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 AT2G42200.1
Common NameAtSPL9, SPL9, T24P15.11
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: 375aa    MW: 40846.6 Da    PI: 8.2276
Description squamosa promoter binding protein-like 9
Gene Model
Gene Model ID Type Source Coding Sequence
AT2G42200.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
          SBP   1 lCqvegCeadlseakeyhrrhkvCevhskapvvlvsgleqrfCqqCsrfhelsefDeekrsCrrrLakhnerrrkkqa 78 
                  +CqvegC +dl++ak y++rh+vC vhsk+p+v+v+g+eqrfCqqCsrfh+l efD ekrsCrrrLa+hnerrrk+q+
                  6**************************************************************************986 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
Gene3DG3DSA:4.10.1100.102.9E-3466135IPR004333Transcription factor, SBP-box
PROSITE profilePS5114131.83871148IPR004333Transcription factor, SBP-box
SuperFamilySSF1036121.96E-4072152IPR004333Transcription factor, SBP-box
PfamPF031105.1E-3274147IPR004333Transcription factor, SBP-box
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0010228Biological Processvegetative to reproductive phase transition of meristem
GO:0048653Biological Processanther development
GO:2000025Biological Processregulation of leaf formation
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:0000017anatomyvascular leaf primordium
PO:0000037anatomyshoot apex
PO:0000230anatomyinflorescence meristem
PO:0000293anatomyguard cell
PO:0008019anatomyleaf lamina base
PO:0009006anatomyshoot system
PO:0009009anatomyplant embryo
PO:0009015anatomyportion of vascular tissue
PO:0009025anatomyvascular leaf
PO:0009052anatomyflower pedicel
PO:0009105anatomyinflorescence branch meristem
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:0007611developmental stagepetal differentiation and expansion stage
PO:0007616developmental stageflowering stage
Sequence ? help Back to Top
Protein Sequence    Length: 375 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-2963147184squamosa promoter binding protein-like 4
Search in ModeBase
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
At.4980.0bud| leaf| silique
Expression -- Microarray ? help Back to Top
Source ID E-value
Expression AtlasAT2G42200-
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: Expressed constitutively during plant development, with a strong increase during flower development. {ECO:0000269|PubMed:10524240, ECO:0000269|PubMed:14573523}.
Functional Description ? help Back to Top
Source Description
TAIREncodes a putative transcriptional regulator that is involved in the vegetative to reproductive phase transition. Expression is regulated by MIR156b. SPL activity nonautonomously inhibits initiation of new leaves at the shoot apical meristem.
UniProtTrans-acting factor that binds specifically to the consensus nucleotide sequence 5'-TNCGTACAA-3'. {ECO:0000250}.
Function -- GeneRIF ? help Back to Top
  1. SPL9 has a role in shoot maturation.
    [PMID: 18278578]
  2. Data demonstrate that miR156 is a quantitative, rather than spatial, modulator of SPL9 expression in leaf primordia and that SPL9 activity nonautonomously inhibits initiation of new leaves at the shoot apical meristem.
    [PMID: 18492871]
  3. One of the miR156 targets, SPL9, negatively regulates anthocyanin accumulation.
    [PMID: 21487097]
  4. Our results uncover a molecular mechanism for plant adaptation to the environment through the miR156-SPLs-DFR pathway, which coordinates development and abiotic stress tolerance.
    [PMID: 25345491]
  5. Analysis of plants carrying microRNA miR156-resistant forms of SQUAMOSA PROMOTER BINDING PROTEIN LIKE (SPL) genes showed that wall ingrowth deposition was increased in SPL9-group.
    [PMID: 28082719]
  6. Results suggest the mechanism by which miR156 and miR157 regulate gene expression of SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPL) transcription factors SPL9 and SPL13.
    [PMID: 29672610]
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 and miR157. {ECO:0000305|PubMed:12202040}.
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 AT2G30432(A), AT5G53200(A)
Regulation -- MicroRNA ? help Back to Top
Source Description
miRTarBaseRegulated by ath-miR156f
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT2G42200
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAJ0116380.0AJ011638.1 Arabidopsis thaliana (ecotype Columbia) mRNA for squamosa promoter binding protein-like 9.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_181749.10.0squamosa promoter binding protein-like 9
SwissprotQ700W20.0SPL9_ARATH; Squamosa promoter-binding-like protein 9
TrEMBLD7LI290.0D7LI29_ARALL; Uncharacterized protein
STRINGAT2G42200.10.0(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. Rhoades MW, et al.
    Prediction of plant microRNA targets.
    Cell, 2002. 110(4): p. 513-20
  4. Schmid M, et al.
    Dissection of floral induction pathways using global expression analysis.
    Development, 2003. 130(24): p. 6001-12
  5. Yamada K, et al.
    Empirical analysis of transcriptional activity in the Arabidopsis genome.
    Science, 2003. 302(5646): p. 842-6
  6. Yamasaki K, et al.
    A novel zinc-binding motif revealed by solution structures of DNA-binding domains of Arabidopsis SBP-family transcription factors.
    J. Mol. Biol., 2004. 337(1): p. 49-63
  7. Gong W, et al.
    Genome-wide ORFeome cloning and analysis of Arabidopsis transcription factor genes.
    Plant Physiol., 2004. 135(2): p. 773-82
  8. Yoo BC, et al.
    A systemic small RNA signaling system in plants.
    Plant Cell, 2004. 16(8): p. 1979-2000
  9. Scheible WR, et al.
    Genome-wide reprogramming of primary and secondary metabolism, protein synthesis, cellular growth processes, and the regulatory infrastructure of Arabidopsis in response to nitrogen.
    Plant Physiol., 2004. 136(1): p. 2483-99
  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. Duarte JM, et al.
    Expression pattern shifts following duplication indicative of subfunctionalization and neofunctionalization in regulatory genes of Arabidopsis.
    Mol. Biol. Evol., 2006. 23(2): p. 469-78
  12. Schwarz S,Grande AV,Bujdoso N,Saedler H,Huijser P
    The microRNA regulated SBP-box genes SPL9 and SPL15 control shoot maturation in Arabidopsis.
    Plant Mol. Biol., 2008. 67(1-2): p. 183-95
  13. Wang JW,Schwab R,Czech B,Mica E,Weigel D
    Dual effects of miR156-targeted SPL genes and CYP78A5/KLUH on plastochron length and organ size in Arabidopsis thaliana.
    Plant Cell, 2008. 20(5): p. 1231-43
  14. 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
  15. Wu G, et al.
    The sequential action of miR156 and miR172 regulates developmental timing in Arabidopsis.
    Cell, 2009. 138(4): p. 750-9
  16. Yu N, et al.
    Temporal control of trichome distribution by microRNA156-targeted SPL genes in Arabidopsis thaliana.
    Plant Cell, 2010. 22(7): p. 2322-35
  17. Chen X, et al.
    SQUAMOSA promoter-binding protein-like transcription factors: star players for plant growth and development.
    J Integr Plant Biol, 2010. 52(11): p. 946-51
  18. Xing S,Salinas M,H
    miR156-targeted and nontargeted SBP-box transcription factors act in concert to secure male fertility in Arabidopsis.
    Plant Cell, 2010. 22(12): p. 3935-50
  19. Gou JY,Felippes FF,Liu CJ,Weigel D,Wang JW
    Negative regulation of anthocyanin biosynthesis in Arabidopsis by a miR156-targeted SPL transcription factor.
    Plant Cell, 2011. 23(4): p. 1512-22
  20. Li S,Yang X,Wu F,He Y
    HYL1 controls the miR156-mediated juvenile phase of vegetative growth.
    J. Exp. Bot., 2012. 63(7): p. 2787-98
  21. Yu S, et al.
    Gibberellin regulates the Arabidopsis floral transition through miR156-targeted SQUAMOSA promoter binding-like transcription factors.
    Plant Cell, 2012. 24(8): p. 3320-32
  22. Stief A, et al.
    Arabidopsis miR156 Regulates Tolerance to Recurring Environmental Stress through SPL Transcription Factors.
    Plant Cell, 2014. 26(4): p. 1792-1807
  23. Cui LG,Shan JX,Shi M,Gao JP,Lin HX
    The miR156-SPL9-DFR pathway coordinates the relationship between development and abiotic stress tolerance in plants.
    Plant J., 2014. 80(6): p. 1108-17
  24. Yu ZX, et al.
    Progressive Regulation of Sesquiterpene Biosynthesis in Arabidopsis and Patchouli (Pogostemon cablin) by the miR156-Targeted SPL Transcription Factors.
    Mol Plant, 2015.
  25. 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
  26. 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
  27. Morea EG, et al.
    Functional and evolutionary analyses of the miR156 and miR529 families in land plants.
    BMC Plant Biol., 2016. 16: p. 40
  28. Hyun Y, et al.
    Multi-layered Regulation of SPL15 and Cooperation with SOC1 Integrate Endogenous Flowering Pathways at the Arabidopsis Shoot Meristem.
    Dev. Cell, 2016. 37(3): p. 254-66
  29. 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
  30. Mahmood K,Xu Z,El-Kereamy A,Casaretto JA,Rothstein SJ
    The Arabidopsis Transcription Factor ANAC032 Represses Anthocyanin Biosynthesis in Response to High Sucrose and Oxidative and Abiotic Stresses.
    Front Plant Sci, 2016. 7: p. 1548
  31. Mao YB, et al.
    Jasmonate response decay and defense metabolite accumulation contributes to age-regulated dynamics of plant insect resistance.
    Nat Commun, 2017. 8: p. 13925
  32. Nguyen ST,Greaves T,McCurdy DW
    Heteroblastic Development of Transfer Cells Is Controlled by the microRNA miR156/SPL Module.
    Plant Physiol., 2017. 173(3): p. 1676-1691
  33. Duan HC, et al.
    ALKBH10B Is an RNA N6-Methyladenosine Demethylase Affecting Arabidopsis Floral Transition.
    Plant Cell, 2017. 29(12): p. 2995-3011
  34. Dotto M,Gómez MS,Soto MS,Casati P
    UV-B radiation delays flowering time through changes in the PRC2 complex activity and miR156 levels in Arabidopsis thaliana.
    Plant Cell Environ., 2018. 41(6): p. 1394-1406
  35. He J, et al.
    Threshold-dependent repression of SPL gene expression by miR156/miR157 controls vegetative phase change in Arabidopsis thaliana.
    PLoS Genet., 2018. 14(4): p. e1007337