Plant Transcription Factor Database
Previous version: v3.0
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID AT4G36930.1
Common NameAP22.25, BHLH24, C7A10.430, EN99, SPT
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 bHLH
Protein Properties Length: 373aa    MW: 40297.6 Da    PI: 6.837
Description bHLH family protein
Gene Model
Gene Model ID Type Source Coding Sequence
AT4G36930.1genomeTAIRView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
          HLH   4 ahnerErrRRdriNsafeeLrellPkaskapskKlsKaeiLekAveYIksLq 55 
                   hn  E+rRR+riN+++  L++l+P++      K +Ka++L +A+eY+k+Lq
                  6*************************7.....5******************9 PP

Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
SuperFamilySSF474595.5E-20195257IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
PROSITE profilePS5088818.063197246IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene3DG3DSA:, basic helix-loop-helix (bHLH) domain
CDDcd000831.05E-16200251No hitNo description
PfamPF000101.0E-13201247IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
SMARTSM003534.0E-18203252IPR011598Myc-type, basic helix-loop-helix (bHLH) domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006355Biological Processregulation of transcription, DNA-templated
GO:0007623Biological Processcircadian rhythm
GO:0009409Biological Processresponse to cold
GO:0010114Biological Processresponse to red light
GO:0010154Biological Processfruit development
GO:0010187Biological Processnegative regulation of seed germination
GO:0048440Biological Processcarpel development
GO:0005634Cellular Componentnucleus
GO:0003677Molecular FunctionDNA binding
GO:0003700Molecular Functiontranscription factor activity, sequence-specific DNA binding
GO:0005515Molecular Functionprotein binding
GO:0046983Molecular Functionprotein dimerization activity
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: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
PO:0025374developmental stageseed dormant stage
Sequence ? help Back to Top
Protein Sequence    Length: 373 aa     Download sequence    Send to blast
Expression -- UniGene ? help Back to Top
UniGene ID E-value Expressed in
Expression -- Microarray ? help Back to Top
Source ID E-value
Expression AtlasAT4G36930-
Expression -- Description ? help Back to Top
Source Description
UniprotDEVELOPMENTAL STAGE: During flower initiation, expressed in the peripheral zone of the shoot apical meristem. Confined to the anlagen of successive flower buds yet to arise. Later expressed in abaxial and adaxial sepal primordia, but not in sepals. When sepals initiate, localized in the region interior to them. Within the gynoecium, detected in the initiating and developing medial regions, and then in the developing septum and stigma. SPT expression also occurs in sub-regions of developing ovules, and in the wall and dehiscence zone of the maturing fruit. As the petals develop, becomes restricted to the adaxial epidermis. In stamen expression increase in the vicinity of the archesporial cells and in cells undergoing divisions to produce sporogenous and secondary parietal cells of the anther locules. Expressed in the tapetum and microspore mother cells until the initiation of meiosis. Also detected in stomium and filaments. {ECO:0000269|PubMed:11245574}.
UniprotTISSUE SPECIFICITY: Expressed in lateral root caps, young leaves, stipules, maturing pith cells of the stem, differentiating vascular cells, shoot apical meristems and flowers. {ECO:0000269|PubMed:11245574}.
Functional Description ? help Back to Top
Source Description
TAIREncodes a transcription factor of the bHLH protein family. Mutants have abnormal, unfused carpels and reduced seed dormancy.
UniProtTranscription factor that plays a role in floral organogenesis. Promotes the growth of carpel margins and of pollen tract tissues derived from them. {ECO:0000269|PubMed:10225997, ECO:0000269|Ref.8}.
Function -- GeneRIF ? help Back to Top
  1. SPATULA is a light-stable repressor of seed germination and mediates the germination response to temperature.
    [PMID: 16303558]
  2. conserved acidic domain is essential for carpel function, supported by conserved amphipathic helix
    [PMID: 18315540]
  3. SPT is necessary in limiting leaf size without dramatically affecting leaf shape by restricting the size of the meristematic region in leaf primordia independently of the AN3-AtGRF5 pathway.
    [PMID: 20040585]
  4. Study show that IND may directly regulate SPT expression through variant E-box.
    [PMID: 20176890]
  5. SPT integrates time of day and temperature signaling to control vegetative growth rate.
    [PMID: 20705468]
  6. Data show that phytochrome B regulates gynoecium formation in association with the transcription factor SPATULA.
    [PMID: 21364315]
  7. SPT acts in an analogous manner to the gibberellin-dependent DELLAs, REPRESSOR OF GA1-3 and GIBBERELLIC ACID INSENSITIVE, which restrain cotyledon expansion alongside SPT.
    [PMID: 21478445]
  8. Over-expression of ALCATRAZ can partially compensate for a loss of SPT function, and over-expression of SPT can fully compensate for loss of ALCATRAZ function.
    [PMID: 21801252]
  9. SPT and IND at least partially mediate their joint functions in gynoecium and fruit development by controlling auxin distribution.
    [PMID: 21990939]
  10. SPT negatively regulates CUC1 and CUC2 expression in the apical part of the gynoecium.
    [PMID: 22514090]
  11. SPATULA (SPT) regulates gynoecium development by activating genes involved in shade avoidance.
    [PMID: 22851763]
  12. The data suggests that SPT plays a role in control of root growth, similar to its roles in above ground tissues.
    [PMID: 23280064]
  13. SPT is a growth repressor that acts to limit the size of meristems in response to environmental signals, perhaps by regulating auxin transport.
    [PMID: 23470719]
  14. SPT has opposite roles in setting seed dormancy in Landsberg erecta and Columbia Arabidopsis ecotypes
    [PMID: 23754415]
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: Down-regulated by the A class gene AP2 in the first whorl and by ARF3/ETT in gynoecium. {ECO:0000269|PubMed:11245574}.
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
Regulation -- ATRM (Manually Curated Upstream Regulators) ? help Back to Top
Source Upstream Regulator (A: Activate/R: Repress)
ATRM AT2G33860 (R), AT4G00120 (A)
Regulation -- ATRM (Manually Curated Target Genes) ? help Back to Top
Source Target Gene (A: Activate/R: Repress)
ATRM AT1G15550(R), AT1G80340(R), AT4G36260(A)
Interaction ? help Back to Top
Source Intact With
BioGRIDAT4G36930, AT5G67110
IntActSearch Q9FUA4
Phenotype -- Mutation ? help Back to Top
Source ID
T-DNA ExpressAT4G36930
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankAF3195400.0AF319540.1 Arabidopsis thaliana SPATULA (SPT) mRNA, complete cds.
GenBankAK2292670.0AK229267.1 Arabidopsis thaliana mRNA for putative bHLH transcription factor (AtbHLH024) / SPATULA (SPT), complete cds, clone: RAFL16-54-P05.
GenBankBT0264620.0BT026462.1 Arabidopsis thaliana At4g36930 mRNA, complete cds.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqNP_568010.10.0transcription factor SPATULA
SwissprotQ9FUA40.0SPT_ARATH; Transcription factor SPATULA
TrEMBLD7MAZ50.0D7MAZ5_ARALL; Putative uncharacterized protein
STRINGAT4G36930.10.0(Arabidopsis thaliana)
Orthologous Group ? help Back to Top
LineageOrthologous Group IDTaxa NumberGene Number
Representative plantOGRP25816128
Publications ? help Back to Top
  1. Alvarez J,Smyth DR
    CRABS CLAW and SPATULA, two Arabidopsis genes that control carpel development in parallel with AGAMOUS.
    Development, 1999. 126(11): p. 2377-86
  2. Nemhauser JL,Feldman LJ,Zambryski PC
    Auxin and ETTIN in Arabidopsis gynoecium morphogenesis.
    Development, 2000. 127(18): p. 3877-88
  3. Riechmann JL, et al.
    Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.
    Science, 2000. 290(5499): p. 2105-10
  4. Heisler MG,Atkinson A,Bylstra YH,Walsh R,Smyth DR
    SPATULA, a gene that controls development of carpel margin tissues in Arabidopsis, encodes a bHLH protein.
    Development, 2001. 128(7): p. 1089-98
  5. Kuusk S,Sohlberg JJ,Long JA,Fridborg I,Sundberg E
    STY1 and STY2 promote the formation of apical tissues during Arabidopsis gynoecium development.
    Development, 2002. 129(20): p. 4707-17
  6. Heim MA, et al.
    The basic helix-loop-helix transcription factor family in plants: a genome-wide study of protein structure and functional diversity.
    Mol. Biol. Evol., 2003. 20(5): p. 735-47
  7. Toledo-Ortiz G,Huq E,Quail PH
    The Arabidopsis basic/helix-loop-helix transcription factor family.
    Plant Cell, 2003. 15(8): p. 1749-70
  8. Nakayama N, et al.
    Gene trap lines define domains of gene regulation in Arabidopsis petals and stamens.
    Plant Cell, 2005. 17(9): p. 2486-506
  9. Penfield S, et al.
    Cold and light control seed germination through the bHLH transcription factor SPATULA.
    Curr. Biol., 2005. 15(22): p. 1998-2006
  10. Fahlgren N, et al.
    Regulation of AUXIN RESPONSE FACTOR3 by TAS3 ta-siRNA affects developmental timing and patterning in Arabidopsis.
    Curr. Biol., 2006. 16(9): p. 939-44
  11. Sohlberg JJ, et al.
    STY1 regulates auxin homeostasis and affects apical-basal patterning of the Arabidopsis gynoecium.
    Plant J., 2006. 47(1): p. 112-23
  12. Balanz
    Patterning the female side of Arabidopsis: the importance of hormones.
    J. Exp. Bot., 2006. 57(13): p. 3457-69
  13. Donohue K,Heschel MS,Chiang GC,Butler CM,Barua D
    Phytochrome mediates germination responses to multiple seasonal cues.
    Plant Cell Environ., 2007. 30(2): p. 202-12
  14. Finch-Savage WE,Cadman CS,Toorop PE,Lynn JR,Hilhorst HW
    Seed dormancy release in Arabidopsis Cvi by dry after-ripening, low temperature, nitrate and light shows common quantitative patterns of gene expression directed by environmentally specific sensing.
    Plant J., 2007. 51(1): p. 60-78
  15. Gremski K,Ditta G,Yanofsky MF
    The HECATE genes regulate female reproductive tract development in Arabidopsis thaliana.
    Development, 2007. 134(20): p. 3593-601
  16. Zentella R, et al.
    Global analysis of della direct targets in early gibberellin signaling in Arabidopsis.
    Plant Cell, 2007. 19(10): p. 3037-57
  17. Groszmann M,Paicu T,Smyth DR
    Functional domains of SPATULA, a bHLH transcription factor involved in carpel and fruit development in Arabidopsis.
    Plant J., 2008. 55(1): p. 40-52
  18. Holdsworth MJ,Bentsink L,Soppe WJ
    Molecular networks regulating Arabidopsis seed maturation, after-ripening, dormancy and germination.
    New Phytol., 2008. 179(1): p. 33-54
  19. Ståldal V,Sohlberg JJ,Eklund DM,Ljung K,Sundberg E
    Auxin can act independently of CRC, LUG, SEU, SPT and STY1 in style development but not apical-basal patterning of the Arabidopsis gynoecium.
    New Phytol., 2008. 180(4): p. 798-808
  20. Penfield S,Josse EM,Halliday KJ
    A role for an alternative splice variant of PIF6 in the control of Arabidopsis primary seed dormancy.
    Plant Mol. Biol., 2010. 73(1-2): p. 89-95
  21. Ichihashi Y,Horiguchi G,Gleissberg S,Tsukaya H
    The bHLH transcription factor SPATULA controls final leaf size in Arabidopsis thaliana.
    Plant Cell Physiol., 2010. 51(2): p. 252-61
  22. Gallego-Bartolomé J, et al.
    Transcriptional diversification and functional conservation between DELLA proteins in Arabidopsis.
    Mol. Biol. Evol., 2010. 27(6): p. 1247-56
  23. Groszmann M,Bylstra Y,Lampugnani ER,Smyth DR
    Regulation of tissue-specific expression of SPATULA, a bHLH gene involved in carpel development, seedling germination, and lateral organ growth in Arabidopsis.
    J. Exp. Bot., 2010. 61(5): p. 1495-508
  24. Sidaway-Lee K, et al.
    SPATULA links daytime temperature and plant growth rate.
    Curr. Biol., 2010. 20(16): p. 1493-7
  25. Tisza V,Kov
    Characterization of FaSPT, a SPATULA gene encoding a bHLH transcriptional factor from the non-climacteric strawberry fruit.
    Plant Physiol. Biochem., 2010 Oct-Nov. 48(10-11): p. 822-6
  26. Foreman J,White J,Graham I,Halliday K,Josse EM
    Shedding light on flower development: phytochrome B regulates gynoecium formation in association with the transcription factor SPATULA.
    Plant Signal Behav, 2011. 6(4): p. 471-6
  27. Josse EM, et al.
    A DELLA in disguise: SPATULA restrains the growth of the developing Arabidopsis seedling.
    Plant Cell, 2011. 23(4): p. 1337-51
  28. Li G, et al.
    Coordinated transcriptional regulation underlying the circadian clock in Arabidopsis.
    Nat. Cell Biol., 2011. 13(5): p. 616-22
  29. Groszmann M,Paicu T,Alvarez JP,Swain SM,Smyth DR
    SPATULA and ALCATRAZ, are partially redundant, functionally diverging bHLH genes required for Arabidopsis gynoecium and fruit development.
    Plant J., 2011. 68(5): p. 816-29
  30. Ichihashi Y, et al.
    Key proliferative activity in the junction between the leaf blade and leaf petiole of Arabidopsis.
    Plant Physiol., 2011. 157(3): p. 1151-62
  31. Girin T, et al.
    INDEHISCENT and SPATULA interact to specify carpel and valve margin tissue and thus promote seed dispersal in Arabidopsis.
    Plant Cell, 2011. 23(10): p. 3641-53
  32. Nahar MA,Ishida T,Smyth DR,Tasaka M,Aida M
    Interactions of CUP-SHAPED COTYLEDON and SPATULA genes control carpel margin development in Arabidopsis thaliana.
    Plant Cell Physiol., 2012. 53(6): p. 1134-43
  33. Reymond MC, et al.
    A light-regulated genetic module was recruited to carpel development in Arabidopsis following a structural change to SPATULA.
    Plant Cell, 2012. 24(7): p. 2812-25
  34. Fuentes S, et al.
    Fruit growth in Arabidopsis occurs via DELLA-dependent and DELLA-independent gibberellin responses.
    Plant Cell, 2012. 24(10): p. 3982-96
  35. Makkena S,Lamb RS
    The bHLH transcription factor SPATULA regulates root growth by controlling the size of the root meristem.
    BMC Plant Biol., 2013. 13: p. 1
  36. Efroni I, et al.
    Regulation of leaf maturation by chromatin-mediated modulation of cytokinin responses.
    Dev. Cell, 2013. 24(4): p. 438-45
  37. Makkena S,Lamb RS
    The bHLH transcription factor SPATULA is a key regulator of organ size in Arabidopsis thaliana.
    Plant Signal Behav, 2013. 8(5): p. e24140
  38. Footitt S,Huang Z,Clay HA,Mead A,Finch-Savage WE
    Temperature, light and nitrate sensing coordinate Arabidopsis seed dormancy cycling, resulting in winter and summer annual phenotypes.
    Plant J., 2013. 74(6): p. 1003-15
  39. Xing S, et al.
    SPL8 and miR156-targeted SPL genes redundantly regulate Arabidopsis gynoecium differential patterning.
    Plant J., 2013. 75(4): p. 566-77
  40. Vaistij FE, et al.
    Differential control of seed primary dormancy in Arabidopsis ecotypes by the transcription factor SPATULA.
    Proc. Natl. Acad. Sci. U.S.A., 2013. 110(26): p. 10866-71
  41. Lenser T,Thei
    Conservation of fruit dehiscence pathways between Lepidium campestre and Arabidopsis thaliana sheds light on the regulation of INDEHISCENT.
    Plant J., 2013. 76(4): p. 545-56
  42. 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