Plant Transcription Factor Database
Previous version: v3.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT1G53160.2
Common NameF12M16.2, FTM6, SPL4
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: 174aa    MW: 20119.6 Da    PI: 10.1381
Description squamosa promoter binding protein-like 4
Gene Model
Gene Model ID Type Source Coding Sequence
AT1G53160.2genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
          SBP   2 CqvegCeadlseakeyhrrhkvCevhskapvvlvsgleqrfCqqCsrfhelsefDeekrsCrrrLakhnerrrkkq 77 
                  Cqv++C+ad++eak yhrrhkvCevh+ka++v++sgl+qrfCqqCsrfh+l+efDe+krsCrrrLa+hnerrrk++
                  **************************************************************************87 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PIRSFPIRSF0375751.4E-651141IPR017238Squamosa promoter-binding protein
Gene3DG3DSA:4.10.1100.103.7E-3349115IPR004333Transcription factor, SBP-box
PROSITE profilePS5114131.95851128IPR004333Transcription factor, SBP-box
SuperFamilySSF1036124.05E-3853131IPR004333Transcription factor, SBP-box
PfamPF031106.1E-3254127IPR004333Transcription factor, SBP-box
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0009908Biological Processflower development
GO:0010321Biological Processregulation of vegetative phase change
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: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:0020148anatomyshoot apical meristem
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: 174 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_A1e-5140127184squamosa promoter binding protein-like 4
Search in ModeBase
Expression -- Microarray ? help Back to Top
Source ID E-value
Expression AtlasAT1G53160-
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}.
UniprotTISSUE SPECIFICITY: Expressed in the rib meristem and inter-primordial tissue of the inflorescence apex. {ECO:0000269|PubMed:10524240}.
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 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. Promotes both vegetative phase change and flowering. {ECO:0000269|PubMed:10524240, ECO:0000269|PubMed:16914499}.
Function -- GeneRIF ? help Back to Top
  1. 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]
Binding Motif ? help Back to Top
Motif ID Method Source Motif file
MP00634PBMTransfer from PK22320.1Download
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, ECO:0000305|PubMed:16914499}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
Regulation -- MicroRNA ? help Back to Top
Source Description
miRTarBaseRegulated by ath-miR156f
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT1G53160
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAJ0116310.0AJ011631.1 Arabidopsis thaliana (ecotype Columbia) mRNA for squamosa promoter binding protein-like 4.
GenBankBT0028560.0BT002856.1 Arabidopsis thaliana clone RAFL15-05-B10 (R20352) putative transcription factor (At1g53160) mRNA, complete cds.
GenBankBT0043910.0BT004391.1 Arabidopsis thaliana clone U20352 putative transcription factor (At1g53160) mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_175723.11e-126squamosa promoter binding protein-like 4
RefseqNP_974014.11e-126squamosa promoter binding protein-like 4
SwissprotQ9S7A91e-128SPL4_ARATH; Squamosa promoter-binding-like protein 4
TrEMBLD7KKE31e-112D7KKE3_ARALL; Squamosa promoter-binding-like protein
STRINGAT1G53160.11e-125(Arabidopsis thaliana)
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. Li J,Brader G,Palva ET
    The WRKY70 transcription factor: a node of convergence for jasmonate-mediated and salicylate-mediated signals in plant defense.
    Plant Cell, 2004. 16(2): p. 319-31
  7. 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
  8. Czechowski T,Bari RP,Stitt M,Scheible WR,Udvardi MK
    Real-time RT-PCR profiling of over 1400 Arabidopsis transcription factors: unprecedented sensitivity reveals novel root- and shoot-specific genes.
    Plant J., 2004. 38(2): p. 366-79
  9. Sunkar R,Zhu JK
    Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis.
    Plant Cell, 2004. 16(8): p. 2001-19
  10. Yoo BC, et al.
    A systemic small RNA signaling system in plants.
    Plant Cell, 2004. 16(8): p. 1979-2000
  11. 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
  12. 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
  13. Cao D,Cheng H,Wu W,Soo HM,Peng J
    Gibberellin mobilizes distinct DELLA-dependent transcriptomes to regulate seed germination and floral development in Arabidopsis.
    Plant Physiol., 2006. 142(2): p. 509-25
  14. Cai X, et al.
    A putative CCAAT-binding transcription factor is a regulator of flowering timing in Arabidopsis.
    Plant Physiol., 2007. 145(1): p. 98-105
  15. 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
  16. 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
  17. 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
  18. Torti S, et al.
    Analysis of the Arabidopsis shoot meristem transcriptome during floral transition identifies distinct regulatory patterns and a leucine-rich repeat protein that promotes flowering.
    Plant Cell, 2012. 24(2): p. 444-62
  19. Kim MH,Sonoda Y,Sasaki K,Kaminaka H,Imai R
    Interactome analysis reveals versatile functions of Arabidopsis COLD SHOCK DOMAIN PROTEIN 3 in RNA processing within the nucleus and cytoplasm.
    Cell Stress Chaperones, 2013. 18(4): p. 517-25