PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT2G33810.1
Common NameSPL3, T1B8.11
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 SBP
Protein Properties Length: 131aa    MW: 15304 Da    PI: 8.15
Description squamosa promoter binding protein-like 3
Gene Model
Gene Model ID Type Source Coding Sequence
AT2G33810.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
          SBP   1 lCqvegCeadlseakeyhrrhkvCevhskapvvlvsgleqrfCqqCsrfhelsefDeekrsCrrrLakhnerrrkkqa 78 
                  +Cqve+C+ad+s+ak+yh+rhkvC++h+kap+v +sgl+qrfCqqCsrfh+lsefDe+krsCrrrLa+hnerrrk+++
                  6**************************************************************************976 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PIRSFPIRSF0375751.5E-591131IPR017238Squamosa promoter-binding protein
Gene3DG3DSA:4.10.1100.104.2E-3346115IPR004333Transcription factor, SBP-box
PROSITE profilePS5114132.25751128IPR004333Transcription factor, SBP-box
SuperFamilySSF1036121.47E-3853130IPR004333Transcription factor, SBP-box
PfamPF031102.1E-3254127IPR004333Transcription factor, SBP-box
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009911Biological Processpositive regulation of flower development
GO:0010228Biological Processvegetative to reproductive phase transition of meristem
GO:0010229Biological Processinflorescence development
GO:0010321Biological Processregulation of vegetative phase change
GO:0030154Biological Processcell differentiation
GO:0005634Cellular Componentnucleus
GO:0005737Cellular Componentcytoplasm
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0046872Molecular Functionmetal ion binding
Plant Ontology ? help Back to Top
PO Term PO Category PO Description
PO:0000013anatomycauline leaf
PO:0000037anatomyshoot apex
PO:0000229anatomyflower meristem
PO:0000230anatomyinflorescence meristem
PO:0000293anatomyguard cell
PO:0008019anatomyleaf lamina base
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: 131 aa     Download sequence    Send to blast
3D Structure ? help Back to Top
PDB ID Evalue Query Start Query End Hit Start Hit End Description
1ul4_A4e-3847127284squamosa promoter binding protein-like 4
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.253640.0flower| silique
Expression -- Microarray ? help Back to Top
Source ID E-value
Expression AtlasAT2G33810-
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Increases during floral transition and stay high thereafter. {ECO:0000269|PubMed:10524240, ECO:0000269|PubMed:14573523, ECO:0000269|PubMed:16914499, ECO:0000269|PubMed:9301089}.
UniprotTISSUE SPECIFICITY: Expressed in vegetative and inflorescence apical meristems, floral meristems, leaf and flower organ primordia, inflorescence stem tissue and to lower extent in roots. {ECO:0000269|PubMed:10524240, ECO:0000269|PubMed:9301089}.
Functional Description ? help Back to Top
Source Description
TAIREncodes a member of the SPL (squamosa-promoter binding protein-like)gene family, a novel gene family encoding DNA binding proteins and putative transcription factors. Contains the SBP-box, which encodes the SBP-domain, required and sufficient for interaction with DNA. It binds DNA, may directly regulate AP1, and is involved in regulation of flowering and vegetative phase change. Its temporal expression is regulated by the microRNA miR156. The target site for the microRNA is in the 3'UTR.
UniProtTrans-acting factor that binds specifically to the consensus nucleotide sequence 5'-TNCGTACAA-3' of AP1 promoter. Binds specifically to the 5'-GTAC-3' core sequence. Promotes both vegetative phase change and flowering. Regulates phase-specific patterns of leaf epidermal differentiation and flowering time, but does not seem to affect leaf shape. {ECO:0000269|PubMed:16095614, ECO:0000269|PubMed:16914499, ECO:0000269|PubMed:9301089}.
Function -- GeneRIF ? help Back to Top
  1. Results show that vegetative phase change in Arabidopsis is regulated by an increase in the expression of SPL3.
    [PMID: 16914499]
  2. Data show that LEAFY, FRUITFULL, and APETALA1 are directly activated by the microRNA-targeted transcription factor SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 3 (SPL3) to control the timing of flower formation.
    [PMID: 19686687]
  3. Data indicate that although miR172 and miR156 play distinct roles in the timing of developmental phase transitions, there is a signaling crosstalk mediated by the SPL3/4/5 genes.
    [PMID: 21373962]
  4. SOC1-SPL module serves as a molecular link that integrates photoperiod and gibberellic acid signals to promote flowering in Arabidopsis.
    [PMID: 21988498]
  5. Overexpression of miR156-resistant SPL3 causes accelerated flowering at a low ambient temperature.
    [PMID: 22427344]
  6. SPL3/4/5 Integrate Developmental Aging and Photoperiodic Signals into the FT-FD Module in Arabidopsis Flowering.
    [PMID: 27815142]
  7. the miR156-SPL3 module mediates regulation of FT expression by NaKR1 in response to potassium conditions.
    [PMID: 29253219]
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: Negatively regulated by microRNAs miR156. {ECO:0000269|PubMed:12202040, ECO:0000269|PubMed:16914499}.
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 AT1G69120(A), AT5G60910(A), AT5G61850(A)
Regulation -- MicroRNA ? help Back to Top
Source Description
miRTarBaseRegulated by ath-miR157a, ath-miR156a, ath-miR156f
Phenotype -- Disruption Phenotype ? help Back to Top
Source Description
UniProtDISRUPTION PHENOTYPE: Plants flower early and have a significantly reduced number of juvenile, adult and cauline leaves, with a shorter petiole and a more acute leaf base in the first two leaves. {ECO:0000269|PubMed:16914499}.
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT2G33810
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAJ0116330.0AJ011633.1 Arabidopsis thaliana (ecotype Landsberg erecta) mRNA for squamosa promoter binding protein-like 3.
GenBankAJ2429590.0AJ242959.1 Arabidopsis thaliana mRNA for Squamosa promoter binding protein-like 3 (SPL3 gene).
GenBankAK1181790.0AK118179.1 Arabidopsis thaliana At2g33810 mRNA for putative squamosa-promoter binding protein, complete cds, clone: RAFL19-50-A02.
GenBankBT0054430.0BT005443.1 Arabidopsis thaliana clone U50647 putative squamosa-promoter binding protein (At2g33810) mRNA, complete cds.
GenBankY094270.0Y09427.1 A.thaliana mRNA for squamosa-promoter binding protein like 3.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_565771.12e-89squamosa promoter binding protein-like 3
SwissprotP930151e-90SPL3_ARATH; Squamosa promoter-binding-like protein 3
TrEMBLA0A178W1W03e-88A0A178W1W0_ARATH; Squamosa promoter-binding-like protein
STRINGAT2G33810.16e-89(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
Representative plantOGRP9717230
Publications ? help Back to Top
  1. Cardon G, et al.
    Molecular characterisation of the Arabidopsis SBP-box genes.
    Gene, 1999. 237(1): p. 91-104
  2. Riechmann JL, et al.
    Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
    Science, 2000. 290(5499): p. 2105-10
  3. Seki M, et al.
    Functional annotation of a full-length Arabidopsis cDNA collection.
    Science, 2002. 296(5565): p. 141-5
  4. Rhoades MW, et al.
    Prediction of plant microRNA targets.
    Cell, 2002. 110(4): p. 513-20
  5. Folta KM,Pontin MA,Karlin-Neumann G,Bottini R,Spalding EP
    Genomic and physiological studies of early cryptochrome 1 action demonstrate roles for auxin and gibberellin in the control of hypocotyl growth by blue light.
    Plant J., 2003. 36(2): p. 203-14
  6. Schmid M, et al.
    Dissection of floral induction pathways using global expression analysis.
    Development, 2003. 130(24): p. 6001-12
  7. Yamada K, et al.
    Empirical analysis of transcriptional activity in the Arabidopsis genome.
    Science, 2003. 302(5646): p. 842-6
  8. L
    A new SBP-box gene BpSPL1 in silver birch (Betula pendula).
    Physiol Plant, 2004. 120(3): p. 491-500
  9. Kidner CA,Martienssen RA
    The role of ARGONAUTE1 (AGO1) in meristem formation and identity.
    Dev. Biol., 2005. 280(2): p. 504-17
  10. Birkenbihl RP,Jach G,Saedler H,Huijser P
    Functional dissection of the plant-specific SBP-domain: overlap of the DNA-binding and nuclear localization domains.
    J. Mol. Biol., 2005. 352(3): p. 585-96
  11. Wu G,Poethig RS
    Temporal regulation of shoot development in Arabidopsis thaliana by miR156 and its target SPL3.
    Development, 2006. 133(18): p. 3539-47
  12. Gandikota M, et al.
    The miRNA156/157 recognition element in the 3' UTR of the Arabidopsis SBP box gene SPL3 prevents early flowering by translational inhibition in seedlings.
    Plant J., 2007. 49(4): p. 683-93
  13. Yamaguchi A, et al.
    The microRNA-regulated SBP-Box transcription factor SPL3 is a direct upstream activator of LEAFY, FRUITFULL, and APETALA1.
    Dev. Cell, 2009. 17(2): p. 268-78
  14. Sanchez SE,Cagnola JI,Crepy M,Yanovsky MJ,Casal JJ
    Balancing forces in the photoperiodic control of flowering.
    Photochem. Photobiol. Sci., 2011. 10(4): p. 451-60
  15. Jung JH,Seo PJ,Kang SK,Park CM
    miR172 signals are incorporated into the miR156 signaling pathway at the SPL3/4/5 genes in Arabidopsis developmental transitions.
    Plant Mol. Biol., 2011. 76(1-2): p. 35-45
  16. Lal S,Pacis LB,Smith HM
    Regulation of the SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE genes/microRNA156 module by the homeodomain proteins PENNYWISE and POUND-FOOLISH in Arabidopsis.
    Mol Plant, 2011. 4(6): p. 1123-32
  17. Jung JH,Ju Y,Seo PJ,Lee JH,Park CM
    The SOC1-SPL module integrates photoperiod and gibberellic acid signals to control flowering time in Arabidopsis.
    Plant J., 2012. 69(4): p. 577-88
  18. Yang L,Wu G,Poethig RS
    Mutations in the GW-repeat protein SUO reveal a developmental function for microRNA-mediated translational repression in Arabidopsis.
    Proc. Natl. Acad. Sci. U.S.A., 2012. 109(1): p. 315-20
  19. Kim JJ, et al.
    The microRNA156-SQUAMOSA PROMOTER BINDING PROTEIN-LIKE3 module regulates ambient temperature-responsive flowering via FLOWERING LOCUS T in Arabidopsis.
    Plant Physiol., 2012. 159(1): p. 461-78
  20. Hwan Lee J,Joon Kim J,Ahn JH
    Role of SEPALLATA3 (SEP3) as a downstream gene of miR156-SPL3-FT circuitry in ambient temperature-responsive flowering.
    Plant Signal Behav, 2012. 7(9): p. 1151-4
  21. Heidari B,Nemie-Feyissa D,Kangasjärvi S,Lillo C
    Antagonistic regulation of flowering time through distinct regulatory subunits of protein phosphatase 2A.
    PLoS ONE, 2013. 8(7): p. e67987
  22. Jorgensen SA,Preston JC
    Differential SPL gene expression patterns reveal candidate genes underlying flowering time and architectural differences in Mimulus and Arabidopsis.
    Mol. Phylogenet. Evol., 2014. 73: p. 129-39
  23. Le MH,Cao Y,Zhang XC,Stacey G
    LIK1, a CERK1-interacting kinase, regulates plant immune responses in Arabidopsis.
    PLoS ONE, 2014. 9(7): p. e102245
  24. 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
  25. Yu N,Niu QW,Ng KH,Chua NH
    The role of miR156/SPLs modules in Arabidopsis lateral root development.
    Plant J., 2015. 83(4): p. 673-85
  26. Lei KJ, et al.
    Modulation of the Phosphate-Deficient Responses by MicroRNA156 and its Targeted SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 3 in Arabidopsis.
    Plant Cell Physiol., 2016. 57(1): p. 192-203
  27. Xu M, et al.
    Developmental Functions of miR156-Regulated SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) Genes in Arabidopsis thaliana.
    PLoS Genet., 2016. 12(8): p. e1006263
  28. Jung JH,Lee HJ,Ryu JY,Park CM
    SPL3/4/5 Integrate Developmental Aging and Photoperiodic Signals into the FT-FD Module in Arabidopsis Flowering.
    Mol Plant, 2016. 9(12): p. 1647-1659
  29. Duan HC, et al.
    ALKBH10B Is an RNA N6-Methyladenosine Demethylase Affecting Arabidopsis Floral Transition.
    Plant Cell, 2017. 29(12): p. 2995-3011
  30. Negishi K,Endo M,Abe M,Araki T
    SODIUM POTASSIUM ROOT DEFECTIVE1 regulates FLOWERING LOCUS T expression via the microRNA156-SQUAMOSA PROMOTER BINDING PROTEIN-LIKE3 module in response to potassium conditions.
    Plant Cell Physiol., 2018. 59(2): p. 404-413
  31. Cardon GH,Höhmann S,Nettesheim K,Saedler H,Huijser P
    Functional analysis of the Arabidopsis thaliana SBP-box gene SPL3: a novel gene involved in the floral transition.
    Plant J., 1997. 12(2): p. 367-77