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 AT1G53230.1
Common NameF12M16.13, TCP3
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: 391aa    MW: 43044.2 Da    PI: 6.8017
Description TEOSINTE BRANCHED 1, cycloidea and PCF transcription factor 3
Gene Model
Gene Model ID Type Source Coding Sequence
AT1G53230.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
          TCP   2 agkkdrhskihTkvggRdRRvRlsaecaarfFdLqdeLGfdkdsktieWLlqqakpaikeltgt............ssssaseceaesssssasnsss 87 
                  +g+kdrhsk++T++g+RdRRvRlsa++a++f+d+qd+LGfd++sk+++WL+++ak ai++l+++                           +a+++ +
                  79**************************************************************4333222222220..............2222222 PP

          TCP  88 gkaaksaakskksqksaasalnla 111
                  +++ k+  ++ ++q ++++++ + 
                  222222223333333333233222 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PfamPF036347.9E-3347159IPR005333Transcription factor, TCP
PROSITE profilePS5136934.58149107IPR017887Transcription factor TCP subgroup
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009733Biological Processresponse to auxin
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
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000013anatomycauline leaf
PO:0000037anatomyshoot apex
PO:0000056anatomyflower bud
PO:0000230anatomyinflorescence meristem
PO:0000293anatomyguard cell
PO:0008019anatomyleaf lamina base
PO:0009006anatomyshoot system
PO:0009009anatomyplant embryo
PO:0009025anatomyvascular leaf
PO:0009052anatomyflower pedicel
PO:0020137anatomyleaf apex
PO:0025022anatomycollective leaf structure
PO:0001054developmental stagevascular leaf senescent stage
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: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: 391 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-1954107154Putative transcription factor PCF6
5zkt_B4e-1954107154Putative transcription factor PCF6
Search in ModeBase
Expression -- Microarray ? help Back to Top
Source ID E-value
Expression AtlasAT1G53230-
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: First observed in the distal and middle regions of cotyledons of torpedo-shaped embryos. Later localized in bending cotyledon, and mature embryos, but no signals were detected in the presumptive shoot apical meristem (SAM) and the boundary region during embryogenesis. During flower development, first observed throughout the floral meristem. Later expressed in rapidly growing floral primordia. Detected to a lower extent in vegetative primordia. During flower development, first observed throughout the floral meristem. Expressed during ovule development (PubMed:25378179). {ECO:0000269|PubMed:10363373, ECO:0000269|PubMed:17307931, 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
TAIREncodes a member of a recently identified plant transcription factor family that includes Teosinte branched 1, Cycloidea 1, and proliferating cell nuclear antigen (PCNA) factors, PCF1 and 2. Regulated by miR319. Involved in heterchronic regulation of leaf differentiation.
UniProtPlays 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). Participates in ovule develpment (PubMed:25378179). {ECO:0000269|PubMed:17307931, ECO:0000269|PubMed:25378179}.
Function -- GeneRIF ? help Back to Top
  1. TCP3 interactions with R2R3-MYBs lead to enhanced flavonoid production, which further negatively modulates the auxin response.
    [PMID: 24118612]
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
Motif logo
Cis-element ? help Back to Top
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source Target Gene (A: Activate/R: Repress)
ATRM AT1G04240(A), AT2G37630(A)
Interaction ? help Back to Top
Source Intact With
BioGRIDAT1G53230, AT1G56650, AT1G58100, AT1G65620, AT1G66370, AT1G66380, AT1G66390, AT1G69690, AT1G71030
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT1G53230
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAC0080070.0AC008007.7 Genomic sequence for Arabidopsis thaliana BAC F12M16 from chromosome I, complete sequence.
GenBankAY0996780.0AY099678.1 Arabidopsis thaliana putative flower development protein cycloidea (At1g53230) mRNA, complete cds.
GenBankBT0002660.0BT000266.1 Arabidopsis thaliana putative flower development protein cycloidea (At1g53230) mRNA, complete cds.
GenBankCP0026840.0CP002684.1 Arabidopsis thaliana chromosome 1 sequence.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_001322492.10.0TEOSINTE BRANCHED 1, cycloidea and PCF transcription factor 3
RefseqNP_564624.20.0TEOSINTE BRANCHED 1, cycloidea and PCF transcription factor 3
SwissprotQ9MAH80.0TCP3_ARATH; Transcription factor TCP3
STRINGAT1G53230.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
Representative plantOGRP18015163
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. Cubas P,Vincent C,Coen E
    An epigenetic mutation responsible for natural variation in floral symmetry.
    Nature, 1999. 401(6749): p. 157-61
  3. Riechmann JL, et al.
    Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
    Science, 2000. 290(5499): p. 2105-10
  4. Lee HS,Chen ZJ
    Protein-coding genes are epigenetically regulated in Arabidopsis polyploids.
    Proc. Natl. Acad. Sci. U.S.A., 2001. 98(12): p. 6753-8
  5. Yamada K, et al.
    Empirical analysis of transcriptional activity in the Arabidopsis genome.
    Science, 2003. 302(5646): p. 842-6
  6. Qin G, et al.
    An indole-3-acetic acid carboxyl methyltransferase regulates Arabidopsis leaf development.
    Plant Cell, 2005. 17(10): p. 2693-704
  7. Arciga-Reyes L,Wootton L,Kieffer M,Davies B
    UPF1 is required for nonsense-mediated mRNA decay (NMD) and RNAi in Arabidopsis.
    Plant J., 2006. 47(3): p. 480-9
  8. Damerval C,Le Guilloux M,Jager M,Charon C
    Diversity and evolution of CYCLOIDEA-like TCP genes in relation to flower development in Papaveraceae.
    Plant Physiol., 2007. 143(2): p. 759-72
  9. Guti
    Qualitative network models and genome-wide expression data define carbon/nitrogen-responsive molecular machines in Arabidopsis.
    Genome Biol., 2007. 8(1): p. R7
  10. 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
  11. 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
  12. L
    Distinct light-initiated gene expression and cell cycle programs in the shoot apex and cotyledons of Arabidopsis.
    Plant Cell, 2008. 20(4): p. 947-68
  13. 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
  14. 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
  15. 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
  16. Giraud E, et al.
    TCP transcription factors link the regulation of genes encoding mitochondrial proteins with the circadian clock in Arabidopsis thaliana.
    Plant Cell, 2010. 22(12): p. 3921-34
  17. Liu Z,Jia L,Wang H,He Y
    HYL1 regulates the balance between adaxial and abaxial identity for leaf flattening via miRNA-mediated pathways.
    J. Exp. Bot., 2011. 62(12): p. 4367-81
  18. Klopffleisch K, et al.
    Arabidopsis G-protein interactome reveals connections to cell wall carbohydrates and morphogenesis.
    Mol. Syst. Biol., 2011. 7: p. 532
  19. 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
  20. 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
  21. Efroni I, et al.
    Regulation of leaf maturation by chromatin-mediated modulation of cytokinin responses.
    Dev. Cell, 2013. 24(4): p. 438-45
  22. Li S,Zachgo S
    TCP3 interacts with R2R3-MYB proteins, promotes flavonoid biosynthesis and negatively regulates the auxin response in Arabidopsis thaliana.
    Plant J., 2013. 76(6): p. 901-13
  23. Danisman S, et al.
    Analysis of functional redundancies within the Arabidopsis TCP transcription factor family.
    J. Exp. Bot., 2013. 64(18): p. 5673-85
  24. Kim SH, et al.
    The Arabidopsis immune adaptor SRFR1 interacts with TCP transcription factors that redundantly contribute to effector-triggered immunity.
    Plant J., 2014. 78(6): p. 978-89
  25. Mar
    Large-scale identification of gibberellin-related transcription factors defines group VII ETHYLENE RESPONSE FACTORS as functional DELLA partners.
    Plant Physiol., 2014. 166(2): p. 1022-32
  26. Wei B, et al.
    The molecular mechanism of sporocyteless/nozzle in controlling Arabidopsis ovule development.
    Cell Res., 2015. 25(1): p. 121-34
  27. 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
  28. Wang X, et al.
    TCP transcription factors are critical for the coordinated regulation of isochorismate synthase 1 expression in Arabidopsis thaliana.
    Plant J., 2015. 82(1): p. 151-62
  29. 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
  30. Alvarez JP,Furumizu C,Efroni I,Eshed Y,Bowman JL
    Active suppression of a leaf meristem orchestrates determinate leaf growth.
    Elife, 2017.
  31. 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
  32. 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
  33. Mazur MJ, et al.
    Arabidopsis TCP Transcription Factors Interact with the SUMO Conjugating Machinery in Nuclear Foci.
    Front Plant Sci, 2017. 8: p. 2043