QW,Howell SH,Chua NH
    The ENHANCER OF SHOOT REGENERATION 2 gene in Arabidopsis regulates CUP-SHAPED COTYLEDON 1 at the transcriptional level and controls cotyledon development.
    Plant Cell Physiol., 2006. 47(11): p. 1443-56
  26. 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
  27. Hibara K, et al.
    Arabidopsis CUP-SHAPED COTYLEDON3 regulates postembryonic shoot meristem and organ boundary formation.
    Plant Cell, 2006. 18(11): p. 2946-57
  28. Sieber P,Wellmer F,Gheyselinck J,Riechmann JL,Meyerowitz EM
    Redundancy and specialization among plant microRNAs: role of the MIR164 family in developmental robustness.
    Development, 2007. 134(6): p. 1051-60
  29. Koyama T,Furutani M,Tasaka M,Ohme-Takagi M
    TCP transcription factors control the morphology of shoot lateral organs via negative regulation of the expression of boundary-specific genes in Arabidopsis.
    Plant Cell, 2007. 19(2): p. 473-84
  30. Xu B, et al.
    Arabidopsis genes AS1, AS2, and JAG negatively regulate boundary-specifying genes to promote sepal and petal development.
    Plant Physiol., 2008. 146(2): p. 566-75
  31. 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
  32. Skirycz A, et al.
    The DOF transcription factor OBP1 is involved in cell cycle regulation in Arabidopsis thaliana.
    Plant J., 2008. 56(5): p. 779-92
  33. Gómez-Mena C,Sablowski R
    ARABIDOPSIS THALIANA HOMEOBOX GENE1 establishes the basal boundaries of shoot organs and controls stem growth.
    Plant Cell, 2008. 20(8): p. 2059-72
  34. Atta R, et al.
    Pluripotency of Arabidopsis xylem pericycle underlies shoot regeneration from root and hypocotyl explants grown in vitro.
    Plant J., 2009. 57(4): p. 626-44
  35. Tamaki H, et al.
    Identification of novel meristem factors involved in shoot regeneration through the analysis of temperature-sensitive mutants of Arabidopsis.
    Plant J., 2009. 57(6): p. 1027-39
  36. Koizumi A,Yamanaka K,Kawano S
    Carpel development in a floral mutant of dioecious Silene latifolia producing asexual and female-like flowers.
    J. Plant Physiol., 2009. 166(16): p. 1832-8
  37. Mon
    Sex determination in plants.
    Plant Signal Behav, 2007. 2(3): p. 178-9
  38. Bazzini AA, et al.
    Virus infection elevates transcriptional activity of miR164a promoter in plants.
    BMC Plant Biol., 2009. 9: p. 152
  39. Koizumi A, et al.
    Two separate pathways including SlCLV1, SlSTM and SlCUC that control carpel development in a bisexual mutant of Silene latifolia.
    Plant Cell Physiol., 2010. 51(2): p. 282-93
  40. De Smet I,Lau S,Mayer U,J
    Embryogenesis - the humble beginnings of plant life.
    Plant J., 2010. 61(6): p. 959-70
  41. 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
  42. Takeda S, et al.
    CUP-SHAPED COTYLEDON1 transcription factor activates the expression of LSH4 and LSH3, two members of the ALOG gene family, in shoot organ boundary cells.
    Plant J., 2011. 66(6): p. 1066-77
  43. Spinelli SV,Martin AP,Viola IL,Gonzalez DH,Palatnik JF
    A mechanistic link between STM and CUC1 during Arabidopsis development.
    Plant Physiol., 2011. 156(4): p. 1894-904
  44. Uberti-Manassero NG,Lucero LE,Viola IL,Vegetti AC,Gonzalez DH
    The class I protein AtTCP15 modulates plant development through a pathway that overlaps with the one affected by CIN-like TCP proteins.
    J. Exp. Bot., 2012. 63(2): p. 809-23
  45. Lampugnani ER,Kilinc A,Smyth DR
    PETAL LOSS is a boundary gene that inhibits growth between developing sepals in Arabidopsis thaliana.
    Plant J., 2012. 71(5): p. 724-35
  46. Nahar MA,Ishida T,Smyth DR,Tasaka M,Aida M
    Interactions of CUP-SHAPED COTYLEDON and SPATULA genes control carpel margin development in Arabidopsis thaliana.
    Plant Cell Physiol., 2012. 53(6): p. 1134-43
  47. Huang T,L
    RBE controls microRNA164 expression to effect floral organogenesis.
    Development, 2012. 139(12): p. 2161-9
  48. Larsson E,Sundstr
    Expression of PaNAC01, a Picea abies CUP-SHAPED COTYLEDON orthologue, is regulated by polar auxin transport and associated with differentiation of the shoot apical meristem and formation of separated cotyledons.
    Ann. Bot., 2012. 110(4): p. 923-34
  49. 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
  50. Qiao M,Xiang F
    A set of Arabidopsis thaliana miRNAs involve shoot regeneration in vitro.
    Plant Signal Behav, 2013. 8(3): p. e23479
  51. Viola IL,G
    Redox modulation of plant developmental regulators from the class I TCP transcription factor family.
    Plant Physiol., 2013. 162(3): p. 1434-47
  52. Pei H, et al.
    An NAC transcription factor controls ethylene-regulated cell expansion in flower petals.
    Plant Physiol., 2013. 163(2): p. 775-91
  53. Galbiati F, et al.
    An integrative model of the control of ovule primordia formation.
    Plant J., 2013. 76(3): p. 446-55
  54. Zhu Q, et al.
    In silico analysis on structure and DNA binding mode of AtNAC1, a NAC transcription factor from Arabidopsis thaliana.
    J Mol Model, 2014. 20(3): p. 2117
  55. 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
  56. 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
  57. Aida M,Ishida T,Fukaki H,Fujisawa H,Tasaka M
    Genes involved in organ separation in Arabidopsis: an analysis of the cup-shaped cotyledon mutant.
    Plant Cell, 1997. 9(6): p. 841-57