PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT3G15030.3
Common NameK15M2.17, MEE35, TCP4
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 TCP
Protein Properties Length: 420aa    MW: 45963.4 Da    PI: 7.2936
Description TCP family protein
Gene Model
Gene Model ID Type Source Coding Sequence
AT3G15030.3genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
          TCP   2 agkkdrhskihTkvggRdRRvRlsaecaarfFdLqdeLGfdkdsktieWLlqqakpaikeltgt........................ssssasecea 75 
                  +g+kdrhsk++T++g+RdRRvRlsa++a++f+d+qd+LGfd++sk+++WL+++ak++i+el+++                        +++s+s   +
                  79**************************************************************9999999999988888887766652222222233 PP

          TCP  76 esssssas.........nsssg........................kaaksaakskksqksaasalnlakesrakara 120
                  ++++++++             g                         ++ +   +++++++++  +nl+++ +++   
  AT3G15030.3 141 QQQQQQQQlqfgvgfngG---GaehpsnnessflppsmdsdsiadtIKSFFPVIGSSTEAPSN--HNLMHNYHHQHPP 213
                  333333333344444440...044444445667777777777776644444444444444444..5555555544444 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF036342.6E-3243147IPR005333Transcription factor, TCP
PROSITE profilePS5136934.01645103IPR017887Transcription factor TCP subgroup
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:0009965Biological Processleaf morphogenesis
GO:0030154Biological Processcell differentiation
GO:0045962Biological Processpositive regulation of development, heterochronic
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0005515Molecular Functionprotein binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000013anatomycauline leaf
PO:0000037anatomyshoot apex
PO:0000056anatomyflower bud
PO:0000293anatomyguard cell
PO:0008019anatomyleaf lamina base
PO:0009006anatomyshoot system
PO:0009009anatomyplant embryo
PO:0009025anatomyvascular leaf
PO:0025022anatomycollective leaf structure
PO:0001054developmental stagevascular leaf senescent stage
PO:0001078developmental stageplant embryo cotyledonary stage
PO:0001081developmental stagemature plant embryo stage
PO:0004507developmental stageplant embryo bilateral stage
PO:0007064developmental stageLP.12 twelve leaves visible stage
PO:0007095developmental stageLP.08 eight leaves visible stage
PO:0007098developmental stageLP.02 two leaves visible stage
PO:0007103developmental stageLP.10 ten leaves visible stage
PO:0007115developmental stageLP.04 four leaves visible stage
PO:0007123developmental stageLP.06 six leaves visible stage
PO:0007611developmental stagepetal differentiation and expansion stage
PO:0007616developmental stageflowering stage
Sequence ? help Back to Top
Protein Sequence    Length: 420 aa     Download sequence    Send to blast
3D Structure ? help Back to Top
PDB ID Evalue Query Start Query End Hit Start Hit End Description
5zkt_A4e-2050103154Putative transcription factor PCF6
5zkt_B4e-2050103154Putative transcription factor PCF6
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.237640.0floral meristem| seed
Expression -- Microarray ? help Back to Top
Source ID E-value
Expression AtlasAT3G15030-
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Expressed in cotyledons during embryogenesis. Expressed during ovule development (PubMed:25378179). {ECO:0000269|PubMed:25378179}.
UniprotTISSUE SPECIFICITY: Expressed in cotyledons, particularly in the vascular region, in leaves, roots, buds, flowers and immature siliques. {ECO:0000269|PubMed:17307931}.
Functional Description ? help Back to Top
Source Description
TAIRArabidopsis thaliana TCP family transcription factor. Regulated by miR319. Involved in heterchronic regulation of leaf differentiation.
UniProtTranscription factor playing a pivotal role in the control of morphogenesis of shoot organs by negatively regulating the expression of boundary-specific genes such as CUC genes, probably through the induction of miRNA (e.g. miR164) (PubMed:12931144, PubMed:17307931). Required during early steps of embryogenesis (PubMed:15634699). Participates in ovule develpment (PubMed:25378179). Activates LOX2 expression by binding to the 5'-GGACCA-3' motif found in its promoter (PubMed:18816164). {ECO:0000269|PubMed:12931144, ECO:0000269|PubMed:15634699, ECO:0000269|PubMed:17307931, ECO:0000269|PubMed:18816164, ECO:0000269|PubMed:25378179}.
Function -- GeneRIF ? help Back to Top
  1. a miRNA-resistant version of TCP4, when expressed in petals and stamens, causes these organs not to develop
    [PMID: 20007771]
  2. Arabidopsis plants with an increased activity of the transcription factor TCP4, which reduces cell proliferation in leaves, have higher miR396 and lower GRF levels.
    [PMID: 20023165]
  3. hyper-activation of TCP4 revealed its role in determining the timing of crucial developmental events, both at the organ and organism level.
    [PMID: 21518050]
  4. TCP4 protein blocks cell cycle of budding yeast, specifically at G1->S transition, by regulating G1 checkpoint control pathway.
    [PMID: 21658370]
  5. These analyses indicate a role for auxin, gibberellic acid and abscisic acid in TCP4-mediated control of leaf growth.
    [PMID: 21904111]
  6. Data show that the expression of TCP4 and IAMT1 that encodes a methyltransferase converting free indole-3-acetic acid (IAA) to methyl-IAA ester (MeIAA) was induced and the induction level was dependent on the abundance of TaWRKY71-1 transcripts.
    [PMID: 23671653]
  7. A small increase in TCP4 activity has an immediate impact on leaf cell number, by significantly reducing cell proliferation through miR319.
    [PMID: 25053833]
  8. Data showed that SPOROCYTELESS (SPL) most likely functions as a transcription repressor by interacting with TCP family transcription factors and the TOPLESS (TPL) co-repressors.
    [PMID: 25527103]
  9. miR319 and its target TCP4 can act as switches that turn on secondary cell wall synthesis and programmed cell death.
    [PMID: 28233945]
  10. Our yeast one-hybrid analysis revealed that class II CIN-TCPs, including TCP4, bind to the CO promoter. TCP4 induces CO expression around dusk by directly associating with the CO promoter in vivo. In addition, TCP4 binds to another flowering regulator, GIGANTEA (GI), in the nucleus, and induces CO expression in a GI-dependent manner
    [PMID: 28628608]
  11. Mutations in MIR319 and gain-of-function mutations in the TCP4 gene conferred resistance against miR319 and impaired the cotyledon boundary and leaf serration formation. Taken together, these findings demonstrate that the MIR319 and TCP gene families underlie robust and multilayer control of leaf development.
    [PMID: 28842549]
  12. Detailed genetic analyses show that GIS and TCP4 work in same pathway and GIS function is required for TCP4-mediated regulation of trichome differentiation.
    [PMID: 29165850]
  13. We induced a microRNA-resistant form of TCP4 at various developmental stages of leaf primordium that lacked the activity of TCP4 and its homologues and followed its effect on growth kinematics. By combining this with spatio-temporal gene expression analysis, we show that TCP4 commits leaf cells within the transition zone to exit proliferation and enter differentiation.
    [PMID: 30742619]
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: Repressed by the miRNA miR-JAW/miR319 (PubMed:12931144, PubMed:18816164). {ECO:0000269|PubMed:12931144, ECO:0000269|PubMed:18816164}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
Interaction ? help Back to Top
Source Intact With
BioGRIDAT3G02150, AT3G27010, AT3G47620, AT4G18390, AT4G27330, AT5G08070, AT5G08330, AT5G51910, AT5G60970, AT1G30210, AT1G35560, AT1G53230, AT1G58100, AT1G65620, AT1G69690
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT3G15030
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAK3167040.0AK316704.1 Arabidopsis thaliana AT3G15030 mRNA, complete cds, clone: RAFL06-89-F15.
GenBankAP0003700.0AP000370.1 Arabidopsis thaliana genomic DNA, chromosome 3, TAC clone:K15M2.
GenBankAY0944440.0AY094444.1 Arabidopsis thaliana AT3g15030/K15M2_17 mRNA, complete cds.
GenBankAY1499570.0AY149957.1 Arabidopsis thaliana At3g15030/K15M2_17 mRNA, complete cds.
GenBankCP0026860.0CP002686.1 Arabidopsis thaliana chromosome 3, complete sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_001189896.10.0TCP family transcription factor 4
RefseqNP_001319557.10.0TCP family transcription factor 4
RefseqNP_188121.10.0TCP family transcription factor 4
RefseqNP_850589.10.0TCP family transcription factor 4
SwissprotQ8LPR50.0TCP4_ARATH; Transcription factor TCP4
TrEMBLB9DFB40.0B9DFB4_ARATH; AT3G15030 protein
STRINGAT3G15030.10.0(Arabidopsis thaliana)
Publications ? help Back to Top
  1. Cubas P,Lauter N,Doebley J,Coen E
    The TCP domain: a motif found in proteins regulating plant growth and development.
    Plant J., 1999. 18(2): p. 215-22
  2. Riechmann JL, et al.
    Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
    Science, 2000. 290(5499): p. 2105-10
  3. Palatnik JF, et al.
    Control of leaf morphogenesis by microRNAs.
    Nature, 2003. 425(6955): p. 257-63
  4. Yamada K, et al.
    Empirical analysis of transcriptional activity in the Arabidopsis genome.
    Science, 2003. 302(5646): p. 842-6
  5. Souret FF,Kastenmayer JP,Green PJ
    AtXRN4 degrades mRNA in Arabidopsis and its substrates include selected miRNA targets.
    Mol. Cell, 2004. 15(2): p. 173-83
  6. Pagnussat GC, et al.
    Genetic and molecular identification of genes required for female gametophyte development and function in Arabidopsis.
    Development, 2005. 132(3): p. 603-14
  7. Qin G, et al.
    An indole-3-acetic acid carboxyl methyltransferase regulates Arabidopsis leaf development.
    Plant Cell, 2005. 17(10): p. 2693-704
  8. Aguilar-Martínez JA,Poza-Carrión C,Cubas P
    Arabidopsis BRANCHED1 acts as an integrator of branching signals within axillary buds.
    Plant Cell, 2007. 19(2): p. 458-72
  9. 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
  10. Ascencio-Ib
    Global analysis of Arabidopsis gene expression uncovers a complex array of changes impacting pathogen response and cell cycle during geminivirus infection.
    Plant Physiol., 2008. 148(1): p. 436-54
  11. Efroni I,Blum E,Goldshmidt A,Eshed Y
    A protracted and dynamic maturation schedule underlies Arabidopsis leaf development.
    Plant Cell, 2008. 20(9): p. 2293-306
  12. Schommer C, et al.
    Control of jasmonate biosynthesis and senescence by miR319 targets.
    PLoS Biol., 2008. 6(9): p. e230
  13. Nag A,King S,Jack T
    miR319a targeting of TCP4 is critical for petal growth and development in Arabidopsis.
    Proc. Natl. Acad. Sci. U.S.A., 2009. 106(52): p. 22534-9
  14. Rodriguez RE, et al.
    Control of cell proliferation in Arabidopsis thaliana by microRNA miR396.
    Development, 2010. 137(1): p. 103-12
  15. Aggarwal P, et al.
    Identification of specific DNA binding residues in the TCP family of transcription factors in Arabidopsis.
    Plant Cell, 2010. 22(4): p. 1174-89
  16. Koyama T,Mitsuda N,Seki M,Shinozaki K,Ohme-Takagi M
    TCP transcription factors regulate the activities of ASYMMETRIC LEAVES1 and miR164, as well as the auxin response, during differentiation of leaves in Arabidopsis.
    Plant Cell, 2010. 22(11): p. 3574-88
  17. Sarvepalli K,Nath U
    Hyper-activation of the TCP4 transcription factor in Arabidopsis thaliana accelerates multiple aspects of plant maturation.
    Plant J., 2011. 67(4): p. 595-607
  18. Aggarwal P, et al.
    The TCP4 transcription factor of Arabidopsis blocks cell division in yeast at G1→S transition.
    Biochem. Biophys. Res. Commun., 2011. 410(2): p. 276-81
  19. Sarvepalli K,Nath U
    Interaction of TCP4-mediated growth module with phytohormones.
    Plant Signal Behav, 2011. 6(10): p. 1440-3
  20. Causier B,Ashworth M,Guo W,Davies B
    The TOPLESS interactome: a framework for gene repression in Arabidopsis.
    Plant Physiol., 2012. 158(1): p. 423-38
  21. Viola IL,Reinheimer R,Ripoll R,Manassero NG,Gonzalez DH
    Determinants of the DNA binding specificity of class I and class II TCP transcription factors.
    J. Biol. Chem., 2012. 287(1): p. 347-56
  22. Li Z,Li B,Shen WH,Huang H,Dong A
    TCP transcription factors interact with AS2 in the repression of class-I KNOX genes in Arabidopsis thaliana.
    Plant J., 2012. 71(1): p. 99-107
  23. Yang X, et al.
    Evolution of double positive autoregulatory feedback loops in CYCLOIDEA2 clade genes is associated with the origin of floral zygomorphy.
    Plant Cell, 2012. 24(5): p. 1834-47
  24. Mecchia MA,Debernardi JM,Rodriguez RE,Schommer C,Palatnik JF
    MicroRNA miR396 and RDR6 synergistically regulate leaf development.
    Mech. Dev., 2013. 130(1): p. 2-13
  25. Efroni I, et al.
    Regulation of leaf maturation by chromatin-mediated modulation of cytokinin responses.
    Dev. Cell, 2013. 24(4): p. 438-45
  26. Qin Z, et al.
    Ectopic expression of a wheat WRKY transcription factor gene TaWRKY71-1 results in hyponastic leaves in Arabidopsis thaliana.
    PLoS ONE, 2013. 8(5): p. e63033
  27. Danisman S, et al.
    Analysis of functional redundancies within the Arabidopsis TCP transcription factor family.
    J. Exp. Bot., 2013. 64(18): p. 5673-85
  28. Zhao J,Favero DS,Peng H,Neff MM
    Arabidopsis thaliana AHL family modulates hypocotyl growth redundantly by interacting with each other via the PPC/DUF296 domain.
    Proc. Natl. Acad. Sci. U.S.A., 2013. 110(48): p. E4688-97
  29. Schommer C,Debernardi JM,Bresso EG,Rodriguez RE,Palatnik JF
    Repression of cell proliferation by miR319-regulated TCP4.
    Mol Plant, 2014. 7(10): p. 1533-44
  30. Wei B, et al.
    The molecular mechanism of sporocyteless/nozzle in controlling Arabidopsis ovule development.
    Cell Res., 2015. 25(1): p. 121-34
  31. Chen GH,Sun JY,Liu M,Liu J,Yang WC
    SPOROCYTELESS is a novel embryophyte-specific transcription repressor that interacts with TPL and TCP proteins in Arabidopsis.
    J Genet Genomics, 2014. 41(12): p. 617-25
  32. Ju Y, et al.
    Arabidopsis JINGUBANG Is a Negative Regulator of Pollen Germination That Prevents Pollination in Moist Environments.
    Plant Cell, 2016. 28(9): p. 2131-2146
  33. Challa KR,Aggarwal P,Nath U
    Activation of YUCCA5 by the Transcription Factor TCP4 Integrates Developmental and Environmental Signals to Promote Hypocotyl Elongation in Arabidopsis.
    Plant Cell, 2016. 28(9): p. 2117-2130
  34. Alvarez JP,Furumizu C,Efroni I,Eshed Y,Bowman JL
    Active suppression of a leaf meristem orchestrates determinate leaf growth.
    Elife, 2017.
  35. Li J, et al.
    RABBIT EARS regulates the transcription of TCP4 during petal development in Arabidopsis.
    J. Exp. Bot., 2016. 67(22): p. 6473-6480
  36. Sun X, et al.
    Activation of secondary cell wall biosynthesis by miR319-targeted TCP4 transcription factor.
    Plant Biotechnol. J., 2017. 15(10): p. 1284-1294
  37. Kubota A, et al.
    TCP4-dependent induction of CONSTANS transcription requires GIGANTEA in photoperiodic flowering in Arabidopsis.
    PLoS Genet., 2017. 13(6): p. e1006856
  38. 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
  39. Bresso EG,Chorostecki U,Rodriguez RE,Palatnik JF,Schommer C
    Spatial Control of Gene Expression by miR319-Regulated TCP Transcription Factors in Leaf Development.
    Plant Physiol., 2018. 176(2): p. 1694-1708
  40. Vadde BVL,Challa KR,Nath U
    The TCP4 transcription factor regulates trichome cell differentiation by directly activating GLABROUS INFLORESCENCE STEMS in Arabidopsis thaliana.
    Plant J., 2018. 93(2): p. 259-269
  41. Challa KR,Rath M,Nath U
    The CIN-TCP transcription factors promote commitment to differentiation in Arabidopsis leaf pavement cells via both auxin-dependent and independent pathways.
    PLoS Genet., 2019. 15(2): p. e1007988